Contacts of the strand formed by residues 689 - 694 (chain A) in PDB entry 2VWX
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 689 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648A THR* 3.3 3.8 - - - -
649A LEU* 2.8 51.0 + - + +
658A ARG* 3.7 29.8 - - - +
661A PHE* 3.9 11.8 - - + -
662A LEU* 3.7 34.5 - - + -
683A VAL 3.3 13.7 - - - +
684A THR* 4.5 1.1 - - + -
686A SER 3.9 9.6 - - - +
687A MET* 4.9 2.0 - - + +
688A PRO* 1.3 74.2 - - - +
690A MET* 1.3 62.8 + - - +
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Residues in contact with MET 690 (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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612A VAL* 4.3 21.3 - - + -
615A VAL* 4.3 19.3 - - + -
617A ILE* 4.1 17.0 - - + -
646A ILE* 3.8 17.0 - - + -
647A LYS 3.1 7.4 - - - +
648A THR* 4.0 12.3 - - + -
661A PHE* 4.5 1.1 - - - -
682A VAL* 3.2 8.7 - - - +
683A VAL* 2.8 48.3 + - + +
686A SER* 6.1 0.4 - - - +
688A PRO* 3.6 32.5 - - + +
689A VAL* 1.3 81.9 - - - +
691A ILE* 1.3 64.6 - - - +
692A LEU* 3.9 12.8 - - + -
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Residues in contact with ILE 691 (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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646A ILE* 3.3 4.0 - - - -
647A LYS* 2.8 35.9 + - + -
661A PHE* 3.3 52.0 - - + +
662A LEU* 4.3 5.8 - - + -
664A GLU* 4.6 10.5 - - - +
665A ALA* 4.1 21.8 - - + +
668A MET* 3.8 23.3 - - + -
679A LEU* 3.8 13.9 - - + -
681A GLY 3.8 3.4 - - - -
682A VAL* 4.4 0.4 - - + -
690A MET* 1.3 76.8 - - - +
692A LEU* 1.3 63.2 + - - +
693A THR* 4.3 1.3 - - + -
1889A 7X4 3.5 19.0 - - + +
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Residues in contact with LEU 692 (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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610A ILE* 3.9 18.6 - - + -
615A VAL* 3.8 29.8 - - + -
634A LEU* 4.3 11.4 - - + -
644A VAL* 4.2 16.6 - - + -
645A ALA 3.3 4.3 - - - +
646A ILE* 4.1 15.0 - - + -
679A LEU* 3.4 8.0 - - - +
680A GLU* 2.8 36.4 + - + -
681A GLY 2.9 21.1 + - - +
683A VAL* 4.4 9.6 - - + -
690A MET* 3.9 25.4 - - + +
691A ILE* 1.3 79.0 - - - +
693A THR* 1.3 57.0 + - - +
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Residues in contact with THR 693 (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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644A VAL* 3.2 9.7 - - - +
645A ALA* 2.9 22.3 + - - +
668A MET* 3.7 26.0 - - + -
677A ILE* 3.7 16.2 - - + -
678A ARG 3.2 15.3 - - - +
679A LEU* 4.4 1.3 - - - -
680A GLU* 4.0 7.9 - - - +
691A ILE* 4.3 0.4 - - + -
692A LEU* 1.3 79.2 - - - +
694A GLU* 1.3 77.9 + - - +
1889A 7X4 3.3 41.8 - - + +
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Residues in contact with GLU 694 (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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643A CYS 4.4 5.4 - - - -
645A ALA 3.9 0.3 + - - -
676A ILE 3.7 1.2 - - - +
677A ILE* 3.6 6.5 - - + -
678A ARG* 2.8 74.6 + - - +
680A GLU* 4.1 5.0 - - - +
693A THR* 1.3 91.2 + - - +
695A PHE* 1.3 60.2 + - - +
696A MET* 3.8 14.3 - - - +
749A ASN* 5.5 0.7 + - - -
755A LYS* 2.7 46.5 + - - +
1889A 7X4 3.2 11.8 - - - -
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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