Contacts of the helix formed by residues 1131 - 1151 (chain B) in PDB entry 4DDG
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 THR1131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1129B GLY 3.6 2.9 + - - +
1130B PHE* 1.3 70.0 - - - +
1132B GLU* 1.3 62.2 + - - +
1133B PHE* 3.5 15.3 - - + -
1134B THR* 2.7 32.5 + - - -
1135B ILE* 3.4 8.2 - - - +
12C ASP* 5.2 7.4 - - - +
96C ALA 3.9 5.8 + - - -
98C THR* 3.4 32.3 - - + +
101C LYS* 4.3 17.1 - - - +
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Residues in contact with GLU1132 (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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1122B LYS* 3.7 26.5 + - - +
1123B GLU* 5.2 5.9 - - - +
1126B VAL* 3.8 40.4 - - + +
1130B PHE 3.3 3.2 + - - -
1131B THR* 1.3 72.8 - - - +
1133B PHE* 1.3 59.4 + - - +
1134B THR 3.1 0.7 + - - -
1135B ILE* 3.2 5.0 + - - +
1136B GLU* 2.9 38.7 + - + +
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Residues in contact with PHE1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131B THR* 3.5 14.6 - - + -
1132B GLU* 1.3 80.3 - - - +
1134B THR* 1.3 87.3 + - + +
1136B GLU* 3.6 13.8 - - - +
1137B ASP* 3.2 19.4 - - - +
5C ARG* 4.9 2.9 - - - -
8C LYS* 3.5 57.2 - - + +
9C GLU* 3.7 20.4 - - + -
12C ASP* 3.6 41.1 - - + -
98C THR* 4.7 8.5 - - + -
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Residues in contact with THR1134 (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 THR* 2.7 20.7 + - - +
1133B PHE* 1.3 107.0 - - + +
1135B ILE* 1.3 74.6 + - - +
1136B GLU 3.1 4.6 + - - -
1137B ASP* 3.3 14.3 - - - +
1138B PHE* 3.1 21.9 - - - -
5C ARG* 3.5 32.5 - - - +
96C ALA* 3.4 23.1 + - - +
98C THR* 4.4 4.9 - - + -
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Residues in contact with ILE1135 (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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1122B LYS* 4.2 11.7 - - + +
1125B LEU* 3.9 29.2 - - + -
1126B VAL* 3.7 27.6 - - + +
1130B PHE* 4.1 18.8 - - + -
1131B THR 3.4 8.1 - - - +
1132B GLU* 3.5 9.6 - - - +
1134B THR* 1.3 90.6 + - - +
1136B GLU* 1.3 61.6 + - - +
1137B ASP 3.3 0.4 - - - -
1138B PHE* 3.4 11.9 + - - +
1139B HIS* 2.9 29.3 + - - +
1174B TYR* 4.3 4.4 - - + -
1177B LEU* 3.9 24.5 - - + -
96C ALA* 4.5 6.3 - - + +
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Residues in contact with GLU1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1122B LYS* 3.5 28.6 + - - +
1132B GLU* 2.9 26.2 + - - +
1133B PHE* 3.6 18.0 - - - +
1134B THR 3.1 0.6 - - - -
1135B ILE* 1.3 80.3 - - - +
1137B ASP* 1.3 58.3 + - - +
1139B HIS* 3.5 5.9 + - - +
1140B ASN* 2.9 45.7 + - - +
8C LYS* 4.2 14.7 + - - -
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Residues in contact with ASP1137 (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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1133B PHE 3.2 15.3 - - - +
1134B THR* 3.3 16.8 - - - +
1136B GLU* 1.3 75.0 - - - +
1138B PHE* 1.3 62.7 + - + +
1140B ASN* 3.1 12.6 + - - +
1141B THR* 2.9 29.6 + - - -
1170B TYR* 3.9 24.9 + - + -
4C LYS* 6.6 0.2 - - - -
5C ARG* 4.4 13.0 + - - +
8C LYS* 3.8 22.6 + - - +
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Residues in contact with PHE1138 (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 THR 3.1 31.2 - - - -
