Contacts of the helix formed by residues 1130 - 1149 (chain M) in PDB entry 6G0L
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 ALA1130 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060M ALA* 3.6 33.4 - - + +
1063M CYS* 5.0 0.2 - - + -
1064M VAL* 3.7 12.3 - - + -
1118M VAL* 3.2 16.0 + - + -
1120M PHE* 3.7 20.2 - - + -
1128M LEU 3.9 0.2 + - - -
1129M ASN* 1.3 73.1 - - - +
1131M GLU* 1.3 65.3 + - - +
1132M SER 3.4 0.4 - - - -
1133M LEU* 3.5 6.0 + - - +
1134M LEU* 3.4 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1131 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064M VAL* 4.5 14.3 - - + +
1071M ARG* 5.7 2.4 + - - -
1117M ALA* 5.7 3.4 - - - +
1118M VAL* 3.4 32.3 - - + +
1129M ASN* 2.9 12.0 + - - +
1130M ALA* 1.3 76.4 - - - +
1132M SER* 1.3 54.2 + - - +
1134M LEU* 3.5 4.9 + - - +
1135M SER* 2.6 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1132 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I A 5.6 1.4 + - - -
1019M TYR* 5.3 0.7 - - - -
1023M LEU* 4.7 14.4 - - - +
1129M ASN* 2.4 41.4 + - - +
1131M GLU* 1.3 67.4 - - - +
1133M LEU* 1.3 52.5 + - - +
1135M SER* 3.4 7.8 + - - -
1136M ARG* 2.6 49.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1133 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019M TYR* 3.6 30.1 - - + +
1022M ILE* 3.7 24.6 - - + +
1023M LEU* 3.8 18.2 - - + -
1056M MET* 4.2 21.3 - - + -
1057M MET* 4.4 17.0 - - + -
1060M ALA* 4.5 16.4 - - + -
1120M PHE* 4.8 3.6 - - + -
1129M ASN 3.4 20.9 - - - +
1130M ALA* 3.5 5.4 + - - +
1131M GLU 3.2 1.0 - - - -
1132M SER* 1.3 75.2 - - - +
1134M LEU* 1.3 62.4 + - + +
1136M ARG* 3.2 3.5 + - - +
1137M VAL* 2.9 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1134 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057M MET* 3.7 24.9 - - + +
1060M ALA* 5.3 3.4 - - + -
1061M LYS* 3.7 36.8 - - + +
1064M VAL* 4.5 22.2 - - + -
1130M ALA 3.4 16.6 + - - +
1131M GLU* 4.1 4.9 - - - +
1133M LEU* 1.3 74.6 - - + +
1135M SER* 1.3 59.2 + - - +
1137M VAL* 3.2 6.3 + - - +
1138M GLU* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1135 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131M GLU* 2.6 24.7 + - - -
1132M SER* 3.4 10.0 + - - -
1134M LEU* 1.3 77.8 - - - +
1136M ARG* 1.3 57.9 + - - +
1138M GLU* 4.3 6.7 - - - -
1139M ASP* 2.9 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022M ILE* 3.8 17.3 - - + +
1023M LEU* 2.4 51.1 + - + +
1026M GLY* 4.8 1.6 - - - -
1132M SER* 2.6 37.3 + - - +
1133M LEU* 3.5 6.5 - - - +
1134M LEU 3.1 0.2 - - - -
1135M SER* 1.3 75.4 + - - +
1137M VAL* 1.3 59.7 + - + +
1139M ASP* 4.6 6.2 + - - +
1140M LEU* 2.9 65.4 + - + +
1192M TYR* 3.3 42.0 - - - -
1258M ASP* 5.0 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022M ILE* 5.3 3.6 - - + -
1026M GLY* 4.7 7.6 - - - -
1027M ASN* 4.6 19.3 - - + +
1053M TYR* 3.9 21.5 - - - +
1057M MET* 4.1 15.9 - - + -
1133M LEU* 2.9 21.0 + - - +
1134M LEU* 3.7 5.4 - - + +
1136M ARG* 1.3 76.0 - - + +
1138M GLU* 1.3 61.0 + - - +
1140M LEU* 4.9 2.2 - - - -
1141M LYS* 2.8 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134M LEU* 2.9 24.6 + - + +
1135M SER* 3.9 7.2 - - - +
1137M VAL* 1.3 79.9 - - + +
1139M ASP* 1.3 57.8 + - - +
1141M LYS* 3.5 30.0 + - - +
1142M TYR* 2.9 23.0 + - - +
1265M ARG* 2.9 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135M SER* 2.9 33.0 + - - +
