Contacts of the strand formed by residues 1636 - 1652 (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 PRO1636 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1547B ASN* 3.4 30.7 - - + +
1549B GLN* 2.9 26.4 + - - +
1627B GLN* 3.4 37.0 - - - +
1629B GLY 3.7 1.1 - - - +
1630B THR* 4.3 1.3 - - + -
1631B TYR* 3.4 4.9 - - - -
1634B GLY 3.8 2.9 - - - +
1635B GLU* 1.4 93.4 - - + +
1637B LYS* 1.3 60.2 + - - +
1638B TYR* 3.8 20.0 - - + +
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Residues in contact with LYS1637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1578B GLU* 3.8 14.9 + - - -
1627B GLN* 3.3 3.7 - - - -
1628B VAL* 2.8 49.8 + - + +
1629B GLY 2.9 19.0 + - - +
1630B THR* 4.1 9.4 - - - +
1631B TYR* 3.6 39.0 - - + +
1635B GLU 3.5 0.4 + - - -
1636B PRO* 1.3 72.3 - - - +
1638B TYR* 1.3 60.4 + - - +
1639B GLU* 3.8 28.9 + - - +
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Residues in contact with TYR1638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1545B MET* 3.6 28.5 - - + -
1546B PRO* 3.9 23.2 - - + +
1547B ASN* 3.4 43.1 + - - +
1549B GLN* 3.4 26.4 + - - -
1551B LYS* 3.3 24.0 + - - +
1578B GLU* 4.7 1.0 - - - +
1625B ILE* 3.6 20.4 - - + -
1626B ASN 3.4 1.6 - - - -
1627B GLN* 3.9 29.2 + - + -
1636B PRO* 3.8 23.5 + - + +
1637B LYS* 1.3 77.5 + - - +
1639B GLU* 1.3 70.5 + - - +
1640B PHE* 5.3 1.4 - - + -
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Residues in contact with GLU1639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1578B GLU* 2.8 27.2 - - - +
1624B LEU 3.5 1.9 - - - +
1625B ILE* 3.6 2.8 - - - +
1626B ASN* 2.9 35.8 + - + +
1628B VAL* 3.4 32.8 - - + -
1637B LYS* 3.8 14.1 + - - +
1638B TYR* 1.3 77.6 - - - +
1640B PHE* 1.3 68.8 + - - +
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Residues in contact with PHE1640 (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* 4.5 0.4 - - + -
1545B MET* 3.7 22.2 - - + -
1551B LYS* 4.0 21.5 - - + -
1553B PHE* 3.6 28.0 - + - -
1563B ILE* 3.9 21.5 - - + -
1580B ASP* 4.6 5.5 - - - +
1582B ASN* 5.9 1.2 + - - -
1605B VAL* 3.8 35.2 - - + -
1623B GLY* 4.6 2.7 - - - -
1624B LEU 3.4 3.6 - - - -
1625B ILE* 3.8 25.1 - - + -
1638B TYR 5.3 0.9 - - - -
1639B GLU* 1.3 81.1 + - - +
1641B ASP* 1.3 60.0 + - - +
1642B TRP* 3.8 34.3 + + + +
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Residues in contact with ASP1641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623B GLY* 3.4 0.8 - - - -
1624B LEU* 2.8 46.2 + - + +
1626B ASN* 4.0 16.4 + - - +
1639B GLU 4.0 0.2 + - - -
1640B PHE* 1.3 72.0 - - - +
1642B TRP* 1.3 62.6 + - - +
1643B LYS* 2.9 36.8 + - - +
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Residues in contact with TRP1642 (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* 3.7 32.8 - + - -
1561B LEU* 4.3 7.8 - - + +
1580B ASP* 2.8 31.8 + - - -
1582B ASN* 4.2 14.4 - - + -
1583B VAL* 3.5 24.4 - - + +
1605B VAL* 3.8 16.8 - - + -
1607B PHE* 3.7 26.5 - + + -
1621B ARG* 3.8 21.3 - - + +
1622B ILE 3.7 1.3 - - - -
1623B GLY* 3.4 33.0 - - - -
1640B PHE* 3.8 24.8 - + + +
1641B ASP* 1.3 69.5 + - - +
1643B LYS* 1.3 59.2 + - - +
1644B TYR 3.4 2.5 - - - -
1645B ASN* 3.0 29.9 + - - +
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Residues in contact with LYS1643 (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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1600B ASP* 2.8 35.8 + - - +
1622B ILE 3.2 3.0 + - - +
1624B LEU* 3.8 19.6 - - + +
1641B ASP* 2.9 30.2 + - - +
1642B TRP* 1.3 75.2 - - - +
1644B TYR* 1.3 86.7 + - + +
1645B ASN* 3.8 4.0 + - - -
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Residues in contact with TYR1644 (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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1599B VAL* 4.2 9.2 - - + -
1600B ASP* 2.6 34.3 + - - -
1620B VAL 4.7 0.2 - - - -
1621B ARG* 3.2 4.3 - - - +
1622B ILE* 2.9 54.2 + - + +
1624B LEU* 5.1 1.3 - - + -
1643B LYS* 1.3 111.2 + - + +
1645B ASN* 1.3 66.1 + - - +
