Contacts of the helix formed by residues 695 - 699 (chain A) in PDB entry 2V3V
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 LEU 695 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ALA 4.2 6.1 - - - +
421A HIS* 3.8 36.3 - - + +
426A LEU* 3.8 11.2 - - + -
430A HIS* 4.0 25.4 - - + +
450A VAL* 4.5 15.0 - - + -
670A MET* 3.4 11.0 - - - +
691A ASP 3.9 2.2 - - - +
692A PRO* 3.6 35.7 - - + +
693A LYS 3.9 1.0 - - - -
694A LYS* 1.3 70.8 - - - +
696A VAL* 1.3 62.0 + - - +
697A ASN 3.2 2.7 - - - -
698A LYS* 3.0 38.6 + - - +
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Residues in contact with VAL 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A SER* 5.1 0.4 - - - -
641A ALA* 5.1 2.9 - - + -
670A MET* 4.2 18.4 - - - -
672A LEU* 4.9 4.7 - - + -
687A VAL* 3.7 31.4 - - + -
688A PRO 3.3 19.5 - - - +
689A PHE* 3.3 35.4 - - + -
694A LYS* 2.9 18.6 + - + +
695A LEU* 1.3 66.5 - - - +
697A ASN* 1.3 58.7 + - - +
698A LYS 3.0 4.9 - - - -
699A LEU* 2.8 27.3 + - + +
700A PHE* 3.3 18.9 - - + -
811A MGD 4.7 2.9 - - - +
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Residues in contact with ASN 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A HIS 3.2 18.6 + - - -
422A THR* 3.5 9.9 + - - +
423A LEU 3.1 21.0 - - - +
424A PRO* 4.0 3.2 - - + +
425A ASN 2.9 14.0 + - - -
426A LEU* 2.9 32.7 + - + -
689A PHE* 4.7 7.9 - - - +
695A LEU 3.2 2.2 + - - -
696A VAL* 1.3 77.1 - - - +
698A LYS* 1.3 59.1 + - - +
699A LEU 3.2 0.8 + - - -
700A PHE* 3.7 10.3 + - - +
713A TYR* 3.3 16.0 - - - -
811A MGD 2.9 41.0 + - - -
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Residues in contact with LYS 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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425A ASN* 4.8 2.3 - - - +
426A LEU* 3.8 21.7 + - + +
427A ASN* 3.6 29.5 + - - +
430A HIS* 4.2 16.8 - - - -
667A ARG* 3.5 19.4 - - - +
668A ASP* 3.7 28.3 + - + +
670A MET* 4.6 11.2 - - + +
695A LEU* 3.0 36.2 + - + +
696A VAL 3.0 1.0 + - - -
697A ASN* 1.3 77.7 - - - +
699A LEU* 1.3 60.7 + - - +
700A PHE 4.5 1.3 - - - +
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Residues in contact with LEU 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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613A LEU* 4.2 12.1 - - + -
663A VAL* 3.7 35.9 - - + +
665A THR* 2.7 38.7 + - + +
667A ARG* 2.9 15.6 + - - -
668A ASP* 3.5 35.2 - - + +
669A ALA* 3.9 6.1 - - - +
670A MET* 4.4 22.0 - - + -
672A LEU* 5.5 0.7 - - + -
687A VAL* 5.1 6.5 - - + -
696A VAL* 2.8 27.0 + - + +
698A LYS* 1.3 78.5 - - - +
700A PHE* 1.3 59.9 + - + +
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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