Contacts of the strand formed by residues 1636 - 1652 (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 PRO1636 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1547A ASN* 3.3 24.7 - - + +
1549A GLN* 2.9 26.2 + - - +
1627A GLN* 3.5 33.7 - - - +
1629A GLY 3.9 0.9 - - - +
1630A THR* 4.3 1.3 - - + -
1631A TYR* 3.4 5.4 - - - -
1634A GLY 3.7 3.1 - - - +
1635A GLU* 1.3 98.2 - - + +
1637A LYS* 1.3 59.7 + - - +
1638A TYR* 3.7 21.5 + - + +
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Residues in contact with LYS1637 (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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1578A GLU* 3.4 28.6 + - - -
1627A GLN* 3.3 4.2 - - - +
1628A VAL* 2.8 55.6 + - + +
1629A GLY 3.0 12.5 + - - +
1630A THR* 4.2 9.4 - - - +
1631A TYR* 3.7 38.6 - - + +
1635A GLU 3.5 0.4 + - - -
1636A PRO* 1.3 72.3 - - - +
1638A TYR* 1.3 62.4 + - - +
1639A GLU* 3.5 22.2 + - - +
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Residues in contact with TYR1638 (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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1545A MET* 3.6 29.8 - - + -
1546A PRO* 4.0 22.8 - - + +
1547A ASN* 3.6 41.2 + - - +
1549A GLN* 3.4 25.2 + - - -
1551A LYS* 3.1 26.1 + - - +
1578A GLU* 4.7 1.0 - - - +
1625A ILE* 3.6 19.7 - - + -
1626A ASN 3.5 1.3 - - - -
1627A GLN* 4.1 28.8 + - + -
1631A TYR* 5.0 0.2 - - - -
1636A PRO* 3.7 26.4 + - + +
1637A LYS* 1.3 75.8 - - - +
1639A GLU* 1.3 69.6 + - - +
1640A PHE* 5.2 1.4 - - + -
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Residues in contact with GLU1639 (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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1578A GLU* 2.7 26.9 - - - +
1624A LEU 3.5 2.1 - - - +
1625A ILE* 3.6 3.3 - - - -
1626A ASN* 2.9 37.7 + - + +
1628A VAL* 3.7 30.2 - - + +
1637A LYS* 3.5 14.7 + - - +
1638A TYR* 1.3 79.8 - - - +
1640A PHE* 1.3 70.1 + - - +
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Residues in contact with PHE1640 (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* 4.5 0.4 - - + -
1545A MET* 3.7 22.2 - - + -
1551A LYS* 4.0 22.7 - - + -
1553A PHE* 3.6 28.0 - + - -
1563A ILE* 3.8 22.4 - - + -
1580A ASP* 4.7 4.7 - - - +
1582A ASN* 6.0 0.3 + - - -
1605A VAL* 3.7 35.0 - - + -
1623A GLY* 4.6 2.7 - - - -
1624A LEU 3.4 3.6 - - - -
1625A ILE* 3.9 24.5 - - + -
1638A TYR 5.2 0.7 - - - -
1639A GLU* 1.3 83.3 + - - +
1641A ASP* 1.3 59.8 + - - +
1642A TRP* 3.8 33.1 + + + +
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Residues in contact with ASP1641 (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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1623A GLY* 4.2 0.7 - - - -
1624A LEU* 2.8 47.2 + - + +
1626A ASN* 4.0 16.6 + - - +
1639A GLU 4.1 0.2 + - - -
1640A PHE* 1.3 71.8 - - - +
1642A TRP* 1.3 63.7 + - - +
1643A LYS* 2.8 35.8 + - - +
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Residues in contact with TRP1642 (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* 3.7 32.5 - + - -
1561A LEU* 4.3 7.6 - - + -
1580A ASP* 2.8 30.9 + - - -
1582A ASN* 4.3 12.8 - - + -
1583A VAL* 3.6 25.3 - - + +
1605A VAL* 3.9 16.2 - - + -
1607A PHE* 3.6 26.2 - + + -
1621A ARG* 3.7 19.5 - - + +
1622A ILE 3.7 1.1 - - - -
1623A GLY* 3.4 33.2 - - - -
1640A PHE* 3.8 25.5 - + + +
1641A ASP* 1.3 70.7 + - - +
1643A LYS* 1.3 59.9 + - - +
1644A TYR 3.4 2.5 - - - -
1645A ASN* 3.0 30.5 + - - +
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Residues in contact with LYS1643 (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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1600A ASP* 2.7 37.3 + - - +
1622A ILE 3.2 2.4 + - - -
1624A LEU* 3.8 18.8 - - + +
1641A ASP* 2.8 30.6 + - - +
1642A TRP* 1.3 74.8 - - - +
1644A TYR* 1.3 87.9 + - + +
1645A ASN* 3.8 4.3 + - - -
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Residues in contact with TYR1644 (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* 4.1 11.9 - - + -
