Contacts of the helix formed by residues 635 - 641 (chain C) in PDB entry 5VOT
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 635 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502C ILE* 3.8 10.7 - - - +
633C ILE 4.2 0.4 - - - -
634C GLU* 1.3 84.9 + - - +
636C ALA* 1.3 62.2 + - - +
637C GLU* 4.4 2.7 - - - -
638C ASP* 3.5 25.1 - - - +
639C LEU* 3.2 29.0 + - - +
723C VAL* 4.9 3.4 - - - +
724C GLY* 5.1 8.3 - - - -
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Residues in contact with ALA 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ILE* 3.7 20.3 - - + +
635C SER* 1.3 72.9 - - - +
637C GLU* 1.3 63.0 + - - +
638C ASP 3.1 1.3 - - - -
639C LEU* 2.9 23.6 + - - +
640C SER* 2.9 11.4 + - - -
667C PHE* 4.6 20.9 - - + -
670C MET* 4.4 15.8 - - + +
703C LEU* 6.3 0.2 - - + -
727C LEU* 4.8 11.7 - - + -
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Residues in contact with GLU 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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635C SER* 4.4 2.6 - - - -
636C ALA* 1.3 78.6 - - - +
638C ASP* 1.3 56.5 + - - +
640C SER* 2.3 30.4 + - - +
641C LYS* 2.9 47.6 + - - +
666C VAL* 4.0 19.0 - - + +
667C PHE* 5.8 0.2 - - - -
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Residues in contact with ASP 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633C ILE* 4.8 16.4 - - + +
634C GLU 4.7 2.5 - - - +
635C SER* 3.5 31.0 - - - +
636C ALA 3.1 0.4 - - - -
637C GLU* 1.3 78.8 - - - +
639C LEU* 1.3 63.8 + - - +
641C LYS* 3.0 18.9 + - - +
642C GLN* 3.2 15.2 + - - +
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Residues in contact with LEU 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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502C ILE* 4.0 26.5 - - + -
504C ILE* 5.7 3.6 - - + -
633C ILE* 5.5 12.1 - - + +
635C SER 3.2 17.9 + - - +
636C ALA* 2.9 9.9 + - - +
638C ASP* 1.3 78.6 - - + +
640C SER* 1.3 61.5 + - - +
642C GLN* 3.2 45.5 + - + +
645C ILE* 4.8 12.3 - - + +
647C TYR* 3.8 30.1 + - + -
670C MET* 5.1 4.5 - - + -
701C ALA* 4.2 22.9 - - + -
703C LEU* 5.3 6.1 - - + -
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Residues in contact with SER 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636C ALA 2.9 7.4 + - - -
637C GLU* 2.3 35.7 + - - +
639C LEU* 1.3 79.3 - - - +
641C LYS* 1.3 57.4 + - - +
642C GLN 3.2 7.5 + - - +
643C THR* 5.9 0.2 - - - +
647C TYR* 4.3 8.7 + - - -
666C VAL* 3.3 27.0 - - - +
669C LYS* 4.0 29.3 - - - +
670C MET* 4.1 11.6 - - - +
769D ASP 4.6 3.3 - - - +
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Residues in contact with LYS 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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637C GLU* 2.9 49.5 + - + +
638C ASP* 3.0 9.1 + - - +
640C SER* 1.3 77.9 - - - +
642C GLN* 1.3 58.1 + - - +
643C THR* 5.8 0.2 - - - -
769D ASP* 4.7 25.0 - - + +
771D GLY 5.1 4.9 - - - +
774D GLY 4.9 10.7 - - - +
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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