Contacts of the helix formed by residues 1127 - 1146 (chain B) in PDB entry 1CM8
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 GLU1127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1126B GLY* 1.3 69.0 - - - +
1128B ASP* 1.3 68.8 + - - +
1130B ILE* 3.5 9.1 + - + +
1131B GLN* 3.1 23.6 + - - +
1279B ASN 5.0 9.1 - - - +
1281B SER* 4.2 23.6 - - - +
1310B TYR* 4.3 3.4 + - - -
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Residues in contact with ASP1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126B GLY 3.4 0.8 - - - -
1127B GLU* 1.3 83.2 - - - +
1129B ARG* 1.3 63.2 + - - +
1131B GLN* 3.4 15.5 + - - +
1132B PHE* 3.1 23.3 + - - +
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Residues in contact with ARG1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119B LEU* 3.7 29.9 - - - +
1123B GLU* 3.5 26.2 + - - -
1125B LEU* 3.6 38.6 - - + +
1126B GLY 2.9 10.9 + - - +
1128B ASP* 1.3 76.3 - - - +
1130B ILE* 1.3 65.6 + - - +
1131B GLN 3.2 0.3 + - - -
1132B PHE* 3.2 6.9 + - - +
1133B LEU* 2.9 33.1 + - + +
1163B GLU 5.6 2.4 + - - -
1165B CYS* 3.6 35.3 - - - -
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Residues in contact with ILE1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125B LEU* 3.4 24.9 - - + -
1126B GLY* 2.9 38.4 + - - +
1127B GLU* 4.0 7.0 - - + +
1129B ARG* 1.3 71.9 - - - +
1131B GLN* 1.3 56.4 + - - +
1133B LEU* 3.6 0.7 + - - +
1134B VAL* 2.9 44.2 + - + +
1216B MET* 4.7 2.9 - - + -
1219B MET* 3.9 38.8 - - + +
1220B ILE* 4.1 27.6 - - + +
1310B TYR* 4.0 11.9 - - - +
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Residues in contact with GLN1131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127B GLU 3.1 14.1 + - - +
1128B ASP* 3.5 20.4 + - - +
1129B ARG 3.1 0.6 - - - -
1130B ILE* 1.3 73.4 - - - +
1132B PHE* 1.3 65.7 + - - +
1134B VAL* 3.3 1.9 + - - +
1135B TYR* 2.9 24.3 + - - +
1310B TYR* 2.7 56.9 + - + +
1311B PHE* 3.9 8.4 - - + -
1313B SER* 3.4 24.7 + - - -
1314B LEU* 3.7 25.3 - - + +
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Residues in contact with PHE1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128B ASP 3.1 10.9 + - - +
1129B ARG* 3.6 9.6 - - - +
1131B GLN* 1.3 81.6 - - - +
1133B LEU* 1.3 64.7 + - + +
1135B TYR* 3.3 10.1 + + - +
1136B GLN* 3.1 58.8 + - + +
1164B ASP 4.3 7.6 - - - -
1165B CYS* 3.5 27.4 - - + -
1166B GLU* 5.0 4.9 - - + -
1314B LEU* 4.2 27.1 - - + -
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Residues in contact with LEU1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B LEU* 3.6 18.8 - - + -
1119B LEU* 4.8 4.3 - - + -
1125B LEU* 4.1 17.0 - - + -
1129B ARG* 2.9 21.8 + - + +
1132B PHE* 1.3 77.3 - - + +
1134B VAL* 1.3 62.7 + - - +
1136B GLN* 3.1 11.5 + - - +
1137B MET* 3.0 28.3 + - + +
1161B VAL* 4.0 25.6 - - + -
1165B CYS* 3.6 29.8 - - + +
1167B LEU* 4.0 8.0 - - + +
1219B MET* 3.4 32.5 - - + -
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Residues in contact with VAL1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130B ILE* 2.9 26.7 + - + +
