Contacts of the helix formed by residues 1141 - 1159 (chain A) in PDB entry 5W0N
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 ASP1141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137A TYR 4.2 1.2 + - - -
1138A SER 3.7 8.8 - - - +
1139A ALA 3.3 2.1 - - - -
1140A ILE* 1.3 87.7 - - + +
1142A PRO* 1.3 80.2 - - - +
1143A ARG* 2.9 66.0 + - - +
1144A VAL* 3.0 32.2 + - + +
1145A LYS 4.0 0.3 + - - -
1188A VAL* 4.5 9.1 - - + +
1228A GLY* 6.1 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A SER 5.1 1.6 - - - +
1140A ILE 4.9 0.9 - - - +
1141A ASP* 1.3 93.0 - - - +
1143A ARG* 1.3 62.1 + - + +
1145A LYS* 3.1 19.8 + - + +
1146A TYR* 3.2 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A ASP* 2.9 34.9 + - - +
1142A PRO* 1.3 77.3 - - + +
1144A VAL* 1.3 63.1 + - - +
1146A TYR* 3.9 9.8 - - + +
1147A LEU* 3.0 31.5 + - + +
1181A LEU* 5.2 0.2 - - - -
1188A VAL* 3.6 25.0 + - + +
1228A GLY* 5.8 3.0 - - - -
1230A ASN* 2.8 47.9 + - - +
1231A THR* 3.9 1.0 - - - -
1232A GLU 2.7 38.8 + - - +
1233A SER* 4.7 0.7 - - - +
1234A VAL* 4.0 21.3 - - + -
1237A LEU* 3.8 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A PHE* 4.1 7.2 - - + -
1137A TYR 3.6 25.8 - - - +
1138A SER* 3.9 10.5 - - - +
1141A ASP* 3.0 22.4 + - + +
1143A ARG* 1.3 78.0 - - - +
1145A LYS* 1.3 61.7 + - - +
1147A LEU* 4.0 1.2 - - - +
1148A CYS* 3.1 30.5 + - - -
1178A LEU* 3.8 27.8 - - + -
1181A LEU* 4.2 15.5 - - + -
1188A VAL* 4.9 2.0 - - + -
1189A ILE* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A TYR* 4.1 32.7 + - + +
1051A GLY* 3.6 31.1 + - - +
1052A PHE* 4.0 7.4 - - + -
1138A SER* 3.9 37.5 - - - +
1139A ALA* 5.9 0.2 - - - +
1141A ASP 5.3 0.2 - - - +
1142A PRO* 3.1 13.2 + - + +
1144A VAL* 1.3 75.8 - - - +
1146A TYR* 1.3 69.9 + - + +
1148A CYS* 3.2 1.0 + - - -
1149A TYR* 2.9 36.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A CYS 3.8 9.3 - - - +
1006A ILE* 4.1 34.7 - - + +
1009A TYR* 3.6 44.3 - + + -
1142A PRO* 3.2 39.0 + - + +
1143A ARG* 3.9 4.0 - - + +
1145A LYS* 1.3 78.1 - - + +
1147A LEU* 1.3 58.4 + - - +
1149A TYR* 3.5 1.7 + - - +
1150A THR* 2.8 33.3 + - - -
1234A VAL* 3.5 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005A CYS* 4.9 1.1 - - - -
1143A ARG 3.0 20.0 + - - +
1144A VAL 4.1 0.9 - - - +
1146A TYR* 1.3 74.0 - - - +
1148A CYS* 1.3 57.0 + - - +
1150A THR* 3.2 3.0 + - - -
1151A MET* 2.7 36.0 + - - +
1177A VAL* 3.9 17.2 - - + +
1180A PHE* 4.9 2.7 - - + -
1181A LEU* 3.6 33.2 - - + -
1234A VAL* 3.9 14.8 - - + +
1237A LEU* 3.8 22.4 - - + +
1238A TRP* 3.5 53.2 - - + +
1241A LEU* 5.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1052A PHE* 3.7 42.8 - - + -
1144A VAL* 3.1 27.5 + - - +
1145A LYS 3.8 0.4 - - - +
1147A LEU* 1.3 77.1 - - - +
1149A TYR* 1.3 58.4 + - - +
1151A MET* 3.5 6.7 + - - +
1152A LYS* 2.9 30.5 + - - +
1174A THR* 4.0 21.0 + - + +
1177A VAL* 3.7 25.6 - - - -
1178A LEU* 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A CYS* 3.7 15.9 - - - +
1009A TYR* 3.5 42.5 - + + +
1013A SER* 3.5 25.6 - - - -
1014A PRO* 4.3 2.3 - - - +
1051A GLY 3.6 22.1 + - - -
1052A PHE* 3.6 14.6 - + - -
1053A GLY 2.7 36.9 + - - -
1054A PHE* 3.3 29.8 - + - -
1145A LYS* 2.9 28.7 + - + +
1146A TYR 3.8 3.4 - - - +
1148A CYS* 1.3 74.7 - - - +
1150A THR* 1.3 59.5 + - - +
1152A LYS* 3.2 2.5 + - - +
1153A VAL* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004A VAL* 5.8 0.7 - - + -
1005A CYS* 3.2 31.7 + - - +
1008A CYS* 3.8 11.8 - - - +
1146A TYR 2.8 22.2 + - - -
1147A LEU* 3.2 7.4 + - - -
1149A TYR* 1.3 77.2 - - - +