1136M ARG* 4.1 8.8 + - - +
1138M GLU* 1.3 77.6 - - - +
1140M LEU* 1.3 60.4 + - + +
1142M TYR* 3.3 6.7 + - - +
1143M LEU* 2.9 28.6 + - - +
1258M ASP* 5.1 10.3 - - - +
1261M LEU* 3.7 36.9 - - + +
1262M SER* 4.9 2.2 + - - -
1265M ARG* 3.2 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024M LYS 4.2 6.3 - - - +
1025M PHE* 3.5 39.0 - - - +
1026M GLY* 3.6 7.0 - - - +
1027M ASN 6.0 0.4 - - - +
1136M ARG* 2.9 44.2 + - + +
1137M VAL* 4.5 2.0 - - - +
1139M ASP* 1.3 77.7 - - + +
1141M LYS* 1.3 58.3 + - - +
1143M LEU* 3.3 12.3 + - + +
1144M LYS* 2.9 41.1 + - + +
1187M VAL* 4.4 26.9 - - + +
1191M GLY* 5.5 0.7 - - - -
1192M TYR* 5.0 8.3 - - + +
1261M LEU* 5.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137M VAL* 2.8 35.0 + - + +
1138M GLU* 3.5 35.5 + - - +
1140M LEU* 1.3 74.1 - - - +
1142M TYR* 1.3 59.3 + - - +
1144M LYS* 3.3 5.6 + - + +
1145M ASN* 2.9 54.4 + - - +
1265M ARG* 5.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138M GLU 2.9 20.7 + - - +
1139M ASP* 3.3 4.7 + - - +
1141M LYS* 1.3 77.1 - - - +
1143M LEU* 1.3 59.4 + - - +
1145M ASN* 4.7 5.4 - - + +
1146M LEU* 2.8 66.7 + - + +
1261M LEU* 5.0 8.3 - - + -
1264M LEU* 3.1 42.0 + - + +
1265M ARG* 3.4 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139M ASP 2.9 17.2 + - - +
1140M LEU* 3.6 12.8 - - + +
1142M TYR* 1.3 77.7 - - - +
1144M LYS* 1.3 62.3 + - + +
1146M LEU* 4.3 7.6 - - + -
1147M ILE* 2.9 54.3 + - + +
1184M LEU* 4.2 25.8 - - + +
1187M VAL* 3.9 22.4 - - + +
1188M PHE* 3.8 36.7 - - + +
1261M LEU* 4.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1144 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025M PHE 6.0 2.7 - - - -
1031M ILE* 6.0 7.7 - - - +
1140M LEU* 2.9 28.1 + - + +
1141M LYS* 3.9 5.8 - - - +
1143M LEU* 1.3 78.0 - - + +
1145M ASN* 1.3 61.6 + - - +
1148M ASN* 2.9 47.1 + - - +
1187M VAL 5.6 1.6 - - - -
1188M PHE* 2.7 53.3 + - + +
1189M LYS 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141M LYS* 2.9 43.4 + - - +
1142M TYR* 4.4 5.7 - - + +
1144M LYS* 1.3 80.2 - - - +
1146M LEU* 1.3 54.2 + - - +
1148M ASN* 4.8 1.1 - - - -
1149M SER* 2.3 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142M TYR* 2.8 60.1 + - + +
1143M LEU* 3.9 9.6 - - + +
1145M ASN* 1.3 79.4 - - - +
1147M ILE* 1.3 64.8 + - + +
1149M SER* 4.6 0.7 - - - -
1150M ASN* 2.9 38.3 + - - +
1158M PHE* 3.9 26.2 - - + -
1160M LEU* 5.7 0.2 - - + -
1184M LEU* 5.8 0.2 - - + -
1264M LEU* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143M LEU* 2.9 40.8 + - + +
1146M LEU* 1.3 76.2 - - + +
1148M ASN* 1.3 60.4 + - - +
1150M ASN 3.2 0.3 + - - -
1151M TYR* 2.8 50.1 + - + +
1155M PRO* 5.0 9.4 - - + +
1158M PHE* 3.6 47.1 - - + -
1184M LEU* 5.6 5.2 - - + +
1185M ILE* 6.3 2.9 - - + -
1188M PHE* 3.6 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144M LYS* 2.9 39.0 + - - +
1145M ASN* 4.7 1.6 - - - +
1147M ILE* 1.3 77.2 - - - +
1149M SER* 1.3 59.2 + - - +
1150M ASN 3.2 1.3 + - - -
1151M TYR 4.3 3.4 - - - -
1152M LYS* 4.0 35.4 + - + +
1188M PHE* 3.2 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1149 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145M ASN* 2.3 34.0 + - - +
1146M LEU* 4.2 3.6 - - - -
1147M ILE 3.2 0.4 - - - -
1148M ASN* 1.3 76.8 - - - +
1150M ASN* 1.3 71.8 + - - +
----------------------------------------------------------
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