1600A ASP* 2.6 35.0 + - - -
1621A ARG* 3.2 4.4 - - - +
1622A ILE* 2.9 54.9 + - + +
1624A LEU* 5.0 1.6 - - + -
1643A LYS* 1.3 110.7 + - + +
1645A ASN* 1.3 65.6 + - - +
1688A LEU 3.7 15.3 - - - +
1689A GLU* 3.7 51.7 + - + -
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Residues in contact with ASN1645 (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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1619A THR* 4.5 6.1 - - + -
1620A VAL 3.6 5.2 - - - -
1621A ARG* 2.8 43.2 + - + +
1642A TRP* 3.0 29.2 + - - +
1643A LYS 3.8 4.4 + - - -
1644A TYR* 1.3 80.4 - - - +
1646A LYS* 1.3 64.9 + - - +
1688A LEU 4.3 3.2 + - - +
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Residues in contact with LYS1646 (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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1619A THR* 3.2 7.5 - - - +
1620A VAL 2.8 41.4 + - - +
1645A ASN* 1.3 76.2 + - - +
1647A LEU* 1.3 74.1 + - + +
1648A VAL* 3.3 3.4 + - + +
1687A TYR* 3.1 61.9 - - + +
1688A LEU* 4.0 18.6 - - + +
1690A SER* 2.9 18.8 + - - -
1691A GLY 2.9 21.3 - - - +
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Residues in contact with LEU1647 (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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1248A LYS* 4.7 1.0 + - - -
1617A ASN* 3.2 31.9 - - - +
1618A GLY 3.4 17.7 - - - +
1619A THR* 4.0 6.2 + - - +
1646A LYS* 1.3 77.4 - - + +
1648A VAL* 1.3 59.9 + - - +
1649A LYS 3.7 22.9 - - - +
1650A PRO* 3.9 20.2 - - + -
1687A TYR* 3.3 13.5 + - - -
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Residues in contact with VAL1648 (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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1248A LYS* 2.9 33.9 + - - +
1618A GLY 2.8 22.0 + - - +
1620A VAL* 3.8 24.0 - - + -
1646A LYS* 3.3 15.5 + - + +
1647A LEU* 1.3 74.2 - - - +
1649A LYS* 1.3 65.0 + - + +
1650A PRO* 4.0 5.0 - - - +
1653A TYR* 4.4 4.5 - - + +
1668A LEU* 4.0 15.7 - - + -
1670A TYR* 4.9 5.7 + - + -
1681A ILE* 4.3 6.8 - - + +
1683A MET* 3.7 24.9 - - - -
1687A TYR* 3.8 13.9 - - + +
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Residues in contact with LYS1649 (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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1617A ASN* 3.6 3.6 + - - -
1618A GLY* 2.9 25.6 + - - -
1647A LEU* 3.7 4.0 - - - +
1648A VAL* 1.3 80.1 - - + +
1650A PRO* 1.4 90.2 + - + +
1651A GLY* 3.7 0.6 - - - +
1652A TYR* 2.8 43.1 + - - +
1653A TYR* 3.5 28.5 - - + -
1670A TYR* 3.8 22.2 - - + +
1672A GLY* 3.5 21.3 + - - -
1679A SER* 6.0 0.4 - - - -
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Residues in contact with PRO1650 (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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1248A LYS* 5.5 2.0 - - - +
1617A ASN* 4.9 2.2 - - - +
1647A LEU* 3.9 25.5 - - + -
1648A VAL 4.0 5.4 - - - +
1649A LYS* 1.4 112.4 + - + +
1651A GLY* 1.3 58.6 + - - +
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Residues in contact with GLY1651 (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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1616A SER* 3.0 28.8 - - - -
1617A ASN 3.1 7.7 + - - +
1649A LYS* 3.7 1.9 + - - +
1650A PRO* 1.3 73.9 - - - +
1652A TYR* 1.3 66.0 + - - -
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Residues in contact with TYR1652 (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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1266A ARG* 5.5 1.9 + - - -
1615A ARG* 3.5 31.3 + - + -
1616A SER* 4.7 0.2 - - - -
1649A LYS* 2.8 31.3 + - - +
1651A GLY* 1.3 71.6 - - - -
1653A TYR* 1.3 60.7 + - - +
1654A ALA* 3.4 32.8 - - + +
1671A GLU* 3.5 9.5 + - - -
1672A GLY* 3.5 16.6 - - - +
1673A THR* 3.4 31.0 - - - -
1674A PRO* 3.6 34.8 + - + +
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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