Contacts of the helix formed by residues 1187 - 1204 (chain A) in PDB entry 1M7N
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 THR1187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1129A VAL* 3.6 14.6 - - - +
1179A GLU* 5.0 3.3 + - + +
1185A VAL* 4.8 10.8 - - + -
1186A PHE* 1.3 81.9 - - - +
1188A THR* 1.3 66.7 + - - +
1189A TYR* 3.0 37.4 + - + +
1190A SER* 2.7 24.8 + - - -
1191A ASP* 3.4 7.3 + - - -
1250A PRO* 5.3 0.2 - - - +
981B ALA* 4.3 3.1 - - - -
982B ASP 4.3 6.1 - - - +
983B VAL* 3.5 31.4 - - + -
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Residues in contact with THR1188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124A ASN* 2.4 40.7 + - - +
1129A VAL* 3.8 12.3 - - - +
1187A THR* 1.3 75.8 - - - +
1189A TYR* 1.3 90.4 + - + +
1191A ASP* 3.0 26.8 + - - +
1192A VAL* 3.2 11.7 + - + +
1255A SER* 6.0 8.0 - - - -
1256A PHE* 4.8 1.0 - - - -
981B ALA* 4.8 2.6 - - - +
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Residues in contact with TYR1189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A GLU* 4.3 0.4 - - - +
1187A THR* 3.1 19.3 - - + +
1188A THR* 1.3 96.1 - - + +
1190A SER* 1.3 61.2 + - - +
1191A ASP 3.0 5.2 - - - -
1192A VAL* 3.1 12.3 + - + +
1193A TRP 3.1 16.8 + - - -
1250A PRO* 3.4 49.8 - - + +
1251A LYS* 3.7 41.4 - - + +
1253A ARG* 3.2 16.1 + - + +
1254A PRO 6.0 0.9 - - - -
1255A SER* 6.4 3.4 - - - -
983B VAL* 6.2 2.5 - - + -
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Residues in contact with SER1190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A SER* 3.3 15.6 + - - -
1179A GLU* 4.3 3.6 + - - -
1180A SER* 3.2 25.4 - - - -
1186A PHE* 3.3 14.8 - - - +
1187A THR* 2.7 37.2 + - - -
1189A TYR* 1.3 77.2 - - - +
1191A ASP* 1.3 60.1 + - - +
1193A TRP* 3.5 7.1 - - - +
1194A SER* 2.9 28.8 + - - -
1253A ARG* 4.0 1.8 - - - +
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Residues in contact with ASP1191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120A MET* 3.3 15.0 - - + +
1124A ASN* 3.5 5.7 + - - -
1129A VAL* 3.3 12.9 - - - +
1130A HIS* 2.9 35.5 + - - +
1131A ARG* 3.4 13.2 + - - -
1132A ASP 5.1 0.2 + - - -
1133A LEU* 3.7 7.0 - - + +
1187A THR 3.4 8.5 + - - +
1188A THR* 3.0 14.2 + - - +
1190A SER* 1.3 81.0 + - - +
1192A VAL* 1.3 58.4 + - - +
1193A TRP 3.1 0.2 - - - -
1194A SER* 3.2 6.9 + - - -
1195A PHE* 2.8 27.9 + - - +
1256A PHE* 3.6 18.6 - - + -
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Residues in contact with VAL1192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188A THR* 3.2 8.9 + - + +
1189A TYR* 3.1 13.5 + - + +
1191A ASP* 1.3 76.8 - - - +
1193A TRP* 1.3 64.8 + - - +
1195A PHE* 3.1 6.2 - - - +
1196A GLY 3.0 18.0 + - - -
1245A CYS* 3.6 34.5 - - - +
1253A ARG* 4.1 9.0 - - + -
1254A PRO* 3.1 29.6 - - + +
1255A SER* 4.1 10.3 - - - -
1256A PHE* 3.8 30.5 - - + -
1259A ILE* 4.3 5.2 - - + -
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Residues in contact with TRP1193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175A TRP 3.4 16.5 - - - -