1135B ILE* 3.4 12.3 + - - +
1136B GLU 3.4 0.4 - - - -
1137B ASP* 1.3 73.5 - - - +
1139B HIS* 1.3 65.9 + - - +
1141B THR* 3.2 4.4 + - - +
1142B PHE* 2.9 23.0 + - - +
1170B TYR* 3.5 53.6 - + - +
1173B VAL* 3.7 35.9 - - + -
1174B TYR* 3.9 27.3 - - + +
1177B LEU* 4.5 4.7 - - + -
5C ARG* 4.0 9.0 - - - -
61C PRO* 4.1 23.6 - - + -
62C PHE* 4.9 1.1 - + - -
95C PRO* 4.2 11.4 - - + -
96C ALA* 4.7 3.8 - - - -
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Residues in contact with HIS1139 (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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1118B SER 3.2 24.7 - - - -
1119B ALA* 3.9 8.7 + - - +
1122B LYS* 3.5 41.5 - - + +
1135B ILE 2.9 18.8 + - - +
1136B GLU 3.6 4.7 - - - +
1138B PHE* 1.3 76.2 - - - +
1140B ASN* 1.3 65.9 + - - +
1142B PHE* 3.3 3.9 + - - +
1143B MET* 2.9 63.1 + - + +
1174B TYR* 3.1 33.0 + - + -
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Residues in contact with ASN1140 (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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1122B LYS* 5.4 0.9 + - - -
1136B GLU* 2.9 34.1 + - - +
1137B ASP* 3.1 13.7 + - - +
1139B HIS* 1.3 85.8 - - - +
1141B THR* 1.3 56.3 + - - +
1143B MET* 3.9 5.0 - - - +
1144B ASP* 2.9 37.0 + - - +
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Residues in contact with THR1141 (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 ASP 2.9 12.6 + - - -
1138B PHE 3.6 7.0 - - - -
1140B ASN* 1.3 75.0 - - - +
1142B PHE* 1.3 58.4 + - - +
1144B ASP* 3.3 7.0 + - - +
1145B LEU* 2.9 41.9 + - + +
1167B THR* 3.3 37.8 + - + +
1170B TYR* 3.8 24.4 - - + +
1171B LEU* 3.8 5.8 - - - +
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Residues in contact with PHE1142 (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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1097B GLY* 6.3 1.3 - - - -
1101B LEU* 5.2 6.3 - - + -
1114B PHE* 3.8 30.3 - + - -
1118B SER* 3.5 30.5 - - - -
1138B PHE 2.9 12.3 + - - +
1139B HIS* 3.3 8.5 + - - +
1141B THR* 1.3 78.0 - - - +
1143B MET* 1.3 62.3 + - - +
1145B LEU* 3.0 9.9 + - + +
1146B ILE* 2.9 35.4 + - + +
1171B LEU* 3.6 28.3 - - + -
1174B TYR* 3.4 38.6 - + + -
1175B LEU* 4.4 19.3 - - + -
1178B LEU* 4.4 5.4 - - + -
1227B LEU* 4.5 7.0 - - + -
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Residues in contact with MET1143 (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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1115B LYS* 4.1 27.1 - - + +
1118B SER* 3.5 25.4 - - - +
1119B ALA* 4.0 21.8 - - + -
1139B HIS* 2.9 57.6 + - + +
1140B ASN* 4.0 4.9 - - - +
1142B PHE* 1.3 74.9 - - - +
1144B ASP* 1.3 57.9 + - - +
1146B ILE* 3.2 12.1 + - + +
1147B GLU* 2.9 27.6 + - - +
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Residues in contact with ASP1144 (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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1140B ASN* 2.9 23.5 + - - +
1141B THR* 3.6 7.9 - - - +
1143B MET* 1.3 75.8 - - - +
1145B LEU* 1.3 63.1 + - + +
1147B GLU* 3.0 23.0 + - - +
1148B GLN* 2.9 39.4 + - - +
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Residues in contact with LEU1145 (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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1101B LEU* 3.9 20.5 - - + +
