Contacts of the strand formed by residues 1616 - 1630 (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 SER1616 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1401A ASN* 2.9 43.2 + - - -
1402A ALA 5.4 0.9 - - - -
1610B PRO* 3.2 17.3 - - - +
1611B ASN 3.4 2.3 + - - -
1612B ALA* 3.4 9.0 - - - +
1614B SER* 2.9 13.5 + - - -
1615B ARG* 1.3 75.0 - - - +
1617B ASN* 1.3 74.6 + - - +
1618B GLY 3.4 2.0 - - - -
1651B GLY 3.0 17.3 - - - -
1652B TYR* 4.8 0.2 - - - -
1653B TYR* 3.5 5.1 + - - +
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Residues in contact with ASN1617 (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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1399A THR* 4.6 0.9 + - - -
1401A ASN* 5.3 0.4 - - - +
1407A PHE* 3.5 41.8 - - + -
1410A GLY* 3.1 28.2 + - - +
1412A LYS 5.5 0.2 - - - +
1611B ASN* 2.8 44.8 + - - +
1612B ALA* 4.3 0.7 - - + -
1616B SER* 1.3 76.9 - - - +
1618B GLY* 1.3 61.4 + - - +
1619B THR* 2.8 19.2 + - - -
1647B LEU* 3.2 21.7 - - - +
1649B LYS 3.7 5.8 - - - -
1650B PRO* 4.9 0.7 - - - -
1651B GLY 3.1 12.2 + - - +
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Residues in contact with GLY1618 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1609B ASN 3.7 1.3 - - - -
1616B SER 3.4 1.4 - - - -
1617B ASN* 1.3 72.9 - - - +
1619B THR* 1.3 53.8 + - - -
1647B LEU* 3.4 4.0 - - - +
1648B VAL* 2.8 36.4 + - - -
1649B LYS 2.9 15.9 + - - -
1653B TYR* 3.3 38.5 - - - +
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Residues in contact with THR1619 (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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1410A GLY 5.0 1.0 + - - -
1607B PHE* 3.7 1.4 - - - +
1608B SER* 3.4 4.7 - - - -
1609B ASN* 3.0 30.3 + - - +
1611B ASN* 3.5 28.6 + - + +
1617B ASN* 2.8 25.0 + - - -
1618B GLY* 1.3 73.0 + - - -
1620B VAL* 1.3 65.4 + - - +
1621B ARG* 4.1 20.0 + - + +
1645B ASN* 4.2 7.0 - - + -
1646B LYS 3.3 26.7 - - - +
1647B LEU* 4.0 7.3 - - - +
1648B VAL* 4.5 0.2 - - - +
1653B TYR* 4.5 1.4 - - - -
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Residues in contact with VAL1620 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1606B ILE* 3.6 28.0 - - + -
1607B PHE 3.2 5.6 - - - +
1608B SER* 4.3 11.0 - - - +
1619B THR* 1.3 78.1 - - - +
1621B ARG* 1.3 63.6 + - - +
1644B TYR 4.2 0.5 - - - +
1645B ASN* 3.7 0.3 - - - -
1646B LYS* 2.8 34.5 + - - +
1648B VAL* 3.8 26.0 - - + -
1658B LEU* 4.4 6.7 - - + -
1666B ILE* 5.2 0.4 - - + -
1668B LEU* 4.0 17.5 - - + -
1683B MET* 4.2 7.0 - - - -
1688B LEU* 3.6 31.9 - - + +
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Residues in contact with ARG1621 (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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1582B ASN* 3.5 25.5 + - - +
1583B VAL* 3.9 28.3 - - - +
1584B LEU 4.3 0.8 - - - +
1605B VAL 3.8 0.2 - - - +
1606B ILE* 3.3 8.1 - - - +
1607B PHE* 2.8 54.9 + - + +
1609B ASN* 4.8 3.0 + - - -
1611B ASN* 3.2 41.0 + - - +
1619B THR* 4.1 13.4 + - + +
1620B VAL* 1.3 80.3 - - - +
1622B ILE* 1.3 64.9 + - - +
1642B TRP* 3.8 25.9 - - + +
1644B TYR 3.2 9.0 - - - +
1645B ASN* 2.8 42.7 + - - +
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Residues in contact with ILE1622 (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* 4.4 8.5 - - + -
1604B ALA* 4.1 10.5 - - + -
1605B VAL 3.4 9.2 - - - +
1606B ILE* 4.0 15.5 - - + -
1621B ARG* 1.3 73.9 - - - +
1623B GLY* 1.3 60.9 + - - +
1624B LEU* 4.0 22.6 + - + -
1641B ASP 3.7 0.3 - - - +
1642B TRP* 3.7 4.1 - - - -
1643B LYS* 3.2 24.6 + - - +
1644B TYR* 2.9 24.5 + - + +
1685B LEU* 4.1 16.4 - - + -
