Contacts of the strand formed by residues 1502 - 1506 (chain D) in PDB entry 5YWB
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 ILE1502 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339D TRP* 5.5 5.2 - - - +
1343D GLY* 3.7 33.7 - - - +
1345D ILE* 4.9 13.7 - - + -
1392D PHE* 4.6 8.7 - - + -
1405D ILE* 5.6 4.5 - - + -
1421D ARG 4.2 3.6 + - - +
1422D LEU* 3.6 32.4 - - + -
1423D SER 2.9 26.3 + - - -
1500D THR* 3.1 6.8 + - - -
1501D SER* 1.3 96.3 - - - +
1503D PHE* 1.3 72.2 + - - +
1504D ILE* 4.3 11.2 - - + -
1532D THR* 3.5 19.5 - - + +
1534D VAL* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1503 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423D SER* 3.6 11.9 - - - -
1425D ILE* 5.4 6.3 - - + -
1495D ALA* 3.6 36.6 - - + -
1496D PHE* 5.3 0.2 - + - -
1499D LYS 5.3 0.4 - - - -
1500D THR* 4.0 21.8 - - - -
1502D ILE* 1.3 80.2 - - - +
1504D ILE* 1.3 72.2 + - - +
1505D MET* 6.0 4.0 - - + -
1528D PHE* 3.4 36.3 - + - -
1531D ARG* 3.5 32.5 - - + -
1532D THR 2.9 10.4 + - - -
1533D VAL* 3.6 29.3 - - + -
1534D VAL* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1504 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1388D PHE* 6.3 2.9 - - + -
1389D SER* 3.3 33.2 - - - +
1392D PHE* 4.5 24.5 - - + -
1393D PHE* 4.8 10.3 - - + -
1422D LEU* 5.0 3.4 - - + -
1423D SER 2.8 17.9 + - - +
1424D ILE* 3.4 16.1 - - + -
1425D ILE* 2.9 29.3 + - - +
1502D ILE* 4.3 15.5 - - + -
1503D PHE* 1.3 88.2 - - - +
1505D MET* 1.3 66.7 + - - +
1506D ASP 4.0 0.9 - - - +
1534D VAL* 3.4 20.9 - - + +
1536D ILE* 5.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425D ILE* 4.0 20.2 - - + -
1492D LEU* 5.9 3.4 - - + -
1503D PHE* 6.0 4.3 - - + -
1504D ILE* 1.3 75.2 - - - +
1506D ASP* 1.3 57.0 + - - +
1507D GLU 3.2 3.1 + - - -
1508D ALA* 3.5 31.6 - - + +
1509D THR* 6.1 0.2 - - - -
1521D GLN* 3.0 34.8 - - - +
1524D VAL* 4.7 17.0 - - + -
1525D MET* 5.8 0.7 - - + -
1533D VAL* 4.4 13.9 - - + -
1534D VAL 2.9 13.9 + - - +
1535D THR* 4.0 23.3 - - + -
1536D ILE* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1506 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1385D LYS* 4.4 8.3 - - - -
1386D SER* 3.4 32.6 - - - -
1389D SER* 4.8 4.2 - - - +
1424D ILE* 4.8 8.1 - - + -
1425D ILE* 2.9 19.5 + - - +
1426D LEU* 3.4 9.0 - - + +
1427D GLN* 3.2 33.3 + - - +
1504D ILE* 4.0 1.0 - - + -
1505D MET* 1.3 67.8 - - - +
1507D GLU* 1.3 84.3 + - - +
1508D ALA 3.7 0.2 + - - -
1536D ILE* 3.6 23.6 - - + +
2504D MG 4.3 0.5 - - - -
----------------------------------------------------------
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