1131B GLN* 3.9 3.6 - - - +
1133B LEU* 1.3 72.6 - - - +
1135B TYR* 1.3 66.3 + - - +
1137B MET* 3.2 10.6 + - + +
1138B LEU* 3.1 30.0 + - + +
1212B VAL* 4.3 15.3 - - + -
1216B MET* 3.5 39.0 - - + -
1219B MET* 3.9 18.2 - - - -
1291B MET* 5.0 1.3 - - + -
1310B TYR* 4.9 0.2 - - + -
1311B PHE* 3.9 20.0 - - + -
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Residues in contact with TYR1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131B GLN 2.9 17.1 + - - +
1132B PHE* 3.4 15.9 - + - +
1134B VAL* 1.3 75.3 - - - +
1136B GLN* 1.3 61.1 + - + +
1138B LEU* 3.2 5.5 + - - +
1139B LYS* 3.0 59.2 + - + +
1142B ARG* 5.5 1.8 + - - -
1306B LEU* 3.4 32.8 - - + -
1311B PHE* 3.8 32.2 - + + -
1314B LEU* 3.5 52.5 + - + -
1315B HIS* 4.2 8.1 - - - -
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Residues in contact with GLN1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085B ASN* 3.2 35.3 + - - +
1132B PHE* 3.1 47.2 + - + +
1133B LEU* 3.1 10.8 + - - +
1135B TYR* 1.3 78.5 - - + +
1137B MET* 1.3 66.2 + - - +
1139B LYS* 4.4 5.2 - - - +
1140B GLY* 3.1 17.8 + - - -
1165B CYS 2.8 27.7 + - - -
1166B GLU* 3.6 5.9 - - - +
1167B LEU* 3.0 32.2 + - + +
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Residues in contact with MET1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B LEU* 4.1 8.7 - - + -
1133B LEU* 3.0 33.9 + - + +
1134B VAL* 3.2 17.2 + - + +
1136B GLN* 1.3 75.5 - - - +
1138B LEU* 1.3 56.1 + - + +
1140B GLY 3.3 0.3 + - - -
1141B LEU* 2.8 35.6 + - + +
1154B LEU* 6.5 0.7 - - + -
1159B LEU* 3.8 29.6 - - + -
1167B LEU* 3.9 23.3 - - + +
1169B ILE* 3.6 10.9 - - + +
1212B VAL* 4.4 27.4 - - + +
1215B ILE* 4.4 10.5 - - - -
1216B MET 5.6 0.4 - - - -
1219B MET* 3.9 26.5 - - + +
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Residues in contact with LEU1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134B VAL* 3.1 14.5 + - + +
1135B TYR 3.5 2.9 - - - +
1136B GLN 3.1 0.2 - - - -
1137B MET* 1.3 73.2 - - - +
1139B LYS* 1.3 60.5 + - - +
1140B GLY 3.2 0.9 - - - -
1141B LEU* 3.5 10.0 - - + +
1142B ARG* 2.7 30.1 + - - +
1209B ILE* 4.1 21.8 - - + -
1212B VAL* 4.1 20.2 - - + -
1291B MET* 4.8 6.7 - - - -
1302B ALA* 4.0 7.0 - - - +
1305B ALA* 3.7 26.0 - - + -
1306B LEU* 3.5 21.6 - - + +
1311B PHE* 3.6 36.6 - - + -
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Residues in contact with LYS1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083B HIS* 3.8 13.5 + - + +
1084B GLU* 6.1 2.2 - - - +
1085B ASN* 3.7 23.7 + - - +
1135B TYR* 3.0 54.5 + - + +
1136B GLN* 3.4 4.2 + - - +
1138B LEU* 1.3 72.4 - - - +
1140B GLY* 1.3 68.2 + - - +
1142B ARG* 3.3 16.9 + - - +
1143B TYR* 3.0 23.0 + - - +
1306B LEU* 3.8 21.5 - - + -
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Residues in contact with GLY1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083B HIS* 4.2 3.1 - - - -
1085B ASN* 3.8 24.5 - - - +
1086B VAL* 4.1 5.7 - - - +
1136B GLN 3.1 10.5 + - - -
1137B MET 3.6 4.3 - - - -
1139B LYS* 1.3 77.5 - - - +
1141B LEU* 1.3 56.0 + - - +
1143B TYR* 3.2 4.9 + - - +
