Contacts of the strand formed by residues 1537 - 1544 (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 LEU1537 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1493B GLN 3.0 5.6 + - - +
1494B SER* 3.0 12.8 + - - -
1495B SER* 3.0 37.1 + - - +
1512B SER* 4.9 0.4 - - - +
1513B PRO* 4.0 19.3 - - + -
1514B ASN* 3.3 27.8 - - - +
1517B ARG* 3.7 11.4 - - - +
1535B PRO 3.6 6.1 - - - +
1536B GLN* 1.3 81.5 - - - +
1538B THR* 1.3 60.9 + - - +
1554B MET* 3.7 31.6 - - + -
1555B ARG 3.6 2.5 - - - -
1556B ASN* 4.0 5.6 - - + -
1562B ASN* 3.5 27.8 - - - +
1577B VAL* 4.4 5.2 - - + -
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Residues in contact with THR1538 (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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1485B TYR* 3.4 24.3 - - - +
1493B GLN* 3.3 44.6 - - + +
1495B SER* 2.7 22.0 + - - -
1536B GLN* 4.4 5.8 - - + +
1537B LEU* 1.3 81.9 - - - +
1539B GLU* 1.3 76.3 + - - +
1540B CYS* 3.5 0.9 + - - -
1555B ARG* 2.9 41.7 + - - +
1556B ASN* 5.1 0.2 - - - -
1587B TYR* 4.0 15.0 - - + +
2692B FSI 4.8 0.2 + - - -
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Residues in contact with GLU1539 (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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1328B ASP* 4.7 0.3 - - - +
1464B ALA* 3.9 10.3 - - + -
1465B PRO* 3.6 16.0 - - + +
1485B TYR* 3.7 25.0 + - + -
1538B THR* 1.3 85.4 + - - +
1540B CYS* 1.3 59.3 + - - +
1554B MET* 3.6 0.3 - - - -
1555B ARG* 2.7 59.5 + - + +
1589B GLN* 3.2 27.6 - - + +
1590B LEU* 5.6 1.6 - - - +
1655B TYR* 2.8 31.7 + - - -
2692B FSI 4.0 12.7 - - - +
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Residues in contact with CYS1540 (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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1464B ALA* 3.4 7.5 - - - +
1465B PRO 4.9 0.2 - - - +
1483B PRO* 3.2 24.3 - - - +
1484B VAL 3.5 24.7 - - - -
1495B SER* 3.8 16.4 - - - -
1496B ALA 3.9 3.1 - - - -
1538B THR 3.8 1.8 - - - +
1539B GLU* 1.3 77.4 - - - +
1541B GLN* 1.3 80.0 + - - +
1552B LEU* 3.8 15.0 - - + -
1553B PHE 3.0 15.7 - - - +
1554B MET* 3.7 15.5 - - + -
1590B LEU* 5.1 3.1 - - - -
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Residues in contact with GLN1541 (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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1464B ALA 3.5 17.8 + - - -
1465B PRO 3.7 9.5 + - - +
1466B GLY* 3.6 3.3 - - - -
1467B ARG* 2.9 52.9 + - - +
1483B PRO* 3.8 6.8 - - - +
1540B CYS* 1.3 90.9 + - - +
1542B VAL* 1.3 60.7 + - - +
1551B LYS 4.0 0.3 - - - +
1552B LEU* 3.7 3.5 - - - -
1553B PHE* 2.8 33.3 + - - +
1589B GLN* 5.2 1.2 + - + -
1590B LEU* 3.4 27.3 - - + +
1591B SER* 4.4 7.2 + - - -
1592B VAL* 3.9 27.2 - - + +
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Residues in contact with VAL1542 (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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1467B ARG 5.4 0.8 + - - +
1468B GLY* 5.0 0.9 - - - -
1469B ILE* 3.3 41.3 - - + +
1481B VAL* 4.1 13.0 - - + +
1483B PRO* 3.9 19.0 - - + +
1497B VAL* 4.8 0.7 - - + -
1541B GLN* 1.3 78.0 - - - +
1543B VAL* 1.3 78.1 + - - +
1550B LEU* 4.0 26.9 - - + -
1551B LYS 3.3 14.8 - - - +
1552B LEU* 3.8 15.0 - - + -
1573B TRP* 4.6 3.4 - - + -
1592B VAL* 4.4 4.6 - - - +
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Residues in contact with VAL1543 (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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1469B ILE* 4.4 7.6 - - + -
1542B VAL* 1.3 82.2 - - - +
1544B GLU* 1.3 60.5 + - - +
1545B MET* 4.1 11.4 - - + -
1550B LEU* 3.4 4.2 - - - -
1551B LYS* 2.9 40.6 + - + +
1553B PHE* 3.8 28.9 - - + -
1592B VAL* 3.9 12.1 - - + +
1593B ILE* 3.6 40.2 - - - +
1594B ASN* 3.5 13.9 - - - +
1605B VAL* 4.1 8.5 - - + -
1640B PHE* 4.5 0.2 - - + -
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Residues in contact with GLU1544 (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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1469B ILE* 4.4 6.3 - - + +
1470B GLN 4.0 1.9 - - - +
1471B ILE* 3.3 15.0 - - - -
1472B LYS* 2.8 29.6 + - - +
1473B ASN* 2.8 46.5 + - - +
1543B VAL* 1.3 74.9 - - - +
1545B MET* 1.3 76.2 + - - +
1548B GLY* 3.4 18.3 - - - +
1549B GLN 3.5 2.7 - - - -
1550B LEU* 4.2 8.3 - - + -
1594B ASN* 2.8 35.5 + - - +
1625B ILE* 4.8 1.2 - - - +
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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