Contacts of the strand formed by residues 1602 - 1610 (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 LYS1602 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1598B LYS* 3.2 9.4 - - - +
1599B VAL 2.8 31.4 + - - +
1600B ASP 3.7 15.3 - - - +
1601B GLY* 1.4 83.1 - - - +
1603B ASP* 1.3 71.9 + - - +
1604B ALA* 3.7 0.9 + - - +
1624B LEU* 4.0 25.5 - - + +
1625B ILE 4.1 7.6 - - - +
1626B ASN* 2.6 33.6 + - - +
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Residues in contact with ASP1603 (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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1546B PRO* 3.0 31.3 - - + +
1597B GLN 5.3 1.2 - - - -
1598B LYS* 2.8 36.6 + - - +
1602B LYS* 1.3 75.4 - - - +
1604B ALA* 1.3 59.8 + - - +
1624B LEU* 3.6 2.8 - - - -
1625B ILE* 2.9 49.3 + - + +
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Residues in contact with ALA1604 (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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1594B ASN* 4.1 4.2 + - - -
1595B TYR* 3.1 36.4 + - + +
1597B GLN 4.5 4.5 + - - +
1599B VAL* 3.9 28.7 - - + -
1602B LYS 3.7 0.9 + - - +
1603B ASP* 1.3 78.3 - - - +
1605B VAL* 1.3 68.3 + - - +
1606B ILE* 5.3 0.4 - - + -
1622B ILE* 4.1 7.2 - - + -
1623B GLY 3.2 10.3 - - - +
1624B LEU* 4.0 9.4 - - + -
1625B ILE* 4.5 2.8 - - - +
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Residues in contact with VAL1605 (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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1543B VAL* 4.1 14.1 - - + -
1545B MET* 4.8 0.2 - - + -
1592B VAL* 4.1 12.3 - - + -
1593B ILE 3.2 15.5 - - - +
1594B ASN* 4.0 16.2 - - - +
1595B TYR 4.3 1.1 - - - +
1604B ALA* 1.3 78.6 - - - +
1606B ILE* 1.3 66.7 + - - +
1622B ILE* 3.4 5.2 - - - +
1623B GLY 2.8 39.4 + - - +
1625B ILE* 4.2 6.5 - - + -
1640B PHE* 3.8 31.0 - - + -
1642B TRP* 3.8 23.3 - - + -
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Residues in contact with ILE1606 (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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1592B VAL* 3.2 5.4 - - - +
1593B ILE* 2.9 44.8 + - + -
1595B TYR* 4.0 30.3 - - + -
1605B VAL* 1.3 82.5 - - - +
1607B PHE* 1.3 63.9 + - - +
1620B VAL* 3.6 26.9 - - + -
1621B ARG 3.3 4.0 - - - +
1622B ILE* 4.0 23.6 - - + -
1658B LEU* 3.5 15.6 - - + +
1666B ILE* 3.9 29.2 - - + -
1685B LEU* 4.8 5.8 - - + -
1688B LEU* 4.5 4.0 - - + -
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Residues in contact with PHE1607 (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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1553B PHE* 3.8 35.0 - + - -
1561B LEU* 4.1 6.5 - - + -
1583B VAL* 3.6 23.3 - - + -
1585B GLU* 6.2 0.2 - - + -
1590B LEU* 4.0 25.6 - - + -
1591B SER 3.3 11.9 - - - -
1592B VAL* 4.0 4.3 - - + -
1606B ILE* 1.3 74.4 - - - +
1608B SER* 1.3 60.9 + - - +
1609B ASN* 3.4 44.4 - - + -
1619B THR 4.9 0.4 - - - -
1620B VAL* 3.2 6.1 - - - +
1621B ARG* 2.8 52.7 + - + +
1642B TRP* 3.7 24.5 - + + -
1658B LEU* 3.7 2.7 - - - -
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Residues in contact with SER1608 (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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1590B LEU* 3.6 1.7 - - - +
1591B SER* 2.8 35.4 + - - +
1607B PHE* 1.3 77.8 - - - +
1609B ASN* 1.3 65.4 + - - +
1619B THR 3.4 6.7 - - - -
1620B VAL* 4.3 5.4 - - - -
1653B TYR* 2.7 29.6 + - - -
1656B SER* 2.7 20.7 + - - -
1658B LEU* 3.8 22.4 - - - -
1668B LEU* 3.8 4.7 - - - +
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Residues in contact with ASN1609 (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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1583B VAL* 4.6 1.6 - - - +
1584B LEU 2.9 26.1 + - - +
1585B GLU* 3.9 16.4 + - - +
1586B PRO* 4.0 1.6 - - - +
1588B CYS 5.7 0.4 + - - -
1589B GLN 4.4 1.3 - - - +
1590B LEU* 3.8 15.7 - - + +
1607B PHE* 3.4 26.9 - - + -
1608B SER* 1.3 77.9 + - - +
1610B PRO* 1.3 82.9 + - + +
1611B ASN* 3.4 6.8 + - - +
1619B THR* 3.0 30.8 + - - +
1621B ARG* 4.8 2.4 + - - -
1653B TYR* 3.6 11.0 - - - -
1656B SER* 4.7 1.6 - - - -
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Residues in contact with PRO1610 (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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1584B LEU 4.0 0.9 - - - +
1586B PRO* 3.3 30.5 - - + +
1588B CYS* 3.9 17.5 - - + -
1589B GLN 4.2 7.2 - - - +
1609B ASN* 1.3 96.6 + - + +
1611B ASN* 1.3 61.5 + - - +
1612B ALA 3.0 6.8 + - - -
1614B SER 3.7 5.6 - - - +
1615B ARG* 4.2 1.3 - - - -
1616B SER 3.2 24.7 - - - +
1617B ASN 4.0 0.9 - - - +
1653B TYR* 3.4 30.7 - - + +
1654B ALA 4.1 9.9 - - - +
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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