Contacts of the strand formed by residues 655 - 659 (chain A) in PDB entry 2VUW
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 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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611A ASP* 3.2 2.1 - - - -
612A LEU* 2.8 53.3 + - + +
628A ILE* 4.5 2.9 - - + -
632A LEU* 4.1 19.5 - - + -
650A LEU* 3.8 19.1 - - + -
651A HIS 4.2 3.1 - - - +
652A TRP 3.8 1.5 + - - +
653A GLY 3.4 0.6 - - - -
654A ASN* 1.3 82.0 - - - +
656A LEU* 1.3 61.1 + - - +
657A LEU* 4.2 10.4 + - + +
683A VAL* 4.0 22.4 - - + -
684A SER 3.9 2.9 - - - -
685A ILE* 5.4 0.2 - - + -
748A LEU* 4.0 25.1 - - + -
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Residues in contact with LEU 656 (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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557A ILE* 4.6 1.8 - - + -
608A GLY* 3.4 23.1 - - - +
609A GLY 4.5 0.4 - - - -
610A ILE 3.6 3.8 - - - +
611A ASP* 3.6 31.4 - - + +
653A GLY 4.1 0.9 - - - +
655A VAL* 1.3 75.4 - - - +
657A LEU* 1.3 63.5 + - - +
682A GLN 3.6 0.9 - - - +
683A VAL* 3.2 7.6 - - - +
684A SER* 2.9 42.0 + - - +
686A ILE* 3.5 29.6 - - + -
1800A 5ID 3.4 57.0 - - + +
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Residues in contact with LEU 657 (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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608A GLY 3.7 1.8 - - - -
609A GLY* 3.4 0.9 - - - -
610A ILE* 2.9 36.7 + - - +
612A LEU* 3.9 21.5 - - + -
615A MSE 4.0 20.7 - - + +
619A LEU* 3.9 27.6 - - + -
628A ILE* 4.0 17.0 - - + -
655A VAL* 4.3 14.8 - - + +
656A LEU* 1.3 81.7 - - - +
658A LYS* 1.3 60.3 + - - +
681A LEU* 4.3 16.8 - - + -
682A GLN 3.7 2.2 - - - -
683A VAL* 3.6 24.9 - - + -
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Residues in contact with LYS 658 (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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606A GLU* 3.0 28.1 + - - +
607A PHE* 3.0 30.9 + - + -
608A GLY* 3.5 17.4 - - - +
609A GLY* 4.2 7.4 - - - +
657A LEU* 1.3 74.9 - - - +
659A LYS* 1.3 73.2 + - - +
681A LEU* 3.4 6.3 - - - -
682A GLN* 2.8 49.5 + - + +
684A SER* 5.4 2.1 + - - -
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Residues in contact with LYS 659 (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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658A LYS* 1.3 91.2 - - - +
660A THR* 1.3 61.5 + - - +
680A GLY 3.4 10.5 - - - +
681A LEU* 4.3 8.7 - - + +
682A GLN* 5.3 0.7 - - - +
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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