1646B LYS 4.3 0.2 - - - -
1688B LEU* 3.7 14.8 - - - +
1689B GLU* 3.6 51.7 + - + -
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Residues in contact with ASN1645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1409A ASN 5.5 2.9 - - - +
1611B ASN* 5.9 1.1 - - - +
1619B THR* 4.2 7.6 - - + -
1620B VAL 3.7 5.2 - - - -
1621B ARG* 2.8 45.4 + - + +
1642B TRP* 3.0 29.3 + - - +
1643B LYS 3.8 4.2 + - - -
1644B TYR* 1.3 82.4 - - - +
1646B LYS* 1.3 60.3 + - - +
1647B LEU 4.2 0.9 + - - -
1688B LEU 4.2 2.9 + - - +
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Residues in contact with LYS1646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619B THR* 3.3 5.4 - - - +
1620B VAL 2.8 42.3 + - - +
1645B ASN* 1.3 75.3 - - - +
1647B LEU* 1.3 72.3 + - + +
1648B VAL* 3.3 3.2 + - + +
1687B TYR* 3.5 55.4 - - + +
1688B LEU* 3.6 22.4 - - + +
1690B SER* 2.8 26.4 + - - +
1691B GLY 3.5 16.7 - - - +
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Residues in contact with LEU1647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395A LYS* 6.1 0.9 - - - +
1399A THR* 3.9 34.1 - - + +
1409A ASN* 4.8 5.8 + - - -
1410A GLY* 3.9 31.5 - - - +
1617B ASN* 3.2 23.1 - - - +
1618B GLY 3.4 18.2 - - - +
1619B THR* 4.0 5.3 + - - +
1645B ASN 4.2 1.2 + - - -
1646B LYS* 1.3 86.2 - - + +
1648B VAL* 1.3 58.9 + - - +
1649B LYS 3.7 22.9 - - - +
1650B PRO* 3.9 9.2 - - + -
1687B TYR* 3.8 10.4 + - - -
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Residues in contact with VAL1648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248B LYS* 4.0 21.7 + - + +
1618B GLY 2.8 18.9 + - - +
1620B VAL* 3.8 24.9 - - + -
1646B LYS* 3.3 11.6 + - + +
1647B LEU* 1.3 78.2 - - - +
1649B LYS* 1.3 68.3 + - + +
1650B PRO* 4.0 6.7 - - - +
1653B TYR* 4.4 4.3 - - + +
1668B LEU* 4.0 15.9 - - + -
1670B TYR* 4.7 5.4 + - + -
1681B ILE* 4.2 7.6 - - + +
1683B MET* 3.0 35.9 - - + -
1687B TYR* 4.2 9.0 - - + -
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Residues in contact with LYS1649 (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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1386A ASN* 5.7 0.2 + - - -
1617B ASN* 3.7 1.0 - - - -
1618B GLY* 2.9 25.3 + - - -
1647B LEU* 3.7 3.6 - - - +
1648B VAL* 1.3 81.4 - - + +
1650B PRO* 1.3 89.0 + - + +
1651B GLY* 3.6 2.8 + - - +
1652B TYR* 2.8 41.6 + - - +
1653B TYR* 3.5 29.8 - - + -
1670B TYR* 3.8 21.8 - - + +
1672B GLY* 3.5 23.0 + - - -
1679B SER* 6.0 0.2 - - - -
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Residues in contact with PRO1650 (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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1385A GLU 4.2 5.0 - - - +
1386A ASN* 3.9 15.2 - - + +
1387A VAL* 3.8 23.8 - - + -
1395A LYS* 5.1 4.3 - - - +
1399A THR* 3.8 28.5 - - + +
1617B ASN* 4.9 2.2 - - - +
1647B LEU* 3.9 16.8 - - + -
1648B VAL 4.0 5.6 - - - +
1649B LYS* 1.3 112.8 + - + +
1651B GLY* 1.3 58.6 + - - +
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Residues in contact with GLY1651 (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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1386A ASN* 3.4 31.7 - - - +
1400A THR 3.7 9.5 + - - -
1401A ASN* 4.8 2.5 - - - -
1402A ALA 5.7 0.9 - - - -
1616B SER* 3.0 27.6 - - - -
1617B ASN 3.1 7.5 + - - +
1649B LYS* 3.6 2.0 + - - +
1650B PRO* 1.3 74.3 - - - +
1652B TYR* 1.3 66.6 + - - -
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Residues in contact with TYR1652 (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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1386A ASN* 4.6 1.2 + - - -
1445A GLU* 6.3 5.6 - - + -
1266B ARG* 5.4 2.6 + - - -
1615B ARG* 3.5 32.6 + - + -
1649B LYS* 2.8 31.3 + - - +
1651B GLY* 1.3 71.5 - - - +
1653B TYR* 1.3 61.0 + - - +
1654B ALA* 3.4 26.6 - - + +
1671B GLU* 3.5 16.7 + - + -
1672B GLY* 3.6 16.2 - - - +
1673B THR* 3.4 31.9 - - - -
1674B PRO* 3.7 34.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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