Contacts of the strand formed by residues 1666 - 1671 (chain B) in PDB entry 2VK7
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 ILE1666 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1593B ILE* 4.8 1.6 - - + -
1595B TYR* 3.8 29.4 - - + -
1606B ILE* 3.9 19.3 - - + -
1620B VAL* 5.2 0.7 - - + -
1658B LEU* 3.6 32.1 - - + -
1659B THR 3.5 4.9 - - - +
1660B GLU* 4.2 10.3 - - + +
1661B LEU* 3.8 3.6 - - - -
1665B ASN* 1.3 82.3 - - - +
1667B GLY* 1.3 63.9 + - - +
1681B ILE 3.9 0.2 - - - +
1682B GLU* 3.3 4.0 - - - +
1683B MET* 2.9 52.6 + - + +
1685B LEU* 4.0 17.7 - - + -
1688B LEU* 4.4 10.1 - - + -
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Residues in contact with GLY1667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B LEU* 3.8 6.5 - - - -
1658B LEU* 3.4 4.5 - - - -
1659B THR* 2.8 37.3 + - - +
1661B LEU* 3.6 8.6 - - - +
1666B ILE* 1.3 78.1 - - - +
1668B LEU* 1.3 62.2 + - - +
1680B TYR* 3.8 17.9 - - - -
1681B ILE 3.3 8.5 - - - -
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Residues in contact with LEU1668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270B LEU* 3.8 1.6 - - - +
1608B SER* 3.8 9.0 - - - +
1620B VAL* 4.0 19.3 - - + -
1648B VAL* 4.0 10.3 - - + -
1653B TYR* 3.4 26.5 - - - +
1656B SER* 4.1 6.7 - - - -
1657B CYS 3.5 17.9 - - - +
1658B LEU* 3.6 24.5 - - + -
1667B GLY* 1.3 75.2 - - - +
1669B LEU* 1.3 60.6 + - - +
1670B TYR* 3.7 19.5 - - + -
1679B SER 3.5 1.4 - - - +
1680B TYR* 3.2 8.5 - - - -
1681B ILE* 2.9 48.4 + - + +
1683B MET* 5.0 4.9 - - - -
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Residues in contact with LEU1669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254B LEU* 3.9 24.7 - - + -
1255B PHE* 4.3 12.1 - - + -
1268B PRO* 3.5 29.8 - - + +
1269B ALA 4.0 17.5 - - - +
1270B LEU* 3.8 13.2 - - + +
1280B ALA* 4.0 18.8 - - + -
1281B SER 4.3 1.3 - - - +
1282B ILE* 4.8 0.7 - - + -
1656B SER* 3.3 2.8 - - - -
1657B CYS 2.9 35.9 + - - +
1668B LEU* 1.3 72.1 - - - +
1670B TYR* 1.3 62.1 + - - +
1678B MET* 4.1 14.6 - - + -
1679B SER 3.2 22.0 - - - +
1680B TYR* 4.2 4.5 - - + +
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Residues in contact with TYR1670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248B LYS* 5.3 0.2 + - - -
1251B PRO* 3.5 26.9 - - - +
1268B PRO* 4.3 2.7 - - - -
1648B VAL* 4.7 5.7 + - + -
1649B LYS* 3.8 35.6 - - + +
1653B TYR* 3.5 38.6 - + + +
1655B TYR 3.6 3.8 - - - -
1656B SER* 4.0 3.4 - - - -
1668B LEU* 3.7 20.6 - - + -
1669B LEU* 1.3 76.2 - - - +
1671B GLU* 1.3 60.3 + - - +
1672B GLY* 3.1 21.2 + - - -
1678B MET* 3.7 5.1 - - - -
1679B SER* 2.8 60.9 + - - -
1681B ILE* 4.1 25.8 - - + +
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Residues in contact with GLU1671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266B ARG* 2.9 43.4 + - - +
1267B ILE 2.8 23.8 + - - -
1268B PRO* 3.7 6.5 - - + -
1652B TYR* 3.5 3.8 - - - -
1653B TYR* 3.4 6.4 - - - -
1654B ALA* 3.0 30.8 + - + +
1655B TYR* 2.9 45.3 + - - +
1670B TYR* 1.3 70.4 - - - +
1672B GLY* 1.3 59.9 + - - +
1673B THR 3.3 13.9 - - - +
1674B PRO 4.5 4.3 - - - +
1678B MET* 3.7 20.6 - - - -
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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