Contacts of the strand formed by residues 642 - 649 (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 SER 642 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A ARG* 3.2 9.5 - - - +
634A LEU* 2.8 52.3 + - - +
640A LYS 3.4 5.9 + - - -
641A GLU* 1.3 74.8 - - - +
643A CYS* 1.3 62.4 + - - +
644A VAL* 4.1 7.4 - - - +
680A GLU* 4.7 12.7 + - - -
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Residues in contact with CYS 643 (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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631A ARG* 4.2 17.0 - - - -
632A GLY 3.6 12.8 - - - -
633A ARG* 4.5 4.9 - - + +
642A SER* 1.3 76.1 - - - +
644A VAL* 1.3 67.1 + - - +
680A GLU* 5.3 0.7 - - - +
694A GLU* 3.9 2.6 - - - -
695A PHE* 3.0 53.2 + - + -
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Residues in contact with VAL 644 (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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631A ARG* 3.5 5.9 - - - +
632A GLY 2.8 45.5 + - - +
633A ARG 4.0 12.6 - - - -
634A LEU* 3.9 18.8 - - + +
642A SER* 4.1 3.6 - - - +
643A CYS* 1.3 81.0 - - - +
645A ALA* 1.3 61.4 + - - +
646A ILE* 3.7 24.9 - - + -
680A GLU* 4.0 24.0 - - + -
692A LEU* 4.2 13.2 - - + -
693A THR 3.3 13.7 - - - +
695A PHE* 3.9 6.3 - - - -
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Residues in contact with ALA 645 (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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621A ILE* 4.8 2.0 - - + -
629A VAL* 4.8 5.6 - - + -
630A CYS 3.2 8.5 - - - +
644A VAL* 1.3 74.5 - - - +
646A ILE* 1.3 60.8 + - - +
647A LYS* 6.0 1.1 - - + -
691A ILE 3.6 1.0 - - - +
692A LEU* 3.3 4.5 - - - -
693A THR* 2.9 34.4 + - - +
695A PHE* 4.0 9.5 - - + +
1888A 7X3 3.4 50.0 - - + +
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Residues in contact with ILE 646 (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* 3.6 25.1 - - + -
616A LYS 4.1 10.3 - - - +
617A ILE* 3.8 17.0 - - + -
628A GLU 3.8 1.0 - - - +
629A VAL* 3.2 4.4 - - - +
630A CYS* 2.7 45.5 + - + +
631A ARG 4.7 0.7 - - - -
632A GLY* 4.1 8.3 - - - +
644A VAL* 3.7 23.3 - - + +
645A ALA* 1.3 78.9 - - - +
647A LYS* 1.3 64.3 + - - +
648A THR* 4.1 9.1 - - + +
690A MET* 3.8 37.0 - - + -
691A ILE 3.4 4.3 - - - +
692A LEU* 4.2 8.1 - - + -
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Residues in contact with LYS 647 (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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624A GLY* 6.2 1.6 - - - -
628A GLU 3.7 5.4 - - - +
629A VAL* 3.9 19.7 - - + -
645A ALA* 4.2 1.1 - - + -
646A ILE* 1.3 73.3 - - - +
648A THR* 1.3 60.2 + - - +
661A PHE* 3.7 22.9 - - + -
664A GLU* 2.6 34.8 + - - +
690A MET* 3.1 8.7 - - - +
691A ILE* 2.9 42.7 + - + +
758A ASP* 5.4 8.1 + - - +
1888A 7X3 3.6 36.1 - - + +
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Residues in contact with THR 648 (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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617A ILE* 4.3 16.6 - - + -
626A PHE 3.6 12.0 - - - +
627A GLY* 3.8 10.2 - - - -
628A GLU* 3.1 28.3 + - + +
630A CYS* 5.0 7.0 - - - -
646A ILE* 4.1 19.1 - - + +
647A LYS* 1.3 79.4 - - - +
649A LEU* 1.3 60.7 + - - +
661A PHE* 3.9 6.2 - - - -
688A PRO* 4.3 15.5 - - + -
689A VAL 3.3 6.7 - - - -
690A MET* 4.2 8.1 - - + -
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Residues in contact with LEU 649 (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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626A PHE* 3.7 41.3 - - + +
627A GLY* 5.5 0.7 - - - -
648A THR* 1.3 78.1 - - - +
657A GLN* 5.0 7.0 - - + +
658A ARG* 3.6 44.6 - - + +
661A PHE* 3.8 27.5 - - + -
688A PRO* 3.6 21.9 - - - +
689A VAL* 2.9 22.2 + - + +
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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