1176A MET 3.4 10.7 + - - -
1177A SER* 3.5 23.8 - - - -
1178A PRO* 3.4 38.1 - - + -
1189A TYR 3.1 11.2 + - - +
1190A SER 3.5 9.0 - - - +
1191A ASP 3.1 0.2 - - - -
1192A VAL* 1.3 77.7 - - - +
1194A SER* 1.3 64.0 + - - +
1196A GLY 3.0 10.0 + - - -
1197A VAL* 3.3 15.1 + - + +
1210A TYR* 4.3 13.3 + - - -
1222A VAL* 3.9 16.6 - - + -
1226A GLY 5.1 0.9 - - - -
1227A LEU* 4.2 12.8 - - + -
1245A CYS 3.7 9.6 + - - -
1246A TRP* 3.2 69.2 + + + -
1247A GLN 4.2 1.8 - - - -
1248A TYR* 5.0 1.3 - + - -
1253A ARG* 3.6 17.0 - - - +
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Residues in contact with SER1194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A ARG 6.0 1.6 - - - -
1133A LEU* 3.6 35.4 + - - +
1175A TRP* 3.0 25.7 + - - +
1176A MET* 4.9 1.4 - - - -
1190A SER 2.9 14.4 + - - -
1191A ASP* 3.2 10.1 + - - -
1193A TRP* 1.3 73.7 - - - +
1195A PHE* 1.3 67.1 + - - +
1197A VAL* 2.8 17.3 + - - +
1198A VAL* 2.9 15.7 + - - +
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Residues in contact with PHE1195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A ALA* 3.6 31.0 - - + -
1116A ILE* 4.0 21.5 - - + -
1117A ALA* 3.8 19.5 - - + -
1133A LEU* 3.6 10.0 - - + +
1191A ASP 2.8 14.4 + - - +
1192A VAL 3.1 9.6 - - - +
1194A SER* 1.3 74.4 - - - +
1196A GLY* 1.3 56.1 + - - +
1198A VAL* 2.9 10.2 + - + +
1199A LEU* 2.9 55.3 + - + +
1241A LEU* 4.0 1.6 - - + -
1245A CYS* 3.7 17.5 - - - -
1256A PHE* 3.7 20.2 - + + -
1259A ILE* 3.7 33.0 - - + -
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Residues in contact with GLY1196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192A VAL 3.0 10.7 + - - -
1193A TRP 3.0 5.1 + - - -
1195A PHE* 1.3 78.6 - - - +
1197A VAL* 1.3 60.2 + - - +
1199A LEU* 3.3 9.6 + - - +
1200A TRP* 3.2 15.2 + - - +
1242A MET* 3.7 5.3 - - - +
1245A CYS* 3.8 18.8 - - - -
1246A TRP* 3.1 24.5 - - - -
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Residues in contact with VAL1197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1174A ARG 3.7 8.5 - - - +
1175A TRP* 3.5 39.0 - - + +
1193A TRP* 3.3 30.0 + - + +
1194A SER 2.8 11.2 + - - +
1196A GLY* 1.3 72.8 - - - +
1198A VAL* 1.3 58.7 + - - +
1200A TRP* 3.1 6.5 - - + +
1201A GLU* 3.0 25.1 + - - +
1209A PRO* 3.7 24.0 - - + -
1210A TYR* 5.0 1.6 - - - +
1228A LEU* 4.4 11.2 - - + -
1246A TRP* 3.7 17.9 - - + +
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Residues in contact with VAL1198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A LEU* 4.7 1.8 - - + -
1116A ILE* 4.1 26.7 - - + -
1133A LEU* 4.1 12.1 - - + -
1134A ALA* 3.4 38.6 - - - +
1135A ALA* 4.4 11.2 - - + +
1138A CYS* 5.1 1.3 - - - -
1175A TRP* 4.7 0.9 - - + -
1194A SER 2.9 16.6 + - - +
1195A PHE* 2.9 11.2 + - + +
1197A VAL* 1.3 75.1 - - - +
1199A LEU* 1.3 66.9 + - + +
1200A TRP 3.0 1.6 - - - -
1201A GLU* 3.0 13.1 + - - +
1202A ILE* 2.9 28.7 + - + +
