Contacts of the strand formed by residues 1493 - 1500 (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 GLN1493 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1353A PHE* 3.7 10.3 - - + -
1354A TRP* 5.1 6.5 - - - -
1485A TYR* 3.4 19.3 - - + -
1486A TYR 3.2 7.0 - - - +
1487A THR* 3.6 21.1 - - + -
1491A GLY 4.5 1.5 + - - +
1492A LYS* 1.3 73.0 - - - +
1494A SER* 1.3 65.3 + - - +
1514A ASN* 3.8 0.5 + - - -
1530A LEU* 4.0 1.4 - - - +
1536A GLN* 2.9 36.4 + - - +
1537A LEU 3.0 21.7 + - - +
1538A THR* 3.3 28.5 - - + +
1587A TYR* 3.0 22.8 + - - -
2693A FSI 3.0 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485A TYR* 3.3 3.5 - - - -
1486A TYR* 2.9 42.9 + - - -
1492A LYS 4.0 1.7 + - - -
1493A GLN* 1.3 72.4 + - - +
1495A SER* 1.4 60.3 + - - +
1512A SER* 3.3 17.3 - - - -
1514A ASN* 2.9 23.2 + - - +
1527A SER* 3.2 30.5 + - - -
1530A LEU* 4.2 4.3 - - - +
1537A LEU 3.0 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484A VAL 3.6 6.7 - - - -
1494A SER* 1.4 73.9 - - - +
1496A ALA* 1.3 61.9 + - - +
1512A SER* 2.6 36.3 + - - -
1513A PRO* 3.2 3.7 - - - +
1537A LEU* 3.0 21.4 + - - +
1538A THR 2.7 26.2 + - - -
1540A CYS* 3.7 13.0 - - - -
1552A LEU* 4.1 4.0 - - - -
1554A MET* 3.7 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1483A PRO* 3.7 0.9 - - - +
1484A VAL* 2.9 37.8 + - + +
1486A TYR* 3.9 18.8 - - + -
1495A SER* 1.3 78.6 - - - +
1497A VAL* 1.3 68.4 + - - +
1509A ILE* 4.1 3.4 - - + -
1510A GLY 3.9 21.5 - - - +
1511A GLU 3.9 9.9 - - - +
1512A SER* 4.2 0.7 - - - +
1513A PRO* 4.6 4.0 - - - -
1540A CYS* 3.9 4.2 - - - -
1552A LEU* 4.6 4.3 - - - -
1573A TRP* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1481A VAL* 3.6 35.0 - - + -
1482A VAL 3.4 4.7 - - - +
1483A PRO* 4.1 10.8 - - + -
1484A VAL* 4.1 2.7 - - - -
1496A ALA* 1.3 81.2 - - - +
1498A ILE* 1.3 63.3 + - - +
1499A TYR* 4.3 8.2 - - + -
1509A ILE* 3.6 2.6 - - - +
1510A GLY 3.0 25.5 + - - +
1511A GLU 5.0 1.8 + - - -
1542A VAL* 4.8 1.6 - - + -
1552A LEU* 4.0 22.2 - - + -
1569A GLY 5.0 0.2 - - - +
1570A GLY* 3.7 33.4 - - - +
1573A TRP* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343A LEU* 4.0 15.7 - - + -
1431A ILE* 4.6 7.0 - - + -
1449A ILE* 4.0 22.9 - - + -
1453A VAL* 3.7 27.1 - - + -
1461A LEU* 5.5 1.3 - - + -
1463A ILE* 5.0 0.2 - - + -
1481A VAL* 3.5 0.9 - - - -
1482A VAL* 2.8 51.7 + - + +
1484A VAL* 4.0 21.5 - - + +
1497A VAL* 1.3 76.7 - - - +
1499A TYR* 1.3 64.1 + - - +
1507A TRP* 3.8 18.2 - - + -
1508A THR 3.1 7.2 - - - +
1509A ILE* 3.8 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479A ARG* 3.3 55.7 + - - -
1480A ILE 3.0 14.8 - - - +
1481A VAL* 4.3 5.4 - - + -
1497A VAL* 4.3 14.6 - - + -
1498A ILE* 1.3 79.0 - - - +
1500A SER* 1.3 61.5 + - - +
1501A ASP* 4.1 8.1 - - - -
1507A TRP* 3.3 8.0 - - - -
1508A THR* 2.8 54.6 + - - +
1509A ILE 4.4 0.8 + - - -
1510A GLY* 4.0 24.0 - - - -
1569A GLY 4.4 2.7 - - - -
1570A GLY 4.2 0.2 - - - -
1571A ALA* 3.8 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478A GLY 4.3 0.7 - - - +
1479A ARG* 3.5 3.4 - - - -
1480A ILE* 2.9 37.5 + - - +
1499A TYR* 1.3 75.0 - - - +
1501A ASP* 1.3 62.1 + - - +
1502A ASP* 2.9 8.3 + - - -
1503A SER 4.7 0.6 + - - -
1504A GLY* 2.9 34.6 + - - -
1506A ASN 2.8 23.4 + - - -
1507A TRP* 3.8 15.7 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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