Contacts of the strand formed by residues 1284 - 1289 (chain A) in PDB entry 4YKN
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 ASN1284 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193A VAL* 3.6 13.9 - - - +
1195A TRP* 2.9 30.2 + - - +
1254A VAL* 3.9 0.5 - - - -
1255A CYS* 3.1 38.5 + - + +
1272A TYR* 3.2 18.8 + - - +
1282A MET* 3.1 27.9 + - - +
1283A PRO* 1.3 72.7 - - - +
1285A LEU* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1192A VAL* 4.9 7.0 - - + -
1193A VAL 2.9 10.7 + - - +
1194A ILE* 3.3 28.8 - - + -
1195A TRP* 2.7 34.7 + - - -
1220A VAL* 4.8 1.3 - - + -
1252A LEU* 3.9 20.6 - - + -
1253A LYS 3.2 10.3 - - - +
1254A VAL* 4.4 1.6 - - - -
1255A CYS* 3.5 2.9 - - - -
1261A PHE* 3.6 39.7 - - + -
1267A LEU* 4.6 16.2 - - + -
1272A TYR* 3.9 16.8 - - + -
1273A ILE* 4.0 4.7 - - + -
1283A PRO* 4.9 4.9 - - + +
1284A ASN* 1.3 83.1 - - - +
1286A MET* 1.3 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195A TRP* 3.4 15.0 - - + +
1196A VAL* 5.3 1.1 - - - -
1197A ILE* 4.2 25.4 - - + +
1252A LEU* 3.7 4.6 - - - -
1253A LYS* 2.6 52.1 + - + +
1255A CYS* 3.8 15.2 - - - +
1285A LEU* 1.3 74.1 - - - +
1287A LEU* 1.3 76.4 + - - +
1288A MET* 3.5 31.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194A ILE* 4.1 14.4 - - + +
1195A TRP 2.7 18.0 + - - +
1196A VAL* 4.0 25.7 - - + +
1197A ILE 5.1 1.2 + - - -
1221A ILE* 4.0 26.9 - - + -
1224A ALA* 5.8 5.8 - - + -
1246A TYR* 4.1 28.5 - - + -
1250A TYR* 3.7 33.7 - - + -
1251A ILE 3.8 9.2 - - - +
1252A LEU* 4.1 7.2 - - + -
1285A LEU 4.2 0.6 - - - -
1286A MET* 1.3 84.8 - - - +
1288A MET* 1.3 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1250A TYR* 3.2 8.2 - - - -
1251A ILE* 2.9 45.5 + - + +
1253A LYS* 3.5 26.2 - - + -
1260A TYR* 3.7 29.2 - - - +
1286A MET* 3.9 27.4 - - + +
1287A LEU* 1.3 75.5 - - - +
1289A ALA* 1.3 73.0 + - - +
1292A SER* 4.6 11.0 - - - -
1293A LEU* 4.9 9.2 - - - -
1296A GLN* 5.2 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A LYS* 3.4 16.6 - - + +
1250A TYR* 3.4 20.1 - - + -
1251A ILE* 5.1 0.7 - - - -
1288A MET* 1.3 79.7 - - - +
1290A LYS* 1.3 66.1 + - - +
1291A GLU* 4.2 9.4 - - + +
1292A SER* 3.0 28.7 + - - +
1293A LEU* 3.3 7.8 + - - +
----------------------------------------------------------
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