Contacts of the helix formed by residues 1092 - 1106 (chain B) in PDB entry 4DAJ
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 ASP1092 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090B SER 4.2 0.6 + - - -
1091B LEU* 1.3 75.5 - - - +
1093B ALA* 1.3 66.5 + - - +
1094B VAL* 3.1 13.5 + - - +
1095B ARG* 2.7 39.7 + - - +
1096B ARG* 2.9 19.3 + - - +
1126B TRP* 5.0 0.9 - - - -
1156B GLY 3.8 18.4 - - - +
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Residues in contact with ALA1093 (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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485B GLU* 4.9 11.9 - - - +
1003B ILE* 5.6 0.5 - - - +
1091B LEU 4.1 0.2 + - - -
1092B ASP* 1.3 73.6 - - - +
1094B VAL* 1.3 63.6 + - + +
1096B ARG* 3.2 14.9 - - - +
1097B ALA* 2.9 23.0 + - - +
1158B TRP* 5.2 2.5 - - + -
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Residues in contact with VAL1094 (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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485B GLU* 5.0 5.8 - - - +
1092B ASP* 3.3 6.5 + - - +
1093B ALA* 1.3 75.5 - - + +
1095B ARG* 1.3 57.4 + - - +
1097B ALA* 2.8 26.7 + - - +
1098B ALA* 3.0 9.7 + - - +
1152B THR* 3.5 25.6 - - + +
1156B GLY 3.5 35.2 - - - +
1157B THR* 3.7 9.0 - - - +
1158B TRP* 3.4 43.3 - - + +
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Residues in contact with ARG1095 (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* 4.1 18.6 - - + +
1092B ASP* 2.7 44.3 + - - +
1094B VAL* 1.3 79.7 - - - +
1096B ARG* 1.3 62.6 + - - +
1098B ALA* 3.1 11.5 + - - +
1099B LEU* 2.9 21.8 + - - +
1126B TRP* 3.2 55.8 - - - +
1152B THR 3.9 9.4 - - - +
1153B PHE* 2.5 35.7 + - + +
1154B ARG 2.6 25.9 + - - -
1155B THR 3.7 2.4 + - - -
1156B GLY* 3.2 19.3 - - - +
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Residues in contact with ARG1096 (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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1088B TYR* 3.1 56.7 + - + +
1089B ASP* 3.1 35.6 + - - +
1091B LEU* 3.1 23.2 + - + +
1092B ASP 2.9 16.5 + - - +
1093B ALA* 3.2 17.5 - - - +
1095B ARG* 1.3 75.2 - - - +
1097B ALA* 1.3 62.7 + - - +
1099B LEU* 2.9 18.9 + - - +
1100B ILE* 2.9 19.6 + - + +
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Residues in contact with ALA1097 (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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1003B ILE* 3.5 30.4 - - + +
1006B MET* 3.9 7.1 - - - +
1007B LEU* 5.8 0.9 - - - +
1093B ALA 2.9 9.7 + - - +
1094B VAL 2.8 16.7 + - - +
1096B ARG* 1.3 72.1 - - - +
1098B ALA* 1.3 59.4 + - - +
1100B ILE* 3.2 17.5 + - - +
1101B ASN* 2.9 20.6 + - - +
1158B TRP* 3.5 22.2 - - + -
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Residues in contact with ALA1098 (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* 3.6 15.6 - - + -
1094B VAL 3.0 6.3 + - - -
1095B ARG* 3.3 12.8 - - - +
1097B ALA* 1.3 75.6 - - - +
1099B LEU* 1.3 55.5 + - - +
1101B ASN* 2.7 28.8 + - - +
1102B MET* 3.0 9.5 + - - +
1149B VAL* 4.3 3.8 - - + +
1152B THR* 3.8 22.7 - - + -
1153B PHE* 3.4 29.8 - - + -
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Residues in contact with LEU1099 (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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1078B ILE* 4.3 16.8 - - + -
1084B LEU* 5.0 12.6 - - + +
1087B VAL* 5.0 7.0 - - + -
1088B TYR* 4.3 33.7 - - + +
1091B LEU* 4.9 8.5 - - + -
1095B ARG 2.9 11.2 + - - +
1096B ARG* 2.9 12.6 + - - +
1098B ALA* 1.3 75.2 - - - +
1100B ILE* 1.3 57.3 + - - +
1102B MET* 3.3 6.3 + - - +
1103B VAL* 2.9 38.1 + - + +
1111B VAL* 4.0 24.0 - - + -
1118B LEU* 5.0 12.1 - - + -