1151A MET* 1.3 56.7 + - - +
1153A VAL* 3.3 2.8 + - - +
1154A PHE* 2.9 28.1 + - - +
1238A TRP* 3.5 40.2 - - + +
1311A PHE* 5.5 0.7 - - + -
1330A PHE* 4.1 15.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A LEU 2.7 20.7 + - - +
1148A CYS* 3.7 4.0 - - - +
1150A THR* 1.3 72.2 - - - +
1152A LYS* 1.3 59.0 + - - +
1154A PHE* 3.2 2.3 + - - +
1155A THR* 3.0 47.6 + - - +
1173A TYR* 3.8 28.7 - - + +
1174A THR* 5.7 0.2 - - - -
1176A MET* 4.4 12.6 - - + -
1177A VAL* 3.6 29.8 - - + -
1238A TRP* 3.9 17.7 - - + -
1241A LEU* 3.7 28.5 - - + -
1245A TYR* 5.0 1.3 - - + -
1304A PHE* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A SER* 3.7 17.2 + - - -
1050A ASN* 5.6 1.0 - - - +
1052A PHE* 2.6 33.6 + - - +
1053A GLY* 4.6 0.6 - - - -
1054A PHE* 3.5 36.8 - - + -
1057A SER* 4.9 4.6 + - - +
1148A CYS 2.9 19.4 + - - +
1149A TYR 3.2 4.5 + - - +
1151A MET* 1.3 74.2 - - - +
1153A VAL* 1.3 65.4 + - - +
1155A THR* 3.4 6.1 + - - +
1156A LYS* 3.1 36.3 + - - +
1170A SER* 3.9 33.8 + - - -
1173A TYR* 6.1 1.8 - - - -
1174A THR* 4.9 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A CYS* 3.9 14.6 - - + -
1012A PHE* 3.6 31.2 - - + -
1054A PHE* 3.6 19.7 - - + -
1149A TYR 2.9 20.4 + - - +
1150A THR 3.7 4.5 - - - +
1152A LYS* 1.3 76.5 - - - +
1154A PHE* 1.3 57.6 + - - +
1156A LYS* 3.3 4.0 + - - +
1157A MET* 2.8 46.7 + - + +
1326A MET* 5.0 1.6 - - + -
1330A PHE* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150A THR 2.9 17.2 + - - +
1151A MET* 3.6 4.0 - - - +
1153A VAL* 1.3 77.3 - - - +
1155A THR* 1.3 75.1 + - + +
1157A MET* 3.2 1.9 + - - +
1158A CYS* 3.0 40.6 + - - -
1160A ILE* 5.1 0.4 - - + -
1238A TRP* 3.9 28.5 - + + -
1242A LEU* 4.5 3.1 - - + -
1303A ALA* 3.4 33.0 - - + -
1304A PHE* 4.2 27.1 - + - -
1307A GLY* 3.8 20.0 - - - -
1311A PHE* 4.3 5.6 - + - -
1330A PHE* 3.8 18.2 - + + -
1335A LEU* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A MET* 3.0 30.4 + - - +
1152A LYS* 3.4 9.0 + - - +
1154A PHE* 1.3 81.2 - - + +
1156A LYS* 1.3 59.2 + - - +
1158A CYS 3.3 0.5 + - - -
1159A ASP 2.9 22.7 + - - -
1160A ILE* 3.0 29.6 + - + +
1161A GLY* 4.5 6.0 - - - -
1170A SER* 5.7 2.3 - - - -
1173A TYR* 3.6 54.9 - - + -
1304A PHE* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A PHE* 4.1 31.4 - - + -
1152A LYS* 3.1 27.7 + - - +
1153A VAL* 3.7 4.3 - - - +
1155A THR* 1.3 78.6 + - - +
1157A MET* 1.3 65.4 + - + +
1159A ASP* 3.1 16.3 + - - +
1161A GLY* 5.3 8.8 + - - +
1170A SER* 6.1 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153A VAL* 2.8 35.8 + - + +
1154A PHE* 3.7 5.2 - - - +
1156A LYS* 1.3 79.7 - - + +
1158A CYS* 1.3 60.3 + - - +
1159A ASP* 3.6 1.7 + - - +
1330A PHE* 3.4 39.0 - - + +
1332A PRO* 3.8 42.3 - - + +
1335A LEU* 5.1 4.5 - - + -
1336A THR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154A PHE* 3.0 29.8 + - - +
1155A THR 3.8 4.0 - - - +
1156A LYS 3.2 0.2 - - - -
1157A MET* 1.3 74.4 - - - +
1159A ASP* 1.3 70.8 + - - +
1160A ILE* 3.5 23.5 - - + +
1299A PHE* 3.6 12.1 - - - -
1303A ALA* 3.8 22.2 - - + -
1335A LEU* 3.8 33.4 - - - -
1336A THR* 3.9 17.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155A THR 2.9 4.2 + - - -
1156A LYS* 3.1 15.0 + - - +
1157A MET 3.3 2.2 - - - +
1158A CYS* 1.3 82.0 - - - +
1160A ILE* 1.3 57.6 + - - +
1161A GLY 3.6 3.1 - - - +
1162A ASP* 5.5 5.4 - - - +
1165A ARG* 5.7 7.3 - - - -
1167A SER* 4.4 4.4 + - - -
1340A LEU* 5.6 5.4 - - - +
1341A ALA* 3.5 32.2 + - + +
----------------------------------------------------------
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