Contacts of the strand formed by residues 1493 - 1500 (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 GLN1493 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353B PHE* 3.7 10.0 - - + -
1354B TRP* 6.3 1.0 - - - -
1485B TYR* 3.3 21.1 - - + -
1486B TYR 3.2 6.5 - - - +
1487B THR* 3.6 20.6 - - + -
1491B GLY 4.4 1.3 - - - +
1492B LYS* 1.3 72.6 - - - +
1494B SER* 1.3 65.3 + - - +
1514B ASN* 3.7 1.0 + - - -
1530B LEU* 4.0 1.2 - - - +
1536B GLN* 2.9 38.5 + - - +
1537B LEU 3.0 19.3 + - - +
1538B THR* 3.3 28.7 - - + +
1587B TYR* 3.0 23.0 + - - -
2692B FSI 3.0 20.6 + - - -
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Residues in contact with SER1494 (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* 3.3 2.4 - - - -
1486B TYR* 2.9 41.2 + - - +
1492B LYS 4.0 1.7 + - - -
1493B GLN* 1.3 72.9 + - - +
1495B SER* 1.3 61.6 + - - +
1512B SER* 3.3 17.9 - - - -
1514B ASN* 2.9 23.1 + - - +
1527B SER* 3.2 30.6 + - - -
1530B LEU* 4.1 4.2 - - - +
1537B LEU 3.0 6.7 + - - -
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Residues in contact with SER1495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484B VAL 3.6 6.5 - - - -
1485B TYR* 4.0 0.2 - - - -
1494B SER* 1.3 73.3 - - - +
1496B ALA* 1.3 61.9 + - - +
1512B SER* 2.6 35.9 + - - -
1513B PRO* 3.2 2.5 - - - +
1537B LEU* 3.0 20.9 + - - +
1538B THR 2.7 25.6 + - - -
1540B CYS* 3.8 12.6 - - - -
1552B LEU* 4.0 3.8 - - - -
1554B MET* 3.7 24.3 - - - +
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Residues in contact with ALA1496 (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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1483B PRO* 3.6 1.7 - - - +
1484B VAL* 2.9 38.0 + - + +
1486B TYR* 3.9 21.1 - - + -
1495B SER* 1.3 78.6 - - - +
1497B VAL* 1.3 68.2 + - - +
1509B ILE* 4.2 3.4 - - + -
1510B GLY 3.9 18.6 - - - +
1511B GLU 3.9 10.1 - - - +
1512B SER* 4.3 0.9 - - - +
1513B PRO* 4.6 0.4 - - - -
1540B CYS* 3.9 4.0 - - - -
1552B LEU* 4.6 8.1 - - - -
1573B TRP* 5.1 0.7 - - - +
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Residues in contact with VAL1497 (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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1481B VAL* 3.6 34.1 - - + -
1482B VAL 3.4 5.6 - - - +
1483B PRO* 4.0 10.1 - - + -
1484B VAL* 4.1 2.9 - - - -
1496B ALA* 1.3 81.8 - - - +
1498B ILE* 1.3 61.8 + - - +
1499B TYR* 4.2 8.6 - - + -
1509B ILE* 3.6 2.3 - - - +
1510B GLY 2.9 26.3 + - - -
1511B GLU 4.9 2.2 + - - -
1542B VAL* 4.8 1.3 - - + -
1552B LEU* 4.0 22.7 - - + -
1570B GLY* 3.6 32.8 - - - +
1573B TRP* 4.3 11.6 - - + -
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Residues in contact with ILE1498 (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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1343B LEU* 4.0 15.5 - - + -
1431B ILE* 4.6 6.7 - - + -
1449B ILE* 4.0 22.0 - - + -
1453B VAL* 3.7 26.0 - - + -
1461B LEU* 5.5 0.9 - - + -
1463B ILE* 4.9 0.2 - - + -
1480B ILE 3.9 0.2 - - - +
1481B VAL* 3.5 0.7 - - - -
1482B VAL* 2.8 51.3 + - + +
1484B VAL* 4.0 22.0 - - + +
1497B VAL* 1.3 74.8 - - - +
1499B TYR* 1.3 64.6 + - - +
1507B TRP* 3.9 17.0 - - + -
1508B THR 3.1 8.7 - - - +
1509B ILE* 3.8 22.2 - - + -
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Residues in contact with TYR1499 (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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1479B ARG* 3.4 53.1 + - + -
1480B ILE 3.0 14.1 - - - +
1481B VAL* 4.3 5.4 - - + -
1497B VAL* 4.2 14.6 - - + -
1498B ILE* 1.3 79.9 - - - +
1500B SER* 1.3 62.1 + - - +
1501B ASP* 4.2 7.6 - - - -
1507B TRP* 3.3 9.3 - - - -
1508B THR* 2.9 58.3 + - + +
1509B ILE 4.4 2.7 + - - -
1510B GLY* 3.9 24.1 - - - -
1569B GLY 4.6 2.0 - - - -
1570B GLY 4.2 7.0 - - - -
1571B ALA* 3.9 18.5 - - + +
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Residues in contact with SER1500 (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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1478B GLY 4.2 1.6 - - - +
1479B ARG* 3.5 2.8 - - - -
1480B ILE* 2.9 36.2 + - - +
1499B TYR* 1.3 74.8 - - - +
1501B ASP* 1.3 61.7 + - - +
1502B ASP* 2.9 8.7 + - - -
1503B SER 4.8 0.2 + - - -
1504B GLY* 2.8 36.8 + - - -
1506B ASN 2.8 24.0 + - - -
1507B TRP* 3.8 15.7 - - - -
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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