Contacts of the helix formed by residues 1141 - 1155 (chain B) in PDB entry 6KJV
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 THR1141 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104B GLN* 3.3 29.3 + - - +
1137B TRP* 3.3 18.1 + - - +
1138B TYR 3.8 2.0 - - - -
1140B GLN* 1.3 91.9 - - + +
1142B PRO* 1.3 67.2 - - - +
1143B ASN 3.5 1.6 - - - -
1144B ARG* 4.3 8.9 - - - +
1145B ALA* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138B TYR* 3.2 32.1 - - + +
1139B ASN* 4.4 5.8 - - - +
1140B GLN 3.6 7.6 - - - +
1141B THR* 1.3 85.2 - - - +
1143B ASN* 1.3 72.8 + - - +
1145B ALA* 3.3 2.2 + - + +
1146B LYS* 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141B THR 3.5 0.6 - - - -
1142B PRO* 1.3 90.7 - - + +
1144B ARG* 1.3 60.9 + - - +
1146B LYS* 3.9 4.3 + - - +
1147B ARG* 3.3 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006B LEU* 3.6 14.3 - - - +
1009B ASP* 3.5 38.7 + - + +
1010B GLU* 2.8 37.0 + - - +
1100B ASN* 2.8 41.1 + - - +
1104B GLN* 3.3 40.9 + - - +
1137B TRP* 5.0 0.9 - - - +
1141B THR* 3.8 12.8 + - - +
1142B PRO 3.3 0.2 - - - -
1143B ASN* 1.3 78.1 - - - +
1145B ALA* 1.3 66.6 + - - +
1147B ARG* 3.3 19.0 + - - +
1148B VAL* 3.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137B TRP* 3.5 33.6 - - + -
1138B TYR* 3.8 28.9 - - + -
1141B THR 3.2 18.6 + - - +
1142B PRO 3.3 3.6 + - - +
1144B ARG* 1.3 79.2 - - - +
1146B LYS* 1.3 56.8 + - - +
1148B VAL 3.3 0.7 + - - -
1149B ILE* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138B TYR* 4.5 15.8 - - + +
1142B PRO 2.9 16.2 + - - +
1143B ASN* 4.3 5.2 - - - +
1144B ARG 3.3 0.2 - - - -
1145B ALA* 1.3 75.7 - - - +
1147B ARG* 1.3 58.0 + - + +
1149B ILE* 3.8 5.9 - - - +
1150B THR* 2.8 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008B ILE* 5.8 4.3 - - - -
1009B ASP* 3.1 32.5 + - - +
1143B ASN* 3.3 31.6 + - - +
1144B ARG* 3.3 29.7 + - - +
1146B LYS* 1.3 77.8 - - + +
1148B VAL* 1.3 63.6 + - - +
1150B THR* 3.3 3.5 + - - -
1151B THR* 3.0 26.6 + - - -
1159B ALA* 3.6 33.5 - - + +
1160B TYR* 3.7 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B MET* 4.4 3.4 - - + -
1097B ALA* 3.7 19.3 - - + +
1100B ASN* 3.6 28.9 - - + +
1101B MET* 4.0 4.0 - - + -
1137B TRP* 3.6 27.6 - - + -
1144B ARG* 3.1 19.0 + - + +
1147B ARG* 1.3 74.4 - - - +
1149B ILE* 1.3 59.1 + - - +
1151B THR* 3.2 8.6 + - - -
1152B PHE* 3.0 56.2 + - + -
1160B TYR* 4.0 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1129B ALA* 3.8 34.9 - - + +
1132B LEU* 3.8 33.2 - - + +
1133B ALA* 4.1 3.1 - - + +
1137B TRP* 3.9 18.2 - - + -
1138B TYR* 3.8 28.7 - - + -
1145B ALA 2.8 27.1 + - - +
1146B LYS* 3.9 4.3 - - - +
1148B VAL* 1.3 72.8 - - - +
1150B THR* 1.3 61.8 + - - +
1152B PHE* 3.2 9.2 + - + +
1153B ARG* 2.8 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146B LYS* 2.8 23.0 + - - +
1147B ARG 3.6 4.0 - - - -
1149B ILE* 1.3 78.4 - - - +
1151B THR* 1.3 58.2 + - - +
1153B ARG* 4.3 26.7 + - - +
1154B THR* 2.8 44.7 + - + +
1156B THR 5.9 0.7 - - - +
1158B ASP* 5.5 4.0 - - + -
1159B ALA* 3.8 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B MET* 4.2 2.5 - - + +
1093B VAL* 3.7 32.8 - - + +
1094B ARG* 3.6 3.4 - - - +
1097B ALA* 3.9 11.4 - - + -
1147B ARG 3.0 15.6 + - - -
1148B VAL* 3.2 8.9 + - - -
1150B THR* 1.3 77.7 - - - +
1152B PHE* 1.3 56.2 + - - +
1154B THR* 4.2 0.4 - - - -
1155B GLY* 2.8 27.2 + - - -
1156B THR 3.5 24.9 + - - +
1157B TRP* 4.4 9.3 - - + -
1159B ALA* 4.7 2.3 - - - +
1160B TYR* 3.9 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B LEU* 4.1 9.9 - - + -
1094B ARG* 2.8 60.4 + - + -
1097B ALA* 3.5 5.2 - - + -
1098B LEU* 3.5 29.8 - - + -
1101B MET* 3.9 18.8 - - - -
1120B LEU* 3.9 37.9 - - + -
1125B TRP* 3.9 10.5 - - - +
1129B ALA* 6.3 1.6 - - - +
1132B LEU* 4.2 19.3 - - + -
1148B VAL* 3.0 47.1 + - + -
1149B ILE* 3.5 7.2 - - + +
1150B THR 3.2 0.2 - - - -
1151B THR* 1.3 77.9 - - - +
1153B ARG* 1.3 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ARG 6.0 0.4 + - - -
171B HIS* 5.7 10.4 - - + +
1094B ARG* 3.6 6.8 + - - -
1125B TRP* 3.6 20.9 - - - +
1126B ASP* 3.8 28.8 + - - +
1129B ALA* 4.1 23.6 - - + -
1149B ILE* 2.8 17.6 + - - +
1150B THR* 3.1 20.1 + - - +
1152B PHE* 1.3 78.1 - - - +
1154B THR* 1.3 82.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B HIS 5.9 4.0 - - - +
173B HIS 5.8 4.0 - - - +
174B CYS* 5.9 4.7 - - + -
1094B ARG* 3.5 10.5 + - - -
1150B THR* 2.8 28.7 + - + +
1153B ARG* 1.3 111.8 - - - +
1155B GLY* 1.3 63.3 + - - +
1156B THR* 3.0 34.1 + - - +
1158B ASP* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE* 3.9 7.8 - - - +
1091B ASP* 4.4 2.8 - - - +
1093B VAL* 3.3 28.9 - - - +
1094B ARG* 3.3 25.1 - - - +
1151B THR 2.8 22.9 + - - -
1154B THR* 1.3 75.1 + - - +
1156B THR* 1.3 60.8 + - - +
----------------------------------------------------------
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