1121B LEU* 5.8 1.1 - - + -
1153B PHE* 3.9 19.2 - - + -
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Residues in contact with ILE1100 (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 GLU* 4.2 17.0 - - + +
1003B ILE* 4.1 32.5 - - + -
1007B LEU* 4.8 8.5 - - + -
1071B VAL* 4.6 10.8 - - + -
1074B ALA* 4.9 7.6 - - + +
1075B VAL* 4.6 15.0 - - + -
1078B ILE* 4.4 17.5 - - + -
1088B TYR* 4.8 12.8 - - + +
1096B ARG* 2.9 22.4 + - + +
1097B ALA* 3.3 17.3 - - - +
1098B ALA 3.2 0.2 - - - -
1099B LEU* 1.3 76.1 - - - +
1101B ASN* 1.3 57.3 + - - +
1103B VAL* 3.6 2.9 + - - +
1104B PHE* 2.9 34.8 + - + +
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Residues in contact with ASN1101 (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* 3.1 32.1 - - + +
1007B LEU* 3.6 21.3 - - + +
1010B ASP* 2.6 32.5 + - - -
1097B ALA 2.9 7.0 + - - +
1098B ALA 2.7 19.5 + - - +
1100B ILE* 1.3 69.1 - - - +
1102B MET* 1.3 64.2 + - - +
1104B PHE* 2.9 12.5 + - - +
1105B GLN* 3.0 12.1 + - - +
1138B TRP* 5.8 1.2 - - - -
1145B ARG* 2.8 24.9 + - - -
1149B VAL* 3.5 11.0 - - + +
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Residues in contact with MET1102 (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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1098B ALA 3.0 8.4 + - - +
1099B LEU* 3.3 9.4 + - - +
1101B ASN* 1.3 76.1 - - - +
1103B VAL* 1.3 64.2 + - - +
1104B PHE 3.0 0.5 + - - -
1105B GLN* 3.1 3.8 + - - +
1106B MET* 3.0 51.5 + - + +
1111B VAL* 3.4 31.1 - - + +
1114B PHE* 3.7 18.6 - - + -
1118B LEU* 6.3 1.1 - - + -
1133B LEU* 4.4 18.6 - - + -
1138B TRP* 4.1 30.3 - - + +
1149B VAL* 4.2 10.1 - - + -
1153B PHE* 3.9 25.1 - - - -
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Residues in contact with VAL1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074B ALA* 3.9 32.7 - - + +
1077B GLY* 5.6 1.1 - - - -
1078B ILE* 3.7 26.0 - - + +
1084B LEU* 5.0 8.7 - - + -
1099B LEU* 2.9 25.0 + - + +
1100B ILE* 4.0 3.8 - - - +
1102B MET* 1.3 75.0 - - - +
1104B PHE* 1.3 57.1 + - - +
1107B GLY* 3.2 32.9 + - - +
1108B GLU* 4.4 7.0 - - + +
1111B VAL* 3.6 26.2 - - + -
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Residues in contact with PHE1104 (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* 3.5 34.8 - - + -
1011B GLU* 4.9 0.9 - - - -
1029B ILE* 3.6 28.9 - - + -
1030B GLY* 3.8 25.0 - - - +
1067B PHE* 4.2 9.9 - + - -
1070B ASP* 3.7 46.0 - - + -
1071B VAL* 3.9 11.2 - - + -
1074B ALA* 4.6 8.5 - - + -
1100B ILE* 2.9 20.2 + - + +
1101B ASN* 2.9 14.1 + - - +
1103B VAL* 1.3 78.9 - - - +
1105B GLN* 1.3 60.6 + - - +
1107B GLY 4.9 0.2 + - - -
1145B ARG* 4.3 6.5 - - - -
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Residues in contact with GLN1105 (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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1011B GLU* 5.1 0.9 - - - +
1020B ASP* 5.3 6.0 + - - +
1021B THR* 5.0 4.6 + - - +
1032B LEU* 5.7 5.4 - - - +
1101B ASN* 3.0 8.3 + - - +
1102B MET* 4.1 3.8 - - - +
1104B PHE* 1.3 80.2 - - - +
1106B MET* 1.3 67.2 + - + +
1107B GLY 3.6 0.2 + - - -
1138B TRP* 3.1 29.4 + - - +
1142B THR* 3.6 27.6 + - - +
1145B ARG* 3.3 45.1 + - - +
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Residues in contact with MET1106 (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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1102B MET* 3.0 51.9 + - + +
1105B GLN* 1.3 79.7 - - + +
1107B GLY* 1.3 59.2 + - - +
1110B GLY* 4.1 21.1 + - - -
1111B VAL* 3.4 17.7 - - + -
1114B PHE* 4.0 15.5 - - + -
1138B TRP* 3.5 49.8 - - + +
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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