Contacts of the helix formed by residues 630 - 643 (chain B) in PDB entry 4P3N
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 CYS 630 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B PRO* 4.2 6.1 - - + -
626B VAL* 5.1 0.7 - - - -
627B GLY 2.9 17.6 + - - +
629B THR* 1.3 82.6 - - - +
631B ASP* 1.3 64.6 + - - +
632B GLU 3.1 3.6 - - - -
633B TYR* 2.9 24.6 + - + +
634B ALA* 3.0 12.5 + - - +
676B VAL* 4.1 15.9 - - + +
677B GLY* 3.5 36.6 - - - +
678B GLU* 3.6 15.3 - - - -
681B LYS* 5.2 4.5 - - + -
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Residues in contact with ASP 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B PRO* 3.4 22.1 - - - +
627B GLY 3.5 0.4 + - - +
628B PRO* 2.9 36.1 + - - +
629B THR 3.4 0.2 - - - -
630B CYS* 1.3 76.6 - - - +
632B GLU* 1.3 61.6 + - - +
634B ALA* 3.8 2.9 + - - +
635B GLN* 3.2 29.6 + - - +
652B LEU* 3.5 38.6 - - + +
654B PRO* 5.9 1.7 - - - +
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Residues in contact with GLU 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B PRO 4.7 0.2 + - - -
629B THR 4.8 4.0 + - - +
630B CYS 3.1 1.0 - - - -
631B ASP* 1.3 78.0 - - - +
633B TYR* 1.3 65.8 + - - +
635B GLN* 3.0 17.8 + - + +
636B LYS* 3.0 20.6 + - + +
681B LYS* 5.7 4.7 - - - +
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Residues in contact with TYR 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B CYS* 2.9 13.1 + - + +
632B GLU* 1.3 80.0 + - - +
634B ALA* 1.3 57.6 + - - +
636B LYS* 2.9 34.5 + - + +
637B VAL* 2.8 46.5 + - + +
676B VAL* 3.5 32.1 - - + -
677B GLY 4.8 0.9 - - - -
680B GLU 3.0 16.7 + - - -
681B LYS* 3.7 45.5 - - + -
684B GLY* 3.2 9.0 - - - -
685B THR 2.7 44.4 + - - -
701B ILE* 4.1 4.2 - - + +
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Residues in contact with ALA 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B VAL* 3.6 16.0 - - + +
625B PRO* 4.1 15.7 - - + -
630B CYS 3.0 12.4 + - - +
631B ASP* 3.9 4.5 - - - +
633B TYR* 1.3 77.3 - - - +
635B GLN* 1.3 62.2 + - - +
637B VAL* 4.4 1.8 - - - -
638B ARG* 3.2 20.1 + - - +
650B ILE* 3.4 24.8 - - + +
676B VAL* 3.7 22.9 - - + -
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Residues in contact with GLN 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B ASP* 3.2 18.7 + - - +
632B GLU* 3.0 20.5 + - + +
634B ALA* 1.3 77.5 - - - +
636B LYS* 1.3 65.4 + - - +
638B ARG* 3.7 4.8 + - - +
639B GLN* 3.2 22.2 + - - +
650B ILE* 4.0 15.9 - - + -
652B LEU* 3.6 20.3 - - + +
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Residues in contact with LYS 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B GLU* 3.0 11.7 + - + +
633B TYR* 2.9 35.4 + - + +
635B GLN* 1.3 75.4 - - - +
637B VAL* 1.3 65.8 + - - +
639B GLN* 3.0 8.8 + - - +
640B GLN* 2.9 53.8 + - + +
684B GLY* 5.8 3.4 - - - -
701B ILE* 6.2 3.2 - - - +
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Residues in contact with VAL 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B VAL* 4.1 16.8 - - + -
633B TYR* 2.8 57.7 + - + +
634B ALA* 3.9 6.1 - - - +
636B LYS* 1.3 76.5 - - + +
638B ARG* 1.3 65.3 + - - +
640B GLN* 3.0 11.6 + - - +
641B PHE* 2.9 45.4 + - + -
674B LEU* 4.5 0.9 - - + -
676B VAL* 4.4 5.2 - - + -
686B VAL* 4.0 16.4 - - + -
701B ILE* 5.0 9.2 - - + -
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Residues in contact with ARG 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B VAL* 3.7 17.3 - - + -
634B ALA 3.2 17.3 + - - +
635B GLN* 4.0 5.3 + - - +
637B VAL* 1.3 77.9 - - - +
639B GLN* 1.3 87.9 + - - +
641B PHE* 3.0 7.2 + - - +
642B HIS* 2.6 61.9 + - - +
648B ALA* 2.8 32.0 + - + +
649B ASP* 3.8 12.2 + - - +
650B ILE* 3.8 28.4 - - + +
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Residues in contact with GLN 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LYS 5.9 0.4 + - - -
635B GLN 3.2 12.3 + - - +
636B LYS* 3.0 13.1 + - - +
638B ARG* 1.3 97.5 + - - +
640B GLN* 1.3 52.7 + - + +
642B HIS* 2.9 23.5 + - - +
643B ASP* 2.7 65.4 + - - +
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Residues in contact with GLN 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636B LYS* 2.9 50.2 + - + +
637B VAL* 3.3 8.7 - - - +
639B GLN* 1.3 77.9 - - + +
641B PHE* 1.3 61.2 + - - +
643B ASP* 3.2 9.8 + - - +
644B ALA* 3.2 20.3 + - - +
701B ILE* 3.0 33.0 - - + +
705B ILE* 3.8 7.7 - - + +
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Residues in contact with PHE 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B VAL* 4.3 9.0 - - + -
637B VAL* 2.9 37.3 + - + -
638B ARG* 3.5 7.9 - - - +
640B GLN* 1.3 76.7 - - - +
642B HIS* 1.3 59.1 + - - +
644B ALA* 2.9 23.8 + - - +
646B PHE* 3.3 32.6 + + + -
648B ALA* 4.1 15.0 - - + -
674B LEU* 3.5 29.2 - - + -
686B VAL* 4.9 2.0 - - + -
701B ILE* 3.9 22.2 - - + -
704B THR* 3.9 19.1 - - + -
705B ILE* 3.6 26.7 - - + -
708B LEU* 3.6 26.5 - - + -
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Residues in contact with HIS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG* 2.9 34.7 + - + +
366A LYS* 4.8 4.1 + - - -
638B ARG* 2.6 42.4 + - - +
639B GLN* 3.2 31.9 - - - +
641B PHE* 1.3 72.9 - - - +
643B ASP* 1.3 63.3 + - - +
644B ALA 3.1 0.4 - - - -
645B LYS* 3.2 16.8 + - - +
646B PHE 3.8 17.6 + - - +
647B MET* 5.7 1.3 - - - -
648B ALA* 4.4 6.5 + - + +
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Residues in contact with ASP 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LYS* 5.6 6.4 - - - +
639B GLN* 2.7 46.6 + - - +
640B GLN* 3.2 10.5 + - - +
641B PHE 3.1 0.4 - - - -
642B HIS* 1.3 79.2 - - - +
644B ALA* 1.3 57.6 + - - +
645B LYS* 3.2 15.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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