1144B ILE* 3.0 38.2 + - - +
1169B ILE* 4.0 7.4 - - - -
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Residues in contact with LEU1141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137B MET 2.8 17.2 + - - +
1138B LEU* 3.5 9.6 - - + +
1139B LYS 3.2 0.2 - - - -
1140B GLY* 1.3 73.8 - - - +
1142B ARG* 1.3 59.5 + - - +
1144B ILE* 3.1 17.7 + - + +
1145B HIS* 2.8 61.9 + - + +
1151B HIS* 5.0 1.6 - - + -
1154B LEU* 3.9 15.9 - - + -
1169B ILE* 3.9 1.5 - - + +
1208B ASP* 3.8 32.8 - - + +
1209B ILE* 3.7 29.6 - - + -
1212B VAL* 3.9 11.0 - - + -
1302B ALA* 4.0 6.1 - - + -
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Residues in contact with ARG1142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B TYR* 5.5 1.8 + - - -
1138B LEU 2.7 20.9 + - - +
1139B LYS* 3.7 23.4 - - - +
1141B LEU* 1.3 71.1 - - - +
1143B TYR* 1.3 56.9 + - - +
1145B HIS* 4.0 2.8 - - - +
1146B ALA* 2.9 37.9 + - + +
1302B ALA* 3.6 12.0 - - + +
1303B GLY* 4.0 24.4 - - - +
1306B LEU* 3.1 28.1 - - + +
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Residues in contact with TYR1143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080B HIS* 4.3 9.5 + - - -
1081B MET* 3.4 24.8 - - + +
1082B ARG* 2.9 45.0 + - - +
1083B HIS* 3.5 42.8 - + + -
1086B VAL* 4.2 8.7 - - + -
1139B LYS 3.0 6.7 + - - +
1140B GLY 3.3 8.3 - - - +
1142B ARG* 1.3 74.7 - - - +
1144B ILE* 1.3 71.3 + - + +
1145B HIS 3.1 0.3 + - - -
1146B ALA* 3.2 5.6 + - - +
1147B ALA* 3.0 31.0 + - + +
1323B VAL* 3.4 36.2 - - + +
1324B GLN 5.3 1.4 + - - -
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Residues in contact with ILE1144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081B MET* 4.3 4.5 - - - -
1086B VAL* 4.0 14.6 - - + -
1140B GLY 3.0 17.9 + - - +
1141B LEU* 3.6 13.7 - - + +
1143B TYR* 1.3 79.5 - - + +
1145B HIS* 1.3 61.8 + - + +
1147B ALA* 3.5 7.3 - - - +
1149B ILE* 2.9 65.0 + - + +
1150B ILE 4.5 0.4 - - - +
1151B HIS* 4.7 10.8 - - + +
1169B ILE* 3.8 26.0 - - + -
1172B PHE* 3.7 31.6 - - + -
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Residues in contact with HIS1145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141B LEU* 2.8 45.6 + - + +
1142B ARG* 4.0 4.0 - - - +
1144B ILE* 1.3 75.2 - - + +
1146B ALA* 1.3 55.1 + - - +
1147B ALA 2.9 4.7 - - - -
1148B GLY* 2.6 26.2 + - - -
1149B ILE 3.1 17.7 - - - -
1150B ILE* 4.5 0.2 - - - -
1205B GLN* 3.1 58.4 + - + +
1208B ASP* 2.9 23.7 + - - -
1209B ILE* 4.9 5.8 - - + -
1302B ALA* 4.3 13.5 + - + +
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Residues in contact with ALA1146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142B ARG* 2.9 28.4 + - + +
1143B TYR 3.8 1.3 - - - +
1145B HIS* 1.3 73.8 - - - +
1147B ALA* 1.3 56.8 + - - +
1148B GLY* 3.0 3.5 + - - -
1323B VAL* 3.3 29.1 - - + +
1325B LYS* 3.9 13.7 - - - +
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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
------------------------------------------------------------
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