Contacts of the helix formed by residues 1142 - 1156 (chain B) in PDB entry 4DJH
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 THR1142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105B GLN* 3.1 29.6 + - - +
1138B TRP* 3.0 21.6 + - - -
1139B TYR 3.8 2.7 - - - -
1141B GLN* 1.3 87.6 - - + +
1143B PRO* 1.3 65.2 - - - +
1144B ASN* 3.5 2.0 - - - -
1145B ARG* 3.4 11.6 + - + -
1146B ALA* 3.0 19.9 + - - +
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Residues in contact with PRO1143 (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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1139B TYR* 3.0 31.6 - - + +
1140B ASN* 3.4 11.9 - - - +
1141B GLN 3.4 9.0 - - - +
1142B THR* 1.3 86.5 - - - +
1144B ASN* 1.3 74.4 + - - +
1146B ALA* 3.1 2.4 + - + +
1147B LYS* 2.8 27.9 + - - +
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Residues in contact with ASN1144 (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 THR 3.5 0.8 - - - -
1143B PRO* 1.3 82.8 - - - +
1145B ARG* 1.3 64.9 + - - +
1147B LYS* 3.4 5.2 + - - +
1148B ARG* 3.3 39.2 + - - +
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Residues in contact with ARG1145 (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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1007B LEU* 3.2 25.1 - - - +
1010B ASP* 3.4 33.7 + - - +
1011B GLU* 3.1 32.9 + - - -
1101B ASN* 2.6 35.8 + - - +
1105B GLN* 3.2 42.2 + - - +
1138B TRP* 5.2 0.2 - - + -
1142B THR* 3.4 14.8 + - - +
1143B PRO 3.3 0.6 - - - -
1144B ASN* 1.3 77.7 - - - +
1146B ALA* 1.3 59.5 - - - +
1148B ARG* 2.9 23.8 + - - +
1149B VAL* 2.8 31.0 + - + +
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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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1138B TRP* 3.5 32.7 - - + +
1139B TYR* 3.7 32.1 - - + -
1142B THR 3.0 18.6 + - - +
1143B PRO 3.1 2.7 + - - +
1145B ARG* 1.3 76.1 - - - +
1147B LYS* 1.3 53.8 + - - +
1149B VAL* 3.2 0.5 + - - +
1150B ILE* 2.7 41.9 + - + +
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Residues in contact with LYS1147 (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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1139B TYR* 4.3 19.2 - - + +
1143B PRO 2.8 18.3 + - - +
1144B ASN* 3.7 5.2 - - - +
1146B ALA* 1.3 77.0 - - - +
1148B ARG* 1.3 56.9 + - + +
1150B ILE* 4.0 4.5 - - - +
1151B THR* 2.9 36.2 + - - +
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Residues in contact with ARG1148 (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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1009B ILE* 4.8 9.5 + - - +
1010B ASP* 2.4 45.8 + - - +
1144B ASN* 3.3 31.3 + - - +
1145B ARG* 2.9 25.6 + - - +
1147B LYS* 1.3 78.9 - - + +
1149B VAL* 1.3 61.8 + - - +
1151B THR* 3.4 0.4 + - - -
1152B THR* 2.9 27.1 + - - -
1160B ALA* 3.5 33.7 - - + +
1161B TYR* 3.9 22.3 - - + +
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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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1006B MET* 4.4 1.6 - - + -
1098B ALA* 3.7 26.6 - - + +
1101B ASN* 3.8 23.8 - - - +
1102B MET* 3.8 7.6 - - + -
1138B TRP* 3.6 25.6 - - + -
1145B ARG* 2.8 25.0 + - + +
1146B ALA 3.7 5.6 - - - +
1148B ARG* 1.3 75.7 - - - +
1150B ILE* 1.3 61.8 + - - +
1152B THR* 3.2 10.3 + - - -
1153B PHE* 3.2 27.2 + - + -
1161B TYR* 3.7 16.2 - - - +
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Residues in contact with ILE1150 (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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1130B ALA* 3.3 33.3 - - + +
1133B LEU* 3.4 38.1 - - + +
1134B ALA* 3.5 22.7 - - + +
1138B TRP* 4.0 13.9 - - + -
1139B TYR* 4.0 14.1 - - + -
1146B ALA 2.7 23.9 + - - +
1147B LYS* 4.0 4.7 - - - +
1149B VAL* 1.3 70.8 - - - +
1151B THR* 1.3 60.8 + - - +
1153B PHE* 3.2 10.9 + - - +
1154B ARG* 2.9 27.5 + - - +
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Residues in contact with THR1151 (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 LYS* 2.9 24.5 + - - +
1148B ARG 3.7 4.5 - - - -
1150B ILE* 1.3 76.3 - - - +
1152B THR* 1.3 53.8 + - - +
1154B ARG* 3.0 34.3 + - - +
1155B THR* 2.7 49.5 + - + +
1159B ASP* 5.5 2.5 - - + -
1160B ALA* 3.9 21.8 - - + +
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Residues in contact with THR1152 (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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1006B MET* 4.0 7.9 - - + +
1094B VAL* 3.7 31.4 - - + +
1095B ARG* 3.6 1.7 + - - +
1098B ALA* 4.0 10.8 - - + -
1148B ARG 2.9 16.4 + - - -
1149B VAL 3.3 9.4 - - - -
1151B THR* 1.3 76.7 - - - +
1153B PHE* 1.3 55.6 + - - +
1155B THR* 4.2 0.2 - - - -
1156B GLY* 2.6 35.0 + - - -
1157B THR 3.6 23.4 + - - +
1158B TRP* 4.9 4.3 - - + -
1160B ALA* 4.1 2.1 - - - +
1161B TYR* 3.5 19.2 - - - -
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Residues in contact with PHE1153 (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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1091B LEU* 4.2 8.7 - - + -
1095B ARG* 2.4 48.8 + - + +
1098B ALA* 3.3 29.6 - - + -
1099B LEU* 3.5 26.2 - - + -
1102B MET* 3.6 23.8 - - - -
1121B LEU* 4.0 33.2 - - + -
1126B TRP* 3.2 19.9 - - + +
1130B ALA* 5.7 2.5 - - + -
1133B LEU* 3.9 22.2 - - + -
1149B VAL* 3.2 18.9 + - + -
1150B ILE* 3.2 10.9 + - + +
1152B THR* 1.3 77.8 - - - +
1154B ARG* 1.3 54.7 + - - +
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Residues in contact with ARG1154 (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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1095B ARG* 3.4 7.4 + - - -
1126B TRP* 3.8 19.3 - - - +
1127B ASP* 3.7 30.7 + - - +
1130B ALA* 4.0 22.4 - - + +
1150B ILE* 2.9 13.6 + - - +
1151B THR* 3.0 42.8 + - - +
1153B PHE* 1.3 77.9 - - - +
1155B THR* 1.3 71.3 + - + +
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Residues in contact with THR1155 (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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1095B ARG* 3.7 6.9 + - - -
1151B THR* 2.7 39.2 + - + +
1154B ARG* 1.3 88.3 - - + +
1156B GLY* 1.3 62.5 + - - +
1157B THR* 2.8 39.6 + - - +
1159B ASP* 4.5 9.6 - - + +
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Residues in contact with GLY1156 (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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258B LEU* 4.4 7.8 - - - +
1092B ASP* 4.4 3.1 - - - +
1094B VAL* 3.5 24.0 - - - +
1095B ARG* 3.1 31.3 - - - +
1152B THR 2.6 23.5 + - - -
1155B THR* 1.3 72.3 - - - +
1157B THR* 1.3 61.3 - - - +
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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