Contacts of the helix formed by residues 395 - 423 (chain B) in PDB entry 6YB9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 395 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B SER* 3.6 15.7 - - - -
263B GLU* 3.8 7.6 + - - +
264B SER* 3.0 31.2 + - - +
266B CYS* 3.8 13.0 - - - -
391B PHE 2.9 13.7 + - - +
392B GLY* 3.6 6.1 + - - +
394B SER* 1.3 76.1 - - - +
396B HIS* 1.3 58.0 + - - +
397B LEU* 3.0 37.4 + - - +
398B VAL* 3.2 22.2 + - + +
399B TRP* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 4.7 0.4 - - + -
178B LYS* 4.1 26.5 - - + +
179B SER* 3.3 35.2 - - - -
182B PRO* 4.4 8.1 - - + +
258B LEU 4.6 1.3 - - - -
259B LEU* 2.6 32.9 + - - -
261B LYS 3.2 26.2 - - - -
263B GLU* 3.1 31.2 + - + +
392B GLY 5.2 0.2 - - - -
394B SER 4.1 0.2 - - - -
395B ASN* 1.3 70.2 + - - +
397B LEU* 1.3 73.3 + - + +
399B TRP* 3.6 7.5 - - - +
400B SER* 2.6 38.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 23.3 - - + -
71B ALA* 5.4 0.5 - - - +
259B LEU 3.8 2.7 - - - +
260B LEU* 3.6 23.3 - - + +
261B LYS 4.0 0.7 - - - -
262B SER* 3.7 31.2 - - - +
395B ASN* 3.0 9.0 + - - +
396B HIS* 1.3 100.7 - - + +
398B VAL* 1.3 64.8 + - + +
400B SER* 3.3 5.8 + - - +
401B LYS* 3.2 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B CYS* 4.4 7.0 - - - -
291B PHE* 3.8 23.8 - - + +
292B GLY 5.5 1.8 - - - +
293B ILE* 4.1 17.7 - - + -
388B ALA* 3.2 46.0 - - + +
391B PHE* 4.5 0.9 - - + -
392B GLY* 4.1 4.3 - - - +
395B ASN* 3.2 31.6 + - + +
397B LEU* 1.3 72.3 - - + +
399B TRP* 1.3 66.9 + - - +
401B LYS* 3.1 7.6 + - - +
402B LEU* 3.1 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLU* 5.9 9.0 - - + -
344A ALA* 3.4 30.8 - - + +
345A TYR* 3.7 28.4 - + - -
506A EDO 5.7 0.2 - - - -
174B GLU* 3.9 36.1 - - + -
175B ILE* 4.0 9.0 - - + -
178B LYS* 3.4 35.9 - - + +
392B GLY* 3.6 26.8 - - - +
395B ASN 3.0 17.2 + - - +
396B HIS* 3.6 8.3 - - - +
397B LEU 3.4 0.2 - - - -
398B VAL* 1.3 76.2 - - - +
400B SER* 1.3 64.0 + - - +
402B LEU* 3.0 11.4 + - - +
403B ARG* 2.9 57.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.6 3.0 - - - +
71B ALA* 3.8 14.0 - - - +
175B ILE* 3.6 32.5 + - - +
178B LYS* 5.2 0.5 - - - +
179B SER* 4.1 8.3 + - - -
396B HIS* 2.6 23.5 + - - +
397B LEU* 3.6 8.5 - - - -
398B VAL 3.2 0.4 - - - -
399B TRP* 1.3 85.4 - - - +
401B LYS* 1.3 61.6 + - - +
403B ARG* 3.4 1.4 + - - +
404B ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLU* 3.2 28.2 + - - +
71B ALA* 3.4 23.0 - - - +
290B ASN 3.4 21.5 - - - +
291B PHE* 3.5 41.3 - - + +
292B GLY* 4.0 6.1 - - - +
397B LEU* 3.2 23.6 + - - +
398B VAL* 3.1 7.9 + - - +
400B SER* 1.3 76.7 - - - +
402B LEU* 1.3 58.3 + - - +
404B ALA 3.9 0.3 - - - -
405B SER* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA* 3.7 23.6 - - + +
291B PHE* 3.5 30.1 - - + -
385B GLN* 4.1 13.9 - - + +
388B ALA* 3.7 15.3 - - + +
389B GLN* 3.6 44.0 - - + +
392B GLY* 4.7 2.5 - - - -
