Contacts of the strand formed by residues 1616 - 1630 (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 SER1616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1610A PRO* 3.2 16.6 - - - +
1611A ASN 3.4 1.9 + - - -
1612A ALA* 3.5 13.3 - - - +
1614A SER* 2.9 23.7 + - - -
1615A ARG* 1.3 75.2 - - - +
1617A ASN* 1.3 74.2 + - - +
1618A GLY 3.4 1.8 - - - -
1651A GLY* 3.0 22.4 - - - -
1652A TYR* 4.7 0.2 - - - -
1653A TYR* 3.4 5.1 + - - +
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Residues in contact with ASN1617 (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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1611A ASN* 2.8 52.1 + - - +
1612A ALA* 4.2 4.7 - - + -
1616A SER* 1.3 78.2 - - - +
1618A GLY* 1.3 60.6 + - - +
1619A THR* 2.9 19.0 + - - -
1647A LEU* 3.2 28.1 - - - +
1649A LYS 3.6 6.5 + - - -
1650A PRO* 4.9 2.6 - - - +
1651A GLY 3.1 10.7 + - - +
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Residues in contact with GLY1618 (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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1609A ASN 3.7 1.8 - - - -
1616A SER 3.4 1.4 - - - -
1617A ASN* 1.3 73.5 - - - +
1619A THR* 1.3 53.6 + - - -
1647A LEU* 3.4 4.0 - - - +
1648A VAL* 2.8 37.5 + - - +
1649A LYS 2.9 14.9 + - - -
1653A TYR* 3.3 39.8 - - - +
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Residues in contact with THR1619 (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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1607A PHE* 3.7 1.4 - - - +
1608A SER* 3.4 4.0 - - - -
1609A ASN* 3.0 30.7 + - - +
1611A ASN* 3.4 24.0 + - + +
1617A ASN* 2.9 22.2 + - - -
1618A GLY* 1.3 71.7 + - - -
1620A VAL* 1.3 64.9 + - - +
1621A ARG* 4.1 28.3 + - + +
1645A ASN* 4.5 4.9 - - + -
1646A LYS 3.2 24.2 - - - +
1647A LEU* 4.0 8.2 - - - +
1648A VAL* 4.5 0.2 - - - +
1653A TYR* 4.5 1.4 - - - -
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Residues in contact with VAL1620 (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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1606A ILE* 3.7 24.0 - - + -
1607A PHE 3.2 9.2 - - - +
1608A SER* 4.3 9.6 - - - -
1619A THR* 1.3 76.2 - - - +
1621A ARG* 1.3 63.7 - - - +
1644A TYR 4.7 0.3 - - - -
1645A ASN* 3.6 0.7 - - - -
1646A LYS* 2.8 34.6 + - - +
1648A VAL* 3.8 20.2 - - + -
1653A TYR* 4.7 0.2 - - - +
1658A LEU* 4.5 7.2 - - + -
1668A LEU* 3.9 24.9 - - + -
1683A MET* 4.2 7.4 - - + -
1688A LEU* 3.7 31.4 - - + +
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Residues in contact with ARG1621 (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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1582A ASN* 3.6 24.4 + - - +
1583A VAL* 4.1 27.6 - - - +
1584A LEU 4.4 0.8 - - - +
1605A VAL 3.9 0.2 - - - +
1606A ILE* 3.3 8.5 - - - +
1607A PHE* 2.8 54.8 + - + +
1609A ASN* 4.8 2.4 + - - -
1611A ASN* 3.2 41.4 + - - +
1619A THR* 4.1 15.5 - - + +
1620A VAL* 1.3 79.3 - - - +
1622A ILE* 1.3 64.8 + - - +
1642A TRP* 3.7 25.8 - - + +
1644A TYR 3.2 9.6 - - - +
1645A ASN* 2.8 34.2 + - - +
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Residues in contact with ILE1622 (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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1599A VAL* 4.5 7.4 - - + -
1604A ALA* 4.1 10.8 - - + -
1605A VAL 3.4 9.2 - - - +
1606A ILE* 4.0 14.8 - - + -
1621A ARG* 1.3 76.0 - - - +
1623A GLY* 1.3 60.1 + - - +
1624A LEU* 4.0 21.7 + - + -
1641A ASP 3.7 0.2 - - - +
1642A TRP* 3.7 3.2 - - - -
1643A LYS* 3.2 24.3 + - - +
1644A TYR* 2.9 26.5 + - + +
1685A LEU* 4.2 15.3 - - + -
1688A LEU* 3.9 25.6 - - + -
1689A GLU* 3.9 34.5 - - + +
