Contacts of the helix formed by residues 1135 - 1148 (chain A) in PDB entry 1DJO
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 ASP1135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1125A SER* 3.7 1.1 - - - -
1126A MET* 2.9 28.5 + - - +
1127A ARG* 2.9 29.7 + - - +
1133A SER 3.4 2.8 + - - +
1134A ALA* 1.3 71.2 - - - +
1136A GLY* 1.3 64.5 + - - +
1137A MET 3.4 2.9 + - - -
1138A LEU* 3.7 7.0 + - - +
1139A ASN* 3.2 38.4 + - - +
1161A MET* 4.8 2.1 - - - +
1179A THR* 3.8 30.1 - - + +
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Residues in contact with GLY1136 (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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1021A ILE* 4.0 16.0 - - - +
1125A SER* 3.6 21.6 - - - -
1127A ARG 4.7 0.8 + - - -
1129A GLY* 6.5 0.4 - - - -
1134A ALA* 3.5 3.8 - - - +
1135A ASP* 1.3 80.2 + - - +
1137A MET* 1.3 68.4 + - - +
1139A ASN* 3.8 2.9 - - - +
1140A LEU* 3.1 26.0 + - - +
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Residues in contact with MET1137 (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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1047A GLY* 5.0 7.2 - - - +
1048A VAL* 4.1 24.7 - - + +
1129A GLY* 5.0 12.8 - - - +
1131A ALA 5.4 0.7 - - - +
1133A SER* 5.2 0.9 - - - +
1134A ALA* 3.4 47.1 - - + +
1135A ASP 3.4 0.6 - - - -
1136A GLY* 1.3 77.1 - - - +
1138A LEU* 1.3 62.7 + - - +
1140A LEU* 3.4 2.9 + - - +
1141A TYR* 3.1 21.7 + - - +
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Residues in contact with LEU1138 (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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1135A ASP* 3.7 6.7 + - - +
1136A GLY 3.5 0.2 - - - -
1137A MET* 1.3 76.0 - - - +
1139A ASN* 1.3 68.7 + - - +
1141A TYR* 3.4 16.3 + - + -
1142A ASN* 2.9 42.5 + - - +
1163A ASP* 3.7 21.5 - - - +
1194A GLU* 6.3 2.0 - - - +
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Residues in contact with ASN1139 (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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1123A VAL* 3.6 18.2 - - + -
1124A GLY 3.2 19.9 + - - +
1125A SER* 4.2 0.4 - - - +
1135A ASP* 3.2 39.6 + - - +
1136A GLY 3.8 3.8 - - - +
1137A MET 3.3 0.2 - - - -
1138A LEU* 1.3 81.8 - - - +
1140A LEU* 1.3 57.1 + - - +
1142A ASN* 3.3 7.1 + - - +
1143A ALA* 2.9 26.9 + - - +
1160A THR* 3.6 8.9 + - - +
1161A MET* 3.6 31.8 - - - +
1162A ASN 3.6 8.0 + - - +
1163A ASP 4.9 2.1 + - - -
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Residues in contact with LEU1140 (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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1014A ILE* 3.9 27.1 - - + -
1021A ILE* 4.6 14.6 - - + -
1044A LEU* 4.6 24.7 - - + +
1045A ILE* 4.9 1.1 - - + +
1048A VAL* 4.5 17.9 - - + -
1051A LEU* 4.6 12.1 - - + -
1095A VAL* 4.1 18.8 - - + -
1097A THR* 4.6 10.3 - - + -
1123A VAL* 4.3 6.2 - - + +
1136A GLY 3.1 17.7 + - - +
1137A MET* 3.8 4.0 - - - +
1139A ASN* 1.3 73.9 - - - +
1141A TYR* 1.3 66.3 + - - +
1143A ALA* 2.9 6.8 + - + +
1144A VAL* 2.9 26.6 + - + +
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Residues in contact with TYR1141 (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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1048A VAL* 4.3 5.8 - - + -
1050A GLU* 3.7 34.1 + - + +
1051A LEU* 3.7 21.0 - - + +
1053A ASP* 5.6 2.8 - - - +
1054A LEU* 3.3 50.1 - - + +
1137A MET 3.1 11.9 + - - +
1138A LEU* 3.6 22.0 - - + +
1140A LEU* 1.3 78.2 - - - +
1142A ASN* 1.3 68.9 + - - +
1144A VAL 3.4 0.5 + - - -
1145A ALA* 2.9 23.9 + - - +
1194A GLU* 4.8 4.0 - - - -
1195A GLY* 4.0 27.2 + - - -
