Contacts of the strand formed by residues 1604 - 1610 (chain A) 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 ALA1604 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1594A ASN* 4.1 3.8 + - - -
1595A TYR* 3.1 36.6 + - + +
1597A GLN 4.6 5.0 + - - +
1599A VAL* 4.0 21.3 - - + -
1602A LYS 3.7 1.1 + - - +
1603A ASP* 1.3 77.9 - - - +
1605A VAL* 1.3 68.3 + - - +
1622A ILE* 4.1 8.5 - - + -
1623A GLY 3.2 11.4 - - - +
1624A LEU* 4.0 16.2 - - + -
1625A ILE* 4.3 2.3 - - - +
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Residues in contact with VAL1605 (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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1543A VAL* 4.1 14.4 - - + -
1545A MET* 4.8 0.2 - - + -
1592A VAL* 4.1 12.3 - - + -
1593A ILE 3.2 14.6 - - - +
1594A ASN* 4.0 17.0 - - - +
1595A TYR 4.3 0.7 - - - +
1604A ALA* 1.3 79.6 - - - +
1606A ILE* 1.3 67.4 + - - +
1622A ILE* 3.4 6.4 - - - +
1623A GLY 2.9 38.8 + - - +
1625A ILE* 4.3 7.0 - - + -
1640A PHE* 3.7 30.5 - - + -
1642A TRP* 3.9 23.8 - - + -
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Residues in contact with ILE1606 (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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1592A VAL* 3.2 5.4 - - - +
1593A ILE* 2.9 46.4 + - + -
1595A TYR* 4.0 30.7 - - + -
1605A VAL* 1.3 82.1 - - - +
1607A PHE* 1.3 62.8 + - - +
1620A VAL* 3.7 25.8 - - + -
1621A ARG 3.3 4.5 - - - +
1622A ILE* 4.0 24.0 - - + -
1658A LEU* 3.4 17.8 - - + +
1666A ILE* 3.9 30.7 - - + -
1685A LEU* 4.9 3.8 - - + -
1688A LEU* 4.8 2.2 - - + -
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Residues in contact with PHE1607 (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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1553A PHE* 3.8 35.0 - + - -
1561A LEU* 4.1 5.8 - - + -
1583A VAL* 3.6 25.1 - - + -
1590A LEU* 4.1 25.1 - - + -
1591A SER 3.3 12.1 - - - -
1592A VAL* 4.0 4.3 - - + -
1606A ILE* 1.3 75.3 - - - +
1608A SER* 1.3 60.3 + - - +
1609A ASN* 3.4 42.8 - - + -
1619A THR 4.9 0.4 - - - -
1620A VAL* 3.2 7.4 - - - +
1621A ARG* 2.8 51.2 + - + +
1642A TRP* 3.6 24.5 - + + -
1658A LEU* 3.7 2.7 - - - -
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Residues in contact with SER1608 (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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1590A LEU* 3.6 1.7 - - - +
1591A SER* 2.8 36.3 + - - +
1607A PHE* 1.3 78.2 - - - +
1609A ASN* 1.3 64.9 + - - +
1619A THR 3.4 7.0 - - - -
1620A VAL* 4.3 3.4 - - - -
1653A TYR* 2.6 28.9 + - - -
1656A SER* 2.7 17.6 + - - -
1658A LEU* 3.8 23.6 - - - -
1668A LEU* 3.7 5.3 - - - +
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Residues in contact with ASN1609 (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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1583A VAL* 4.6 2.1 - - - +
1584A LEU 2.9 25.9 + - - +
1585A GLU* 3.9 17.2 + - - +
1586A PRO* 4.0 1.2 - - - +
1588A CYS 5.7 0.2 + - - -
1589A GLN 4.4 1.6 - - - +
1590A LEU* 3.9 15.0 - - + +
1607A PHE* 3.4 27.0 - - + -
1608A SER* 1.3 79.2 + - - +
1610A PRO* 1.3 84.0 + - + +
1611A ASN* 3.4 5.7 + - - +
1618A GLY* 3.7 0.2 - - - -
1619A THR* 3.0 30.4 + - - +
1621A ARG* 4.8 2.9 + - - -
1653A TYR* 3.6 10.8 - - - -
1656A SER* 4.7 1.6 - - - -
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Residues in contact with PRO1610 (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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1584A LEU 3.9 1.0 - - - +
1586A PRO* 3.4 30.5 - - + +
1588A CYS* 3.9 16.2 - - + -
1589A GLN 4.3 7.9 - - - +
1609A ASN* 1.3 98.4 + - + +
1611A ASN* 1.3 60.3 + - - +
1612A ALA 3.0 7.2 + - - -
1614A SER 3.6 6.1 - - - +
1615A ARG* 4.1 2.0 - - - -
1616A SER 3.2 24.0 - - - +
1617A ASN 4.0 0.9 - - - +
1653A TYR* 3.3 30.7 - - + +
1654A ALA 4.1 9.2 - - - +
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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