1141B THR* 2.9 37.1 + - + +
1142B PHE* 3.0 7.6 + - - +
1144B ASP* 1.3 78.2 - - + +
1146B ILE* 1.3 60.7 + - - +
1147B GLU 3.5 0.2 + - - -
1148B GLN* 3.4 33.1 + - - +
1149B VAL* 3.6 18.5 + - - +
1158B LEU* 4.9 5.1 - - + +
1161B SER* 4.1 9.4 - - - -
1162B PHE* 4.5 16.6 - - + -
1167B THR* 4.1 20.2 - - + +
1168B SER* 5.6 1.1 - - - +
1171B LEU* 3.6 31.0 - - + -
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Residues in contact with ILE1146 (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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1101B LEU* 4.3 7.9 - - + -
1104B LEU* 5.4 0.4 - - + -
1111B LEU* 4.1 19.5 - - + -
1114B PHE* 3.8 31.9 - - + -
1115B LYS* 4.2 22.9 - - + -
1118B SER* 3.2 30.5 - - - +
1142B PHE* 2.9 22.8 + - + +
1143B MET* 3.5 18.6 - - + +
1144B ASP 3.2 0.2 - - - -
1145B LEU* 1.3 76.5 - - - +
1147B GLU* 1.3 58.2 + - - +
1149B VAL* 3.1 12.1 - - + +
1150B GLU* 2.9 26.0 + - - +
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Residues in contact with GLU1147 (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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1143B MET 2.9 11.1 + - - +
1144B ASP* 3.0 34.5 + - - +
1146B ILE* 1.3 75.9 - - - +
1148B GLN* 1.3 63.0 + - - +
1149B VAL 3.1 1.8 - - - -
1150B GLU* 3.1 34.9 + - + +
1151B LYS* 4.1 3.8 + - - +
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Residues in contact with GLN1148 (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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1144B ASP* 2.9 23.4 + - - +
1145B LEU* 3.4 28.8 - - - +
1147B GLU* 1.3 76.9 - - - +
1149B VAL* 1.3 57.9 + - - +
1151B LYS 3.3 12.8 - - - +
1153B THR* 3.2 30.6 - - + +
1157B ASP* 4.1 2.8 - - - +
1158B LEU* 3.8 16.8 + - + +
1161B SER* 2.5 32.0 + - - -
1167B THR* 5.6 1.2 - - - +
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Residues in contact with VAL1149 (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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1101B LEU* 3.4 39.7 - - + +
1104B LEU* 4.4 4.2 - - + +
1105B LEU* 3.5 37.1 - - + +
1111B LEU* 3.2 26.3 - - + +
1145B LEU 3.6 7.2 + - - +
1146B ILE* 3.1 27.1 + - + +
1147B GLU 3.1 0.6 - - - -
1148B GLN* 1.3 79.2 - - - +
1150B GLU* 1.3 68.1 + - - +
1151B LYS 3.6 1.6 - - - -
1152B GLN* 3.9 10.0 + - - +
1158B LEU* 4.9 5.2 - - + -
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Residues in contact with GLU1150 (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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1111B LEU* 3.4 27.5 - - + +
1115B LYS* 3.0 39.6 + - - +
1146B ILE 2.9 11.3 + - - +
1147B GLU* 3.1 34.3 + - + +
1149B VAL* 1.3 80.2 - - - +
1151B LYS* 1.3 60.1 + - + +
1152B GLN* 3.6 1.7 + - - +
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Residues in contact with LYS1151 (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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1147B GLU 4.1 3.1 + - - +
1148B GLN 3.3 12.0 - - - +
1149B VAL 3.9 0.2 - - - -
1150B GLU* 1.3 78.4 - - + +
1152B GLN* 1.3 69.0 + - - +
1153B THR* 3.2 4.0 + - - -
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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