Contacts of the strand formed by residues 615 - 623 (chain A) in PDB entry 2VWV
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 VAL 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A ILE* 3.9 22.9 - - + -
611A ASP 4.2 4.5 - - - +
612A VAL* 3.0 21.6 + - + +
613A SER 3.2 4.1 - - - +
614A TYR* 1.3 82.8 - - - +
616A LYS* 1.3 62.9 + - - +
617A ILE* 4.0 6.4 + - + +
633A ARG 3.7 4.5 - - - +
646A ILE* 3.6 29.2 - - + -
690A MET* 4.0 31.2 - - + -
692A LEU* 3.9 17.0 - - + -
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Residues in contact with LYS 616 (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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614A TYR 4.1 0.6 + - - -
615A VAL* 1.3 73.5 - - - +
617A ILE* 1.3 68.2 + - - +
618A GLU* 4.1 16.3 - - + +
632A GLY* 3.0 6.4 - - - -
633A ARG* 2.8 52.0 + - + +
641A GLU* 6.0 0.2 - - - +
646A ILE* 4.1 0.9 - - - +
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Residues in contact with ILE 617 (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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615A VAL* 3.9 6.9 + - + -
616A LYS* 1.3 75.4 - - - +
618A GLU* 1.3 78.5 + - - +
620A VAL* 5.9 0.7 - - + -
630A CYS* 3.7 20.9 - - + -
631A ARG 4.1 2.2 - - - -
646A ILE* 3.8 21.5 - - + -
648A THR* 4.3 23.8 - - + -
688A PRO* 5.9 2.9 - - + -
690A MET* 4.5 11.7 - - - -
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Residues in contact with GLU 618 (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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616A LYS* 4.1 12.3 - - + +
617A ILE* 1.3 93.8 - - - +
619A GLU* 1.3 72.0 + - - +
620A VAL* 3.4 2.3 + - - +
630A CYS* 4.0 0.7 - - - +
631A ARG* 2.5 56.7 + - - +
632A GLY* 4.0 9.1 - - - -
633A ARG* 3.0 38.5 + - - +
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Residues in contact with GLU 619 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618A GLU* 1.3 80.1 - - - +
620A VAL* 1.3 73.2 + - - +
621A ILE* 3.9 14.5 - - + +
630A CYS* 3.2 1.7 - - - -
631A ARG* 2.8 58.2 + - - +
1888A 7X3 6.1 0.5 - - - +
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Residues in contact with VAL 620 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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617A ILE* 5.9 0.2 - - + -
618A GLU 3.4 2.4 + - - +
619A GLU* 1.3 84.0 - - - +
621A ILE* 1.3 60.8 + - - +
622A GLY 3.7 22.2 - - - +
628A GLU* 3.7 37.9 - - + +
629A VAL 3.7 6.7 - - - +
630A CYS* 3.9 12.3 - - - -
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Residues in contact with ILE 621 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619A GLU* 3.7 21.0 + - - +
620A VAL* 1.3 77.3 - - - +
622A GLY* 1.3 56.8 + - - +
629A VAL* 2.8 20.9 + - + +
630A CYS 4.1 5.6 - - - +
631A ARG* 4.0 26.5 - - + +
645A ALA* 4.8 1.3 - - + -
695A PHE* 4.1 12.8 - - + -
1888A 7X3 3.2 86.7 - - + +
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Residues in contact with GLY 622 (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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620A VAL* 3.7 13.9 - - - +
621A ILE* 1.3 79.8 - - - +
623A ALA* 1.3 60.9 + - - -
628A GLU* 4.0 3.3 - - - +
629A VAL* 3.2 27.0 + - - +
1888A 7X3 3.7 15.3 - - - -
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Residues in contact with ALA 623 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A GLY* 1.3 73.9 - - - -
624A GLY* 1.3 61.0 + - - +
627A GLY 4.0 2.9 - - - -
628A GLU* 4.9 1.1 - - - +
1888A 7X3 3.2 18.7 + - - +
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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