Contacts of the helix formed by residues 380 - 400 (chain B) in PDB entry 1Q6X
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 SER 380 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B VAL* 4.2 4.9 - - - +
378B LYS* 3.8 5.4 + - - -
379B CYS* 1.3 76.5 - - - +
381B PRO* 1.3 72.9 - - - +
382B GLU* 3.5 21.3 + - - +
383B THR* 3.2 19.9 + - - -
384B GLN* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B CYS 4.9 0.2 - - - +
380B SER* 1.3 90.7 - - - +
382B GLU* 1.3 63.1 + - + +
384B GLN* 3.4 13.9 + - + +
385B GLY* 3.1 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B VAL* 4.0 24.5 - - + +
262B LYS* 3.7 24.2 + - - +
380B SER* 3.2 19.6 + - - +
381B PRO* 1.3 77.4 - - + +
383B THR* 1.3 66.0 + - - +
385B GLY* 3.0 12.9 + - - -
386B HIS* 3.0 27.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 4.4 9.9 - - + -
245B LEU* 4.5 8.1 - - + -
256B ALA 5.2 0.2 + - - -
259B VAL* 3.8 9.5 - - - +
260B LEU* 3.5 31.8 - - + +
378B LYS 4.8 1.9 + - - -
379B CYS* 3.8 17.9 - - + -
380B SER* 3.2 25.7 + - - -
382B GLU* 1.3 79.9 - - - +
384B GLN* 1.3 64.4 + - - +
386B HIS* 3.1 12.5 + - - +
387B LEU* 2.9 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B CYS* 4.3 6.7 - - - -
380B SER 2.9 13.1 + - - +
381B PRO* 3.6 16.0 + - + +
382B GLU 3.2 0.2 - - - -
383B THR* 1.3 76.0 - - - +
385B GLY* 1.3 68.3 + - - +
387B LEU* 3.3 14.5 + - + +
388B ALA* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PRO 3.1 9.4 + - - -
382B GLU* 3.0 9.0 + - - -
384B GLN* 1.3 85.9 - - - +
386B HIS* 1.3 63.5 + - - +
388B ALA* 3.5 6.7 + - - +
389B SER* 3.2 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 3.9 15.3 - - + -
248B ASP* 5.0 0.2 - - - +
252B GLU 6.1 0.2 - - - -
255B LYS* 4.3 18.6 + - + +
256B ALA* 3.5 37.2 + - + +
259B VAL* 3.9 21.2 - - + +
382B GLU* 3.0 23.3 + - + +
383B THR* 3.1 12.0 + - - +
385B GLY* 1.3 76.4 - - - +
387B LEU* 1.3 58.7 + - - +
389B SER* 3.4 8.6 + - - -
390B SER* 3.0 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PRO* 4.1 25.6 - - + -
241B PRO* 3.7 33.2 - - + +
242B ILE* 4.5 2.5 - - + -
244B LEU* 3.7 17.8 - - + +
245B LEU* 3.6 26.7 - - + -
379B CYS* 4.4 7.0 - - - -
383B THR* 2.9 28.8 + - + +
384B GLN* 3.6 11.7 - - + +
385B GLY 3.3 0.2 - - - -
386B HIS* 1.3 76.6 - - - +
388B ALA* 1.3 57.9 + - - +
390B SER* 3.7 0.8 - - - -
391B ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLN* 3.3 17.5 + - - +
385B GLY* 3.8 8.1 - - - +
386B HIS 3.4 0.2 - - - -
387B LEU* 1.3 79.6 - - - +
389B SER* 1.3 61.3 + - - +
391B ALA* 3.4 7.4 + - - +
392B GLU* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASP* 4.3 7.0 - - - -
385B GLY 3.2 14.7 + - - -
386B HIS* 3.7 11.8 - - - -
387B LEU 3.3 0.2 - - - -
388B ALA* 1.3 76.3 - - - +
390B SER* 1.3 62.0 + - - +
392B GLU* 3.2 8.4 + - - +
393B LYS* 2.9 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 3.8 28.3 - - - +
245B LEU* 3.7 14.4 - - - +
247B SER* 4.6 1.7 + - - -
248B ASP* 3.1 29.9 + - - +
386B HIS 3.0 18.1 + - - -
387B LEU 3.7 4.5 - - - -
