Contacts of the helix formed by residues 392 - 410 (chain B) in PDB entry 3PU3
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 PRO 392 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLU* 5.8 3.1 - - - +
390B GLN 3.8 4.9 - - - +
391B LEU* 1.3 93.4 - - + +
393B PRO* 1.3 74.4 - - + +
394B HIS* 3.5 31.2 - - + +
395B LEU* 3.2 28.1 + - + +
396B VAL* 3.2 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU 3.4 2.2 - - - +
392B PRO* 1.3 85.9 - - + +
394B HIS* 1.3 59.0 + - - +
396B VAL* 3.0 11.7 + - + +
397B GLN* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B EDO 6.5 0.4 - - - -
45B EDO 3.3 23.3 + - - -
119B GLU* 5.3 12.1 - - + -
339B SER 3.7 20.6 - - - -
340B LEU* 4.1 17.4 - - + +
342B VAL* 5.3 0.2 - - - +
392B PRO* 3.5 29.0 - - + +
393B PRO* 1.3 80.2 - - - +
395B LEU* 1.3 66.8 + - + +
397B GLN* 3.8 6.0 - - - -
398B GLY* 2.8 21.7 + - - -
452B EDO 3.2 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B EDO 4.4 6.7 - - - +
339B SER* 3.8 31.2 - - - +
342B VAL* 6.0 2.0 - - + -
373B MET* 4.5 3.6 - - + -
376B HIS* 5.9 4.0 - - - +
377B LEU* 4.3 29.1 - - + +
380B ALA* 5.9 3.1 - - + -
381B PHE* 5.0 0.7 - - - -
391B LEU* 4.6 17.7 - - + -
392B PRO* 3.2 28.6 + - + +
394B HIS* 1.3 94.0 - - + +
396B VAL* 1.3 61.3 + - - +
398B GLY* 3.7 1.9 - - - +
399B ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PHE* 4.4 11.2 - - + -
391B LEU* 3.5 24.5 - - + +
392B PRO 3.2 16.4 - - - +
393B PRO* 3.0 10.0 + - + +
395B LEU* 1.3 78.2 - - - +
397B GLN* 1.3 58.3 + - - +
399B ALA* 3.1 9.2 + - - +
400B LYS* 3.1 28.3 + - - +
439B ILE* 4.8 11.5 - - + +
442B SER* 3.5 29.6 - - - +
443B GLU* 5.6 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B EDO 5.1 5.3 + - - +
343B GLU* 3.4 22.8 + - - -
393B PRO 2.8 14.6 + - - +
394B HIS* 3.9 6.5 - - - +
396B VAL* 1.3 74.6 - - - +
398B GLY* 1.3 63.7 + - - +
400B LYS* 3.4 24.8 + - - +
401B ILE* 3.1 39.6 + - + +
452B EDO 4.3 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B VAL* 3.8 22.3 - - - +
377B LEU* 4.6 1.3 - - - -
394B HIS 2.8 19.8 + - - -
395B LEU* 3.4 3.6 + - - -
396B VAL 3.2 0.6 - - - -
397B GLN* 1.3 78.1 - - - +
399B ALA* 1.3 55.2 + - - +
401B ILE* 3.2 3.6 + - - +
402B LEU* 2.9 39.5 + - - +
452B EDO 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.9 19.0 - - + +
381B PHE* 3.8 26.2 - - + -
395B LEU 2.9 14.2 + - - +
396B VAL 3.3 9.6 - - - +
398B GLY* 1.3 72.6 - - - +
400B LYS* 1.3 61.9 + - - +
402B LEU* 3.8 2.1 - - - +
403B ASN* 2.8 32.2 + - - +
435B LEU* 5.0 8.0 - - + +
439B ILE* 3.8 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 3.1 13.9 + - - +
397B GLN* 3.6 26.9 - - - +
398B GLY 3.2 0.2 - - - -
399B ALA* 1.3 77.2 - - - +
401B ILE* 1.3 66.1 + - + +
403B ASN* 3.2 2.5 + - - +
404B GLY* 3.0 20.8 + - - -
439B ILE* 3.8 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B VAL* 4.0 7.2 - - + +
343B GLU* 3.5 34.1 - - + +
346B MET* 3.4 33.9 - - + -
397B GLN* 3.1 34.4 + - + +
398B GLY* 3.6 5.8 - - - +
400B LYS* 1.3 79.6 - - + +
402B LEU* 1.3 62.5 + - - +
