Contacts of the helix formed by residues 1449 - 1454 (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 ILE1449 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1343B LEU* 4.2 9.6 - - + -
1431B ILE* 3.0 43.0 + - + +
1433B LEU* 4.2 11.7 - - + -
1447B GLN* 3.7 39.3 - - - +
1448B ASN* 1.3 69.8 - - - +
1450B ASN* 1.3 66.1 + - - +
1451B PHE* 3.1 9.9 - - + -
1452B GLN* 3.0 22.6 + - + +
1453B VAL* 3.4 12.1 + - + +
1498B ILE* 4.0 14.8 - - + -
1507B TRP* 3.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360B SER* 2.9 32.6 + - - +
1362B PHE* 3.8 3.1 - - + -
1429B SER 2.9 24.4 + - - +
1430B TYR* 3.3 13.5 - - - -
1431B ILE* 3.0 29.0 + - - +
1448B ASN* 3.1 14.4 + - - +
1449B ILE* 1.3 78.2 - - - +
1451B PHE* 1.3 59.2 + - - +
1453B VAL* 4.1 4.4 - - - +
1454B LYS* 2.9 53.8 + - - +
1461B LEU* 4.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360B SER* 4.5 6.3 - - - -
1362B PHE* 3.7 37.1 - + + -
1369B GLU* 3.7 37.1 - - + +
1447B GLN* 4.9 13.9 - - + -
1448B ASN 3.5 23.8 - - - -
1449B ILE* 3.0 8.8 + - + -
1450B ASN* 1.3 79.0 - - - +
1452B GLN* 1.3 90.2 + - + +
1454B LYS 4.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447B GLN* 5.8 1.6 + - - -
1449B ILE* 3.0 13.0 + - - +
1451B PHE* 1.3 110.0 - - + +
1453B VAL* 1.3 62.1 + - + +
1454B LYS 3.9 0.2 - - - -
1505B LYS 4.4 1.8 - - - +
1506B ASN* 2.8 35.4 + - - +
1507B TRP* 2.9 51.3 + - + +
1508B THR* 4.2 6.4 - - - -
1509B ILE* 4.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1431B ILE* 4.2 13.5 - - + -
1449B ILE* 3.5 21.3 - - + +
1450B ASN* 3.2 7.6 + - - -
1452B GLN* 1.3 85.9 - - + +
1454B LYS* 1.3 62.3 + - - +
1455B LYS* 3.9 1.3 + - - -
1458B MET* 4.4 0.5 - - - +
1461B LEU* 3.6 22.1 - - + +
1498B ILE* 3.7 32.5 - - + -
1507B TRP* 3.7 27.1 - - + -
1508B THR 4.0 6.7 - - - -
1509B ILE* 3.3 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357B GLY 3.9 0.4 + - - -
1359B GLY 2.9 24.3 + - - +
1360B SER* 3.9 16.2 - - - -
1428B THR* 2.7 29.9 + - - -
1429B SER* 3.1 18.8 + - - +
1450B ASN* 2.9 35.8 + - - +
1451B PHE 5.1 3.1 - - - +
1452B GLN 3.9 0.6 - - - -
1453B VAL* 1.3 78.1 - - - +
1455B LYS* 1.3 70.9 + - - +
1456B ASP 4.2 0.2 + - - -
1458B MET* 3.6 15.9 - - + -
1459B LYS 2.8 22.1 + - - -
1461B LEU* 3.7 27.6 - - + -
----------------------------------------------------------
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