Contacts of the strand formed by residues 1482 - 1487 (chain A) in PDB entry 6XAF
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 ILE1482 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1435A LEU* 4.1 19.3 - - + -
1447A VAL* 3.4 20.9 - - + +
1449A LEU* 3.9 21.8 - - + -
1473A LEU* 3.1 45.1 - - + +
1474A LEU* 3.5 30.7 - - + +
1475A ASN* 5.0 11.7 + - - +
1479A PHE* 5.1 0.9 - - + -
1480A PRO 3.3 10.8 + - - +
1481A ALA* 1.3 72.2 - - - +
1483A ARG* 1.3 61.1 + - - +
1484A ASP 3.5 23.1 + - - +
1485A TYR* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1444A SER 5.6 3.4 + - - -
1446A PRO* 3.9 20.6 - - + +
1447A VAL 3.0 10.7 + - - +
1448A ILE* 5.4 2.0 - - + -
1474A LEU* 6.1 0.2 - - - -
1481A ALA* 3.5 30.0 + - + +
1482A ILE* 1.3 74.5 - - - +
1484A ASP* 1.3 65.6 + - - +
1507A GLU* 3.4 44.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1447A VAL 4.0 2.0 + - - -
1448A ILE* 3.5 10.4 - - + +
1449A LEU 3.1 20.8 + - - -
1474A LEU* 6.0 0.4 - - - -
1482A ILE* 3.4 8.4 - - - +
1483A ARG* 1.3 80.2 - - - +
1485A TYR* 1.3 88.4 + - - +
1486A HIS* 3.4 26.6 + - + -
1499A LYS* 4.4 8.1 + - - -
1503A THR* 3.7 23.2 + - + +
1507A GLU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1449A LEU* 3.2 27.4 - - + -
1466A MET* 3.8 30.4 - - + -
1469A ILE* 4.2 14.1 - - + -
1470A THR* 3.8 18.5 - - + +
1474A LEU* 3.6 37.6 - - + +
1484A ASP* 1.3 95.0 + - - +
1486A HIS* 1.3 68.7 + - - +
1487A PHE* 4.0 18.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419A TYR* 4.7 0.5 + - - -
1448A ILE* 3.8 7.0 - - + +
1449A LEU 2.8 8.7 + - - +
1450A VAL* 4.5 5.4 - - + -
1451A GLY 2.8 25.7 + - - -
1484A ASP* 3.4 37.0 + - + -
1485A TYR* 1.3 77.8 - - - +
1487A PHE* 1.3 71.9 + - - +
1488A VAL* 4.6 8.7 - - + -
1496A ALA* 4.6 4.9 - - + -
1499A LYS* 4.1 15.9 + - + +
1500A LEU* 3.8 41.2 - - + +
1503A THR* 3.5 28.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1419A TYR* 3.2 24.9 - - - -
1421A LEU* 3.5 33.7 - - + -
1451A GLY* 3.4 7.2 - - - +
1454A LEU* 3.7 21.6 - - + +
1462A ARG* 3.8 44.8 + - + +
1465A CYS* 4.3 4.3 - - + -
1466A MET* 4.1 29.6 - - + -
1469A ILE* 4.2 11.9 - - + -
1485A TYR* 4.0 21.3 - + - -
1486A HIS* 1.3 79.5 - - - +
1488A VAL* 1.3 66.6 + - - +
1496A ALA* 3.9 11.6 - - - +
----------------------------------------------------------
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