404B GLY* 3.2 2.4 + - - -
405B ALA* 3.1 18.2 + - - +
452B EDO 3.7 15.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
217B TRP* 4.3 7.2 - - + -
342B VAL* 4.0 18.8 - - + -
346B MET* 4.5 8.1 - - - -
370B CYS* 4.0 36.1 - - + +
373B MET* 3.8 19.1 - - + -
374B GLY* 4.7 5.8 - - - +
377B LEU* 3.4 32.1 - - + -
398B GLY 2.9 18.5 + - - +
399B ALA* 3.8 3.4 - - - +
401B ILE* 1.3 73.8 - - - +
403B ASN* 1.3 60.7 + - - +
405B ALA* 2.8 8.2 + - + +
406B PHE* 2.7 46.3 + - + -
435B LEU* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ALA 2.8 22.7 + - - +
400B LYS* 3.8 3.6 - - - +
402B LEU* 1.3 72.1 - - - +
404B GLY* 1.3 60.8 + - - +
406B PHE* 3.4 8.3 + - - +
407B ARG* 2.9 56.4 + - - +
432B ILE* 3.1 35.6 + - - +
435B LEU* 3.2 33.0 - - + +
436B ALA* 3.6 11.3 - - - +
439B ILE* 4.3 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B EDO 3.2 24.2 + - - -
400B LYS 3.0 13.4 + - - -
401B ILE* 3.6 4.3 - - - -
403B ASN* 1.3 78.4 - - - +
405B ALA* 1.3 59.9 + - - +
407B ARG* 3.4 6.9 + - - +
408B SER* 3.0 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B MET* 3.6 31.2 - - + -
401B ILE 3.1 9.2 + - - +
402B LEU* 2.8 12.8 + - + +
404B GLY* 1.3 75.7 - - - +
406B PHE* 1.3 62.5 + - + +
408B SER* 3.0 11.6 + - - -
409B TRP* 2.9 44.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B CYS* 3.2 36.3 - - + -
371B TRP* 3.5 42.2 - + + -
374B GLY* 3.8 15.0 - - - -
402B LEU* 2.7 37.5 + - + -
403B ASN* 3.7 17.7 - - - +
405B ALA* 1.3 70.2 - - - +
407B ARG* 1.3 63.0 + - - +
409B TRP* 3.0 21.1 + + - -
410B THR* 2.9 27.5 + - - +
431B LEU* 4.0 6.7 - - + -
432B ILE* 3.6 20.2 - - + -
435B LEU* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B EDO 4.0 24.5 - - - +
403B ASN* 2.9 47.2 + - - +
404B GLY* 3.5 8.1 - - - +
406B PHE* 1.3 75.9 - - - +
408B SER* 1.3 62.6 + - - +
410B THR* 3.4 14.8 + - - -
411B LYS* 3.5 15.8 + - - +
432B ILE* 3.6 27.8 + - + +
433B LYS* 5.6 0.8 - - - +
436B ALA* 3.6 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B EDO 4.5 7.8 + - - -
404B GLY 3.0 12.9 + - - -
405B ALA* 3.0 16.5 + - - -
407B ARG* 1.3 77.2 - - - +
409B TRP* 1.3 60.6 + - - +
411B LYS* 2.6 27.6 - - - +
418B HIS* 4.9 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B MET* 4.0 12.3 - - + +
349B TYR* 4.2 12.3 - + - -
366B PHE* 4.6 0.2 - + - -
367B GLU* 3.4 55.7 + - + -
370B CYS* 3.8 22.7 - - + -
371B TRP* 3.8 22.4 - + + +
405B ALA* 2.9 38.0 + - + +
406B PHE* 3.0 32.3 + + - +
408B SER* 1.3 78.4 + - - +
410B THR* 1.3 59.0 + - - +
411B LYS 3.2 8.1 + - - -
416B ALA 4.4 8.0 + - - -
418B HIS* 3.4 55.0 - + + +
419B GLU 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B TRP* 3.5 17.9 - - + -
406B PHE 2.9 17.3 + - - +
407B ARG* 3.5 5.4 + - - -
408B SER 3.4 0.4 - - - -
409B TRP* 1.3 80.0 - - + +
411B LYS* 1.3 60.2 + - - +
412B LYS 4.4 0.4 - - - -
416B ALA 5.8 0.4 - - - +
428B PRO* 3.5 33.7 - - + -
429B SER* 5.4 2.6 + - - -
432B ILE* 3.4 15.0 - - + +
----------------------------------------------------------
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