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Residues in contact with ASN1142 (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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1138A LEU* 2.9 40.8 + - - +
1139A ASN* 3.7 8.1 + - - +
1141A TYR* 1.3 86.7 - - - +
1143A ALA* 1.3 60.6 + - - +
1145A ALA* 3.5 5.3 - - - +
1146A VAL* 2.9 36.4 + - - +
1160A THR* 4.1 8.9 - - - +
1163A ASP* 4.1 21.0 + - - +
1192A VAL* 3.7 38.2 + - + +
1194A GLU* 5.0 2.6 + - - -
1195A GLY 4.6 4.3 + - - -
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Residues in contact with ALA1143 (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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1095A VAL* 3.7 13.1 - - + +
1121A VAL* 3.8 13.7 - - + +
1123A VAL* 3.8 23.6 - - + -
1139A ASN 2.9 11.0 + - - +
1140A LEU* 2.9 10.1 + - - +
1142A ASN* 1.3 77.4 - - - +
1144A VAL* 1.3 56.6 + - - +
1146A VAL* 3.3 2.9 + - - +
1147A ALA* 2.9 29.8 + - - +
1160A THR* 3.3 20.6 + - - +
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Residues in contact with VAL1144 (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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1012A VAL* 4.8 5.6 - - + -
1014A ILE* 4.1 23.3 - - + -
1051A LEU* 4.0 20.0 - - + -
1054A LEU* 3.9 20.9 - - + -
1055A ALA* 4.6 1.8 - - + -
1057A VAL* 4.1 22.2 - - + -
1095A VAL* 4.1 11.9 - - + -
1140A LEU* 2.9 19.2 + - + +
1141A TYR 3.8 6.7 - - - +
1143A ALA* 1.3 73.0 - - - +
1145A ALA* 1.3 64.8 + - - +
1147A ALA* 3.7 1.7 - - - -
1148A SER* 2.8 41.4 + - - +
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Residues in contact with ALA1145 (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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1054A LEU* 3.8 21.9 - - + +
1141A TYR* 2.9 19.2 + - + +
1142A ASN* 3.5 10.8 - - - +
1144A VAL* 1.3 79.6 - - - +
1146A VAL* 1.3 60.5 + - - +
1148A SER* 3.7 4.7 + - - -
1149A ASN* 3.5 20.4 + - - +
1192A VAL* 4.5 4.7 - - + -
1195A GLY* 3.8 31.7 - - - +
1197A SER* 4.8 1.6 + - - -
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Residues in contact with VAL1146 (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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1121A VAL* 4.0 8.3 - - + -
1142A ASN 2.9 20.9 + - - +
1143A ALA 3.8 3.6 - - - +
1145A ALA* 1.3 73.7 - - - +
1147A ALA* 1.3 63.3 + - - +
1148A SER 3.1 1.6 - - - -
1149A ASN* 3.2 6.8 + - - -
1152A SER* 2.7 39.4 + - - +
1158A LEU* 3.7 24.9 - - + -
1160A THR* 3.8 13.9 - - + -
1165A ILE* 4.3 8.3 - - + -
1192A VAL* 3.5 29.8 - - + -
1197A SER* 3.6 16.2 - - - +
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Residues in contact with ALA1147 (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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1012A VAL* 4.0 14.5 - - + +
1092A ASP* 4.5 1.9 - - - +
1093A GLY* 3.5 20.7 + - - -
1094A ILE 4.3 10.8 - - - +
1095A VAL* 3.7 20.0 - - + -
1119A PRO* 4.0 19.8 - - + +
1121A VAL* 4.2 9.6 - - + +
1143A ALA 2.9 17.7 + - - +
1144A VAL 3.2 3.8 + - - +
1146A VAL* 1.3 76.1 - - - +
1148A SER* 1.3 60.9 + - - +
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Residues in contact with SER1148 (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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1010A ALA* 4.0 24.9 - - - +
1012A VAL* 3.4 17.4 - - - +
1054A LEU* 3.9 15.2 + - - -
1055A ALA* 3.4 12.6 - - - +
1092A ASP* 6.1 0.2 - - - -
1144A VAL* 2.8 23.3 + - - +
1145A ALA* 4.0 6.5 - - - -
1146A VAL 3.1 0.2 - - - -
1147A ALA* 1.3 77.3 - - - +
1149A ASN* 1.3 61.9 + - - +
1150A LYS 3.7 1.9 + - - -
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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