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Residues in contact with LEU1199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A MET* 5.5 0.4 - - + +
1113A ALA* 3.4 34.8 - - + -
1195A PHE* 2.9 31.2 + - + +
1196A GLY* 3.3 11.2 + - - +
1198A VAL* 1.3 76.0 - - + +
1200A TRP* 1.3 65.2 + - - +
1202A ILE* 3.4 15.8 + - + +
1203A ALA* 3.2 20.3 + - - +
1238A LEU* 4.3 20.4 - - + +
1241A LEU* 3.5 46.2 - - + -
1242A MET* 3.8 18.1 - - + +
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Residues in contact with TRP1200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196A GLY 3.2 9.9 + - - +
1197A VAL* 3.1 14.8 - - - +
1199A LEU* 1.3 77.4 - - - +
1201A GLU* 1.3 69.8 + - - +
1203A ALA* 3.0 5.3 + - - +
1204A THR* 2.9 46.9 + - + +
1207A GLU* 3.0 39.5 - - + -
1208A GLN 3.8 13.0 - - - -
1209A PRO* 3.6 27.8 - - + -
1210A TYR 4.7 1.3 - - - -
1211A GLN* 5.8 1.1 - - + -
1228A LEU* 4.0 31.2 - - + +
1229A ASP* 3.2 22.9 + - + -
1231A PRO* 3.9 17.1 - - + +
1239A PHE* 5.6 0.4 - + - -
1242A MET* 3.8 22.6 - - - -
1246A TRP* 4.2 3.4 - + + -
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Residues in contact with GLU1201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085A LYS* 3.9 17.5 - - - +
1088A LEU* 4.1 2.8 - - + +
1135A ALA* 2.8 48.3 + - + +
1136A ARG 4.4 0.3 + - - -
1175A TRP* 3.1 36.2 + - + +
1197A VAL 3.0 13.6 + - - +
1198A VAL* 3.0 16.6 + - + +
1200A TRP* 1.3 77.3 - - + +
1202A ILE* 1.3 63.6 + - - +
1204A THR* 3.7 7.9 - - - -
1205A LEU 3.1 3.5 + - - -
1206A ALA* 2.6 37.2 + - - +
1207A GLU 4.4 11.0 - - - +
1209A PRO* 4.9 0.7 - - + -
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Residues in contact with ILE1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1084A LEU* 4.2 17.3 - - + -
1088A LEU* 4.0 15.2 - - + +
1104A PRO* 5.4 2.5 - - + +
1109A MET* 3.6 30.3 - - + +
1112A MET* 3.7 46.2 - - + -
1113A ALA 4.4 2.2 - - - +
1116A ILE* 4.2 18.6 - - + -
1198A VAL* 2.9 21.9 + - + +
1199A LEU* 3.6 26.0 - - + +
1200A TRP 3.2 0.2 + - - -
1201A GLU* 1.3 73.8 - - - +
1203A ALA* 1.3 60.3 + - - +
1205A LEU* 3.5 18.7 + - - +
1238A LEU* 5.4 1.1 - - + -
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Residues in contact with ALA1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A ARG* 5.1 1.6 + - - -
1109A MET* 4.1 19.5 - - + -
1199A LEU 3.2 8.6 + - - +
1200A TRP* 3.0 9.4 + - - +
1202A ILE* 1.3 76.6 - - - +
1204A THR* 1.3 57.4 + - - +
1205A LEU* 3.1 11.4 + - - +
1231A PRO* 4.1 10.3 - - + +
1232A ASP 5.1 6.2 - - - +
1234A CYS* 4.0 30.5 - - + +
1238A LEU* 4.6 3.6 - - + -
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Residues in contact with THR1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A ARG* 3.4 13.2 + - - +
1200A TRP* 2.9 45.7 + - + +
1201A GLU* 3.5 5.7 + - - -
1203A ALA* 1.3 74.2 - - - +
1205A LEU* 1.3 68.4 + - - +
1206A ALA 3.1 0.2 + - - -
1207A GLU* 3.0 44.8 + - + +
1231A PRO* 3.3 29.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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