Contacts of the helix formed by residues 630 - 644 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625C PRO* 3.8 4.6 - - + +
626C VAL* 5.3 0.7 - - - -
627C GLY* 2.8 17.6 + - - +
629C THR* 1.3 87.6 + - - +
631C ASP* 1.3 61.9 + - - +
632C GLU 3.2 2.9 - - - -
633C TYR* 3.5 7.9 + - + +
634C ALA* 3.1 25.3 + - - +
676C VAL* 3.8 21.0 - - + +
677C GLY* 3.4 36.6 - - - -
678C GLU* 3.5 11.9 - - - -
681C LYS* 4.5 8.1 - - - -
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Residues in contact with ASP 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C PRO* 3.7 20.0 - - - +
627C GLY 4.3 0.2 - - - -
628C PRO* 2.8 35.8 + - - +
629C THR 3.4 0.2 - - - -
630C CYS* 1.3 78.7 - - - +
632C GLU* 1.3 61.1 + - - +
634C ALA* 3.6 2.9 - - - +
635C GLN* 3.2 29.1 + - - +
652C LEU* 3.8 36.1 - - + +
654C PRO* 5.8 2.3 - - - +
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Residues in contact with GLU 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LYS* 4.2 23.6 + - - -
628C PRO 4.6 0.4 + - - -
629C THR 4.7 5.5 + - - +
630C CYS 3.2 0.6 - - - -
631C ASP* 1.3 77.7 - - - +
633C TYR* 1.3 65.7 - - - +
635C GLN* 2.9 16.1 + - + +
636C LYS* 2.9 20.4 + - - +
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Residues in contact with TYR 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C THR 5.4 0.4 + - - +
630C CYS* 3.5 8.5 + - - +
632C GLU* 1.3 78.0 - - - +
634C ALA* 1.3 63.2 + - - +
636C LYS* 2.9 27.0 + - + +
637C VAL* 2.9 35.0 + - + +
676C VAL* 3.3 34.8 - - + -
680C GLU 3.4 5.6 - - - -
681C LYS* 3.5 50.5 - - + -
684C GLY* 3.1 10.1 - - - -
685C THR 2.8 43.2 + - - -
701C ILE* 3.6 11.3 - - + +
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Residues in contact with ALA 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623C VAL* 3.9 18.3 - - + +
625C PRO* 4.0 22.4 - - + -
630C CYS 3.1 17.9 + - - +
631C ASP 3.6 5.8 - - - +
633C TYR* 1.3 76.3 - - - +
635C GLN* 1.3 62.1 + - - +
637C VAL* 2.9 16.3 + - - +
638C ARG* 3.0 15.6 + - - +
650C ILE* 3.7 16.4 - - + -
652C LEU* 4.6 0.2 - - + -
676C VAL* 4.5 8.3 - - + -
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Residues in contact with GLN 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631C ASP* 3.2 12.1 + - - +
632C GLU* 2.9 17.4 + - + +
634C ALA* 1.3 79.4 - - - +
636C LYS* 1.3 62.5 + - - +
638C ARG* 4.1 6.0 + - - +
639C GLN* 3.3 21.0 + - - +
650C ILE* 3.6 20.8 - - + +
652C LEU* 3.5 24.8 - - + +
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Residues in contact with LYS 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632C GLU 2.9 10.9 + - - +
633C TYR* 3.1 31.9 - - + +
635C GLN* 1.3 74.7 - - - +
637C VAL* 1.3 67.3 + - - +
639C GLN* 3.0 16.9 + - - +
640C GLN* 3.0 42.5 + - + +
701C ILE* 5.6 2.9 - - + -
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Residues in contact with VAL 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623C VAL* 4.1 14.6 - - + -
633C TYR* 2.9 49.9 + - + +
634C ALA 2.9 6.7 + - - +
636C LYS* 1.3 75.3 - - + +
638C ARG* 1.3 65.9 + - - +
640C GLN* 3.0 13.3 + - - +
641C PHE* 2.9 45.0 + - + -
674C LEU* 4.2 4.0 - - + -
676C VAL* 4.5 2.5 - - + -
686C VAL* 4.0 19.5 - - + -
701C ILE* 4.2 12.6 - - + -
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Residues in contact with ARG 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623C VAL* 3.7 21.3 - - + +
634C ALA 3.0 12.6 + - - +
635C GLN* 4.1 6.9 + - - +
637C VAL* 1.3 75.5 - - - +
639C GLN* 1.3 88.3 + - - +
641C PHE* 3.0 8.7 + - - +
642C HIS* 2.7 61.3 + - - +
648C ALA* 3.1 31.2 + - - +
649C ASP* 3.7 14.5 - - - +
650C ILE* 3.7 31.0 - - + +
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Residues in contact with GLN 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635C GLN 3.3 12.9 + - - +
636C LYS* 3.0 12.2 + - - +
638C ARG* 1.3 95.9 + - - +
640C GLN* 1.3 58.5 - - + +
642C HIS* 2.9 25.9 + - - +
643C ASP* 2.8 60.7 + - - +
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Residues in contact with GLN 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636C LYS* 3.0 44.7 + - + +
637C VAL* 3.0 8.0 + - - +
639C GLN* 1.3 78.1 - - + +
641C PHE* 1.3 57.1 + - - +
643C ASP* 2.9 23.6 + - - +
644C ALA* 3.0 13.0 + - - +
701C ILE* 3.3 36.1 - - + +
705C ILE* 4.2 12.9 - - + +
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Residues in contact with PHE 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621C VAL* 4.1 15.0 - - + -
637C VAL* 2.9 34.5 + - + +
638C ARG* 3.5 8.5 - - - +
640C GLN* 1.3 76.6 - - - +
642C HIS* 1.3 61.0 + - - +
644C ALA* 3.4 6.3 + - - -
646C PHE* 3.3 46.7 + + + +
648C ALA* 4.0 15.3 - - + -
674C LEU* 3.5 24.9 - - + -
686C VAL* 5.2 2.2 - - + -
701C ILE* 3.9 14.4 - - + -
704C THR* 3.2 22.4 - - - -
705C ILE* 3.5 29.4 - - + -
708C LEU* 3.5 25.6 - - + -
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Residues in contact with HIS 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638C ARG* 2.7 43.4 + - - +
639C GLN* 2.9 32.0 + - - +
641C PHE* 1.3 75.0 - - - +
643C ASP* 1.3 60.1 + - - +
644C ALA 3.2 0.2 - - - -
645C LYS* 3.3 16.6 + - - -
646C PHE 4.0 14.8 + - - +
647C MET* 5.6 9.3 - - + +
648C ALA* 4.2 8.1 + - + +
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Residues in contact with ASP 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639C GLN* 2.8 41.0 + - - +
640C GLN* 2.9 11.7 + - - +
642C HIS* 1.3 79.6 - - - +
644C ALA* 1.3 58.5 + - - +
645C LYS* 3.2 6.2 + - - +
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Residues in contact with ALA 644 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640C GLN 3.0 10.8 + - - +
641C PHE 3.7 3.4 - - - +
642C HIS 3.2 0.8 - - - -
643C ASP* 1.3 77.0 - - - +
645C LYS* 1.3 63.4 + - - +
646C PHE* 3.3 34.3 + - + -
705C ILE* 4.0 16.8 - - + -
709C GLN* 3.4 29.0 + - - +
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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