398B VAL* 3.1 17.6 + - + +
399B TRP* 3.0 15.5 + - - +
401B LYS* 1.3 77.0 - - - +
403B ARG* 1.3 55.2 + - - +
405B SER* 3.2 8.0 + - - -
406B ILE* 3.1 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLU* 6.1 0.7 - - - -
344A ALA* 4.2 7.7 - - + +
167B HIS 4.8 2.4 + - - -
170B GLN* 4.4 8.3 + - - +
171B ALA* 3.6 33.0 - - + +
174B GLU* 3.1 40.6 + - + +
175B ILE* 4.0 13.7 - - + -
399B TRP* 2.9 46.7 + - + +
400B SER 3.7 4.0 - - - +
402B LEU* 1.3 74.3 - - - +
404B ALA* 1.3 64.2 + - - +
406B ILE* 3.3 30.2 + - - +
407B LEU* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 3.4 25.8 - - - +
72B GLY* 4.2 3.1 - - - -
73B ILE* 3.7 34.3 - - + +
171B ALA* 5.6 0.4 - - - -
175B ILE* 4.2 2.2 - - + +
400B SER 2.9 17.2 + - - +
403B ARG* 1.3 74.3 - - - +
405B SER* 1.3 59.2 + - - +
407B LEU* 3.1 6.1 + - - +
408B ASN* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 5.3 9.5 - - - -
385B GLN* 5.8 1.6 + - - -
401B LYS 3.0 18.9 + - - -
402B LEU* 3.4 9.0 - - - -
403B ARG 3.2 0.2 - - - -
404B ALA* 1.3 75.9 - - - +
406B ILE* 1.3 64.2 + - - +
408B ASN* 4.2 6.5 - - - +
409B THR* 2.8 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A SER 5.2 0.7 - - - +
341A GLY 4.0 21.3 - - - +
342A ASN* 4.0 11.7 - - - +
343A THR* 3.4 44.4 - - - +
344A ALA* 3.7 6.1 - - - +
385B GLN* 6.1 3.1 - - - +
402B LEU* 3.1 15.0 + - + +
403B ARG* 3.5 28.5 - - - +
405B SER* 1.3 75.4 - - - +
407B LEU* 1.3 64.1 + - - +
409B THR* 3.8 4.5 - - - -
410B TRP* 3.2 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.7 28.7 - - + -
74B LYS 6.2 0.2 - - - +
164B ILE 5.0 0.2 - - - +
167B HIS* 3.9 17.9 - - + +
168B ALA* 3.9 42.6 - - + +
171B ALA* 4.0 11.7 - - + -
403B ARG* 3.3 12.0 + - - +
404B ALA* 3.1 8.6 + - - +
406B ILE* 1.3 79.6 - - - +
408B ASN* 1.3 59.4 + - - +
410B TRP* 3.0 9.5 + - + +
411B ILE* 2.8 59.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLY* 2.8 33.7 + - - +
73B ILE* 5.0 1.1 - - - +
74B LYS* 4.6 19.4 + - - +
404B ALA* 2.8 25.6 + - - +
405B SER* 3.4 6.3 + - - +
407B LEU* 1.3 77.6 - - - +
409B THR* 1.3 56.8 + - - +
411B ILE* 3.3 19.4 + - - +
412B SER* 2.9 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A SER 6.1 0.4 - - - +
371A GLY* 6.0 7.5 - - - +
405B SER* 2.8 24.5 + - - -
406B ILE* 3.8 5.6 - - - -
408B ASN* 1.3 77.6 - - - +
410B TRP* 1.3 61.0 + - - +
412B SER* 3.2 10.9 + - - +
413B LEU* 3.2 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASN* 6.0 1.6 - - - -
163B ASP* 3.6 27.4 - - - -
164B ILE* 4.0 14.1 - - + -
167B HIS* 3.5 61.7 + + + -
406B ILE* 3.2 12.9 + - + +
407B LEU* 3.0 11.5 + - + +
409B THR* 1.3 75.7 - - - +
411B ILE* 1.3 78.2 + - + +
413B LEU* 3.2 16.8 + - + +
414B LYS* 3.1 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS* 6.5 1.1 - - + -
164B ILE* 4.0 33.7 - - + +
168B ALA* 5.4 2.0 - - + -
407B LEU* 2.8 43.8 + - + +
408B ASN* 3.6 18.6 - - - +
410B TRP* 1.3 90.6 - - + +
412B SER* 1.3 57.2 + - - +
414B LYS* 3.2 8.3 + - - +