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Residues in contact with GLY1623 (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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1604A ALA* 3.2 4.7 - - - -
1605A VAL* 2.9 45.2 + - - +
1622A ILE* 1.3 71.2 - - - +
1624A LEU* 1.3 65.0 + - - -
1625A ILE* 3.9 0.9 + - - +
1640A PHE* 4.7 2.5 - - - -
1641A ASP 3.3 8.5 - - - -
1642A TRP* 3.4 27.9 - - - -
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Residues in contact with LEU1624 (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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1599A VAL* 3.7 42.0 - - + +
1600A ASP* 4.1 14.8 - - + +
1602A LYS* 4.1 20.6 - - + +
1603A ASP 3.6 1.6 - - - -
1604A ALA* 4.0 12.6 - - + -
1622A ILE* 4.1 7.4 - - + +
1623A GLY* 1.3 74.1 - - - -
1625A ILE* 1.3 63.6 + - - +
1626A ASN* 3.7 4.1 + - - +
1639A GLU 3.5 0.5 - - - +
1640A PHE* 3.4 4.2 - - - -
1641A ASP* 2.8 54.7 + - + +
1643A LYS* 3.8 34.1 - - + +
1644A TYR* 5.0 0.9 - - + -
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Residues in contact with ILE1625 (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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1544A GLU 4.9 3.6 - - - +
1545A MET* 3.8 30.3 - - + -
1546A PRO* 4.4 12.6 - - + -
1594A ASN* 5.0 2.0 - - - +
1602A LYS* 3.9 15.1 - - - +
1603A ASP* 2.8 39.9 + - + +
1604A ALA 4.3 1.3 - - - +
1605A VAL* 4.3 13.2 - - + -
1623A GLY 4.6 2.9 - - - +
1624A LEU* 1.3 74.2 - - - +
1626A ASN* 1.3 69.9 + - - +
1638A TYR* 3.6 33.7 - - + -
1639A GLU 3.6 4.5 - - - +
1640A PHE* 3.9 20.9 - - + -
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Residues in contact with ASN1626 (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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1602A LYS* 2.9 38.3 + - - +
1624A LEU* 3.9 13.3 + - - +
1625A ILE* 1.3 77.5 - - - +
1627A GLN* 1.3 67.4 + - - +
1628A VAL* 3.6 11.2 + - + +
1638A TYR* 3.5 4.4 - - - -
1639A GLU* 2.9 35.5 + - + +
1640A PHE 5.5 0.2 - - - -
1641A ASP* 4.0 18.6 + - - +
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Residues in contact with GLN1627 (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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1625A ILE* 4.9 0.2 - - - +
1626A ASN* 1.3 74.6 - - - +
1628A VAL* 1.3 64.9 + - - +
1629A GLY* 2.9 30.6 + - - +
1630A THR* 3.9 8.7 - - - +
1636A PRO* 3.5 27.6 - - + +
1637A LYS 3.3 11.4 - - - +
1638A TYR* 4.1 19.5 + - + -
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Residues in contact with VAL1628 (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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1626A ASN* 4.0 15.9 - - + +
1627A GLN* 1.3 77.1 - - - +
1629A GLY* 1.3 63.2 + - - +
1630A THR 3.7 0.3 + - - -
1637A LYS* 2.8 36.7 + - + +
1639A GLU* 3.7 31.9 - - + +
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Residues in contact with GLY1629 (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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1627A GLN* 2.9 26.5 + - - +
1628A VAL* 1.3 75.7 - - - +
1630A THR* 1.3 64.9 + - - -
1637A LYS 3.0 12.5 + - - -
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Residues in contact with THR1630 (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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1627A GLN* 3.9 11.9 - - - +
1628A VAL 3.7 1.0 + - - +
1629A GLY* 1.3 81.4 - - - +
1631A TYR* 1.3 71.4 + - - +
1634A GLY* 3.7 18.7 - - - +
1635A GLU 3.2 15.3 - - - +
1636A PRO* 4.3 0.4 - - + -
1637A LYS* 4.0 10.4 - - - +
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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