Contacts of the helix formed by residues 695 - 703 (chain A) in PDB entry 2VGE
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 THR 695 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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665A HIS* 3.9 2.5 - - - -
686A VAL 4.8 0.4 - - - -
687A ASN* 3.4 27.8 + - + +
688A SER 3.6 2.5 - - - -
689A PRO* 4.3 7.2 - - + -
693A GLY 4.2 4.7 - - - +
694A TRP* 1.3 77.2 - - - +
696A PRO* 1.3 76.7 - - - +
697A LEU* 3.4 16.8 + - - +
698A HIS* 3.0 38.9 + - + +
699A CYS* 3.2 12.3 + - - -
718A ALA 5.3 1.2 + - - -
721A ALA* 4.2 17.6 - - + +
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Residues in contact with PRO 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A LEU* 3.8 21.5 - - + -
665A HIS* 3.9 20.9 - - + +
668A ILE* 3.3 31.8 - - + +
685A ASN 4.1 4.3 - - - +
686A VAL 3.3 34.1 - - - +
688A SER* 3.3 15.7 - - - +
695A THR* 1.3 85.3 - - - +
697A LEU* 1.3 61.3 + - - +
699A CYS* 3.3 2.7 + - - +
700A ALA 3.0 18.5 + - - -
712A LEU* 3.5 9.2 - - + +
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Residues in contact with LEU 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A VAL 4.6 1.8 + - - +
687A ASN* 5.9 0.7 - - - +
695A THR* 3.1 9.1 + - - +
696A PRO* 1.3 79.9 - - - +
698A HIS* 1.3 63.8 + - - +
700A ALA* 3.3 2.1 + - - +
701A ALA* 3.0 23.4 + - - +
709A CYS* 4.0 40.8 - - + +
712A LEU* 3.7 14.0 - - + +
713A VAL* 4.2 6.7 - - + -
717A ALA* 4.2 17.9 - - + -
718A ALA 4.2 19.3 - - - +
719A ILE* 4.2 20.4 - - + -
730A ALA* 3.5 24.2 - - + -
748A LEU* 4.5 7.0 - - + -
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Residues in contact with HIS 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693A GLY 3.8 8.5 - - - -
694A TRP* 3.8 18.3 - - + -
695A THR* 3.0 44.0 + - + +
697A LEU* 1.3 79.1 - - - +
699A CYS* 1.3 61.5 + - - +
701A ALA* 3.5 2.1 + - - +
702A SER* 3.1 24.3 + - - -
721A ALA* 3.1 28.4 + - + -
722A THR 3.9 0.2 - - - -
723A THR* 3.7 24.4 - - + +
728A ALA 3.0 20.1 + - - -
729A THR 3.6 7.2 - - - -
730A ALA* 3.5 25.2 + - + +
733A LYS* 4.0 10.5 - - + +
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Residues in contact with CYS 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A HIS* 3.5 29.4 - - - +
668A ILE* 4.0 14.6 - - + -
669A CYS* 4.2 17.9 - - - -
690A ASP* 5.3 1.6 - - - -
694A TRP* 4.0 22.2 - - + -
695A THR 3.2 14.7 + - - -
696A PRO* 3.7 6.7 - - + +
697A LEU 3.3 0.2 - - - -
698A HIS* 1.3 73.8 - - - +
700A ALA* 1.3 64.3 + - - +
702A SER* 3.0 22.1 + - - -
703A CYS* 3.3 14.7 + - - -
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Residues in contact with ALA 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A ILE* 3.6 10.7 - - + +
696A PRO 3.0 17.2 + - - +
697A LEU 3.3 2.9 + - - +
699A CYS* 1.3 76.0 - - - +
701A ALA* 1.3 60.5 + - - +
703A CYS* 3.3 4.0 + - - +
704A ASN 3.1 2.9 + - - -
705A ASP* 2.9 29.2 + - - -
708A ILE* 3.9 29.2 - - + -
709A CYS* 3.6 20.0 - - - -
712A LEU* 3.9 6.1 - - + -
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Residues in contact with ALA 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A LEU 3.0 16.6 + - - +
698A HIS 3.8 4.3 - - - +
700A ALA* 1.3 73.3 - - - +
702A SER* 1.3 55.2 + - - +
703A CYS 3.0 5.2 - - - -
704A ASN* 2.7 31.8 + - - +
709A CYS* 3.8 7.1 - - - -
730A ALA* 3.1 29.6 - - + +
733A LYS* 3.9 2.0 - - + -
734A CYS* 3.2 10.5 - - - +
744A CYS* 4.2 4.7 - - - -
748A LEU* 3.7 17.5 - - + -
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Residues in contact with SER 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A CYS* 5.9 0.7 - - - -
694A TRP* 3.7 24.8 - - - -
698A HIS 3.1 13.9 + - - -
699A CYS* 3.0 17.2 + - - -
701A ALA* 1.3 76.2 - - - +
703A CYS* 1.3 55.4 + - - +
704A ASN 3.3 0.9 - - - -
733A LYS* 3.1 21.9 + - - -
735A ASP* 3.4 18.8 - - - +
738A ARG* 2.5 27.3 + - - -
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Residues in contact with CYS 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668A ILE* 4.7 5.2 - - - +
669A CYS* 4.2 32.5 - - - -
699A CYS 3.3 15.0 + - - +
700A ALA* 3.3 10.2 + - - +
701A ALA 3.0 0.8 - - - -
702A SER* 1.3 81.9 + - - +
704A ASN* 1.3 71.3 + - - +
705A ASP* 3.0 11.1 + - + +
738A ARG* 3.6 21.9 - - - +
739A GLU 4.6 2.9 - - - +
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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