415B GLN* 3.0 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASN 2.9 15.1 + - - -
409B THR* 3.2 15.2 + - - +
410B TRP 3.3 0.4 - - - -
411B ILE* 1.3 78.0 - - - +
413B LEU* 1.3 56.3 + - - +
415B GLN* 3.3 9.0 + - - +
416B ALA* 2.9 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 3.2 29.8 + - + +
410B TRP* 3.2 17.5 + - + +
412B SER* 1.3 72.7 + - - +
414B LYS* 1.3 58.6 + - - +
416B ALA* 3.3 8.1 + - + +
417B ASP* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLN* 3.5 17.8 - - - +
160B THR* 4.2 38.2 + - + +
163B ASP* 2.9 27.9 + - - -
164B ILE* 4.5 4.5 - - + -
410B TRP* 3.1 51.3 + - + +
411B ILE* 3.4 8.7 - - - +
413B LEU* 1.3 74.6 - - - +
415B GLN* 1.3 57.4 + - - +
417B ASP* 3.4 6.3 + - - +
418B LYS* 3.0 28.1 + - - +
421B ARG* 4.8 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B THR* 4.4 4.9 - - - +
161B GLU* 5.1 2.7 + - - +
164B ILE* 3.9 22.4 - - - +
411B ILE* 3.0 28.1 + - + +
412B SER* 3.7 10.1 - - - +
413B LEU 3.2 0.2 - - - -
414B LYS* 1.3 72.3 - - - +
416B ALA* 1.3 59.5 + - - +
418B LYS* 3.3 20.3 + - - +
419B LYS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B SER 2.9 16.7 + - - +
413B LEU* 3.8 9.4 - - + +
415B GLN* 1.3 72.1 - - - +
417B ASP* 1.3 65.6 + - - +
419B LYS* 3.4 10.6 + - + +
420B ILE* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU 2.9 17.8 + - - +
414B LYS* 3.8 6.5 - - - +
416B ALA* 1.3 72.9 - - - +
418B LYS* 1.3 60.1 + - - +
420B ILE* 3.2 16.0 - - - +
421B ARG* 3.0 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 4.5 10.7 - - - +
156B LEU 5.0 1.8 + - - -
160B THR* 4.2 15.5 - - + +
161B GLU* 2.7 34.6 + - - +
414B LYS 3.0 14.5 + - - +
415B GLN* 3.3 18.8 + - - +
417B ASP* 1.3 78.3 - - - +
419B LYS* 1.3 62.2 + - - +
421B ARG* 3.5 39.2 - - - +
422B GLU* 3.5 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLN 3.0 13.4 + - - +
416B ALA* 3.6 13.5 - - + +
417B ASP 3.3 0.2 - - - -
418B LYS* 1.3 75.9 - - - +
420B ILE* 1.3 60.5 + - + +
422B GLU* 3.1 41.8 + - - +
423B CYS* 3.8 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ALA 3.1 13.1 + - - +
417B ASP* 3.2 23.8 - - - +
419B LYS* 1.3 77.4 - - + +
421B ARG* 1.3 68.4 + - + +
423B CYS* 3.1 33.1 + - + +
424B ASN* 3.8 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B THR* 3.5 19.4 + - - -
414B LYS* 4.8 2.8 + - - +
417B ASP* 3.0 53.5 + - - +
418B LYS* 3.5 43.8 + - - +
419B LYS 3.2 0.2 - - - -
420B ILE* 1.3 77.7 - - + +
422B GLU* 1.3 60.8 + - - +
424B ASN* 3.2 23.8 + - - +
425B LEU* 3.2 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LYS* 3.6 26.6 - - - +
419B LYS* 3.1 22.7 + - - +
421B ARG* 1.3 71.5 - - + +
423B CYS* 1.3 58.0 + - - +
424B ASN 3.1 10.1 + - - -
425B LEU* 3.7 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LYS* 3.8 18.4 - - - -
420B ILE* 3.1 22.8 + - + +
422B GLU* 1.3 74.2 - - - +
424B ASN* 1.3 61.6 + - - +
425B LEU 3.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il