389B SER* 1.3 76.4 - - - +
391B ALA* 1.3 57.9 + - - +
393B LYS* 3.2 3.0 + - - +
394B LEU* 2.8 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 3.8 16.3 - - + +
305B CYS* 3.8 25.3 - - - -
387B LEU 3.0 18.5 + - - +
388B ALA* 3.7 8.3 - - - +
390B SER* 1.3 78.0 - - - +
392B GLU* 1.3 62.9 + - - +
394B LEU* 3.4 3.2 + - - +
395B GLN* 3.2 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ALA 3.2 8.5 + - - +
389B SER* 3.2 10.8 + - - +
391B ALA* 1.3 79.0 - - - +
393B LYS* 1.3 65.0 + - + +
395B GLN* 3.2 17.2 + - + +
396B ARG* 3.1 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ASP* 3.3 31.3 + - - +
249B GLY* 4.7 4.2 - - - +
252B GLU* 4.6 15.8 + - - +
389B SER* 2.9 18.7 + - - +
390B SER* 3.5 6.7 - - - +
392B GLU* 1.3 77.8 - - + +
394B LEU* 1.3 63.5 + - - +
396B ARG* 3.2 44.6 + - - +
397B ILE* 3.4 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 4.8 7.0 - - + -
244B LEU* 3.8 19.7 - - + -
247B SER* 4.1 24.5 - - - +
301B HIS* 4.5 19.3 - - + +
304B GLY* 3.9 12.1 - - - -
305B CYS 3.8 23.3 - - - +
309B GLY* 4.0 20.2 - - - +
314B TYR* 5.5 1.3 - - - +
390B SER 2.8 19.6 + - - +
391B ALA 3.9 4.0 - - - +
393B LYS* 1.3 73.5 - - - +
395B GLN* 1.3 64.0 + - - +
397B ILE* 3.0 32.5 + - + +
398B VAL* 3.0 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLY 4.2 3.5 + - - +
304B GLY* 3.4 31.3 - - - -
305B CYS* 3.8 14.8 - - - +
306B SER* 4.8 7.3 + - - +
391B ALA 3.2 12.4 + - - +
392B GLU* 3.2 13.0 + - + +
394B LEU* 1.3 79.4 - - - +
396B ARG* 1.3 57.5 + - + +
398B VAL* 3.2 15.0 + - - +
399B LYS* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLU* 3.1 42.1 + - + +
393B LYS* 3.5 34.1 - - - +
394B LEU 3.2 0.8 - - - -
395B GLN* 1.3 77.5 - - + +
397B ILE* 1.3 58.4 + - + +
399B LYS* 4.0 5.4 - - - +
400B ASN* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 4.0 26.5 - - + -
103B PRO* 4.1 16.6 - - + +
104B VAL* 3.5 35.4 - - + -
105B ASN* 4.4 8.7 - - - +
247B SER 4.8 2.2 - - - +
301B HIS* 4.8 8.1 - - + -
393B LYS* 3.4 14.8 + - + +
394B LEU* 3.0 18.6 + - + +
396B ARG* 1.3 75.6 - - + +
398B VAL* 1.3 66.2 + - - +
400B ASN* 3.9 4.4 - - - +
401B LEU* 3.1 24.6 + - - +
588B PHE* 6.5 0.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
301B HIS* 3.9 39.6 + - + +
303B GLY* 3.9 11.4 - - - +
304B GLY* 3.6 30.7 - - - +
394B LEU* 3.0 20.1 + - + +
395B GLN* 3.5 18.6 - - - +
397B ILE* 1.3 77.8 - - - +
399B LYS* 1.3 62.6 + - - +
401B LEU* 3.6 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLN* 2.9 17.6 + - - +
396B ARG* 4.0 5.6 - - - +
398B VAL* 1.3 79.7 - - - +
400B ASN* 1.3 60.2 + - - +
401B LEU 3.7 0.9 + - - +
589B HIS* 3.4 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ARG 2.9 20.5 + - - +
397B ILE* 3.2 5.8 + - - +
399B LYS* 1.3 76.8 - - - +
401B LEU* 1.3 62.8 + - - +
402B ASP 3.3 0.7 + - - -
588B PHE* 3.4 26.1 - - + +
589B HIS* 2.9 30.9 + - - +
590B SER* 2.9 50.9 + - - +
----------------------------------------------------------
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