1688B LEU* 3.9 28.9 - - + -
1689B GLU* 3.9 29.6 - - + +
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Residues in contact with GLY1623 (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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1604B ALA* 3.2 3.7 - - - -
1605B VAL* 2.8 42.8 + - - +
1622B ILE* 1.3 72.9 - - - +
1624B LEU* 1.3 65.2 + - - -
1625B ILE* 3.9 1.4 + - - +
1640B PHE* 4.7 3.6 - - - -
1641B ASP 3.4 7.4 - - - -
1642B TRP* 3.4 27.3 - - - -
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Residues in contact with LEU1624 (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* 3.7 43.5 - - + +
1600B ASP* 4.1 12.6 - - + +
1602B LYS* 4.0 20.6 - - + +
1603B ASP 3.6 1.3 - - - -
1604B ALA* 4.0 6.3 - - + -
1622B ILE* 4.0 15.0 - - + -
1623B GLY* 1.3 73.6 - - - -
1625B ILE* 1.3 63.2 + - - +
1626B ASN* 3.8 3.6 + - - +
1639B GLU 3.5 0.5 - - - +
1640B PHE* 3.4 4.0 - - - -
1641B ASP* 2.8 53.5 + - + +
1643B LYS* 3.8 34.3 - - + +
1644B TYR* 5.1 0.9 - - + -
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Residues in contact with ILE1625 (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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1544B GLU 4.8 3.8 - - - +
1545B MET* 3.7 30.7 - - + -
1546B PRO* 4.3 14.8 - - + -
1594B ASN* 5.0 2.0 - - - +
1602B LYS* 4.1 11.8 - - - +
1603B ASP* 2.9 42.1 + - + +
1604B ALA 4.3 1.8 - - - +
1605B VAL* 4.2 13.5 - - + -
1623B GLY 4.5 2.7 - - - +
1624B LEU* 1.3 73.4 - - - +
1626B ASN* 1.3 69.5 + - - +
1638B TYR* 3.6 31.0 - - + -
1639B GLU 3.6 4.7 - - - +
1640B PHE* 3.8 21.1 - - + -
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Residues in contact with ASN1626 (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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1602B LYS* 2.6 38.5 + - - +
1624B LEU* 4.0 14.3 + - - +
1625B ILE* 1.3 77.0 + - - +
1627B GLN* 1.3 64.9 + - - +
1628B VAL* 3.5 15.8 + - + +
1638B TYR* 3.4 5.1 - - - -
1639B GLU* 2.9 37.7 + - + +
1641B ASP* 4.0 18.8 + - - +
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Residues in contact with GLN1627 (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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1625B ILE 4.4 0.2 - - - -
1626B ASN* 1.3 73.4 - - - +
1628B VAL* 1.3 64.2 + - - +
1629B GLY* 3.1 29.7 + - - +
1630B THR* 4.0 8.1 - - - +
1636B PRO* 3.4 30.8 - - + +
1637B LYS 3.3 8.7 - - - +
1638B TYR* 3.9 20.1 + - + -
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Residues in contact with VAL1628 (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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1626B ASN* 4.0 17.0 - - + +
1627B GLN* 1.3 76.2 - - - +
1629B GLY* 1.3 62.6 + - - +
1637B LYS* 2.8 34.5 + - + +
1639B GLU* 3.4 35.2 - - + -
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Residues in contact with GLY1629 (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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1627B GLN* 3.1 21.4 + - - +
1628B VAL* 1.3 77.1 - - - +
1630B THR* 1.3 64.0 + - - -
1637B LYS 2.9 18.8 + - - -
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Residues in contact with THR1630 (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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1627B GLN* 4.0 11.2 - - - +
1628B VAL 4.0 0.8 + - - -
1629B GLY* 1.3 79.9 - - - +
1631B TYR* 1.3 70.0 + - - +
1634B GLY* 3.7 21.3 - - - +
1635B GLU 3.1 11.9 - - - +
1636B PRO* 4.3 0.2 - - + -
1637B LYS* 3.9 12.2 - - - +
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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