Contacts of the strand formed by residues 1204 - 1212 (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 LYS1204 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195A TRP* 4.1 31.8 - - + -
1196A VAL 3.3 12.3 - - - +
1197A ILE* 5.0 2.2 - - + -
1202A ASN 3.9 10.8 - - - +
1203A ASP* 1.3 75.3 - - - +
1205A GLN* 1.3 63.8 + - - +
1206A LYS 4.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194A ILE 4.2 0.2 - - - +
1195A TRP* 3.7 2.9 - - - -
1196A VAL* 3.0 37.3 + - + +
1198A VAL* 4.4 20.8 - - + +
1203A ASP 4.3 0.2 + - - -
1204A LYS* 1.3 76.4 - - - +
1206A LYS* 1.3 61.3 + - - +
1207A TYR* 4.4 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193A VAL* 3.9 16.2 - - + +
1194A ILE 3.4 4.7 - - - -
1195A TRP* 3.6 45.3 - - + -
1204A LYS 4.2 0.6 + - - -
1205A GLN* 1.3 74.2 - - - +
1207A TYR* 1.3 74.3 + - - +
1208A THR* 4.3 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193A VAL* 3.7 1.5 - - - -
1194A ILE* 2.8 54.2 + - + +
1196A VAL* 4.5 19.1 - - + -
1205A GLN* 4.4 23.4 - - + +
1206A LYS* 1.3 82.6 - - - +
1208A THR* 1.3 63.2 + - - +
1209A LEU* 3.8 12.6 + - + +
1224A ALA* 5.4 10.3 - - + -
1227A LYS* 4.7 20.2 - - + +
1228A LYS* 3.0 53.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A ILE* 3.6 28.3 - - + -
1192A VAL 3.6 6.1 - - - +
1193A VAL* 4.3 13.2 - - + +
1206A LYS* 4.3 19.9 + - - +
1207A TYR* 1.3 71.7 - - - +
1209A LEU* 1.3 62.6 + - - +
1227A LYS* 3.3 31.2 - - - +
1282A MET* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A ILE* 3.3 9.4 - - - +
1192A VAL* 2.8 40.7 + - + +
1194A ILE* 3.7 22.7 - - + -
1207A TYR* 4.1 12.6 - - + +
1208A THR* 1.3 82.6 - - - +
1210A LYS* 1.3 63.0 + - - +
1211A ILE* 4.2 7.4 - - + -
1220A VAL* 3.6 31.9 - - + +
1223A GLU* 4.1 21.3 - - + +
1224A ALA* 3.7 15.9 - - - +
1226A ARG* 6.0 0.2 - - - +
1227A LYS* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A GLN* 3.3 42.7 + - + +
1190A ILE 3.5 6.7 - - - +
1191A ILE* 4.3 20.6 - - + -
1209A LEU* 1.3 72.9 - - - +
1211A ILE* 1.3 66.9 + - - +
1223A GLU* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A GLN* 3.2 9.0 - - - +
1190A ILE* 2.8 49.0 + - + +
1192A VAL* 4.3 18.2 - - + -
1209A LEU* 4.7 4.7 - - + -
1210A LYS* 1.3 81.3 - - - +
1212A ASN* 1.3 85.0 + - - +
1215A CYS* 3.8 20.6 - - - -
1219A GLN 5.1 0.9 - - - +
1220A VAL* 4.1 15.9 - - + -
1223A GLU* 3.5 38.4 - - + +
1267A LEU* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1188A GLY* 3.5 9.3 - - - +
1189A GLN* 3.7 21.8 + - - +
1211A ILE* 1.3 89.1 - - - +
1213A HIS* 1.3 67.1 + - + +
1214A ASP* 3.3 18.3 + - - +
1215A CYS* 3.4 20.0 - - + +
----------------------------------------------------------
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