Contacts of the helix formed by residues 1092 - 1106 (chain C) in PDB entry 5B2G
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1091C LEU* 1.3 73.1 - - - +
1093C ALA* 1.3 64.7 - - - +
1094C VAL* 3.1 28.6 + - + +
1095C ARG* 3.3 39.4 + - - +
1096C ARG* 2.9 27.1 + - - +
1156C GLY 4.1 3.8 - - - +
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Residues in contact with ALA1093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092C ASP* 1.3 75.5 - - - +
1094C VAL* 1.3 60.5 + - + +
1096C ARG* 3.4 17.2 - - - +
1097C ALA* 3.0 27.0 + - - +
1158C TRP* 4.9 2.1 - - + -
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Residues in contact with VAL1094 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092C ASP* 3.1 17.2 - - - +
1093C ALA* 1.3 77.4 - - + +
1095C ARG* 1.3 60.7 + - - +
1096C ARG 3.1 1.3 - - - -
1097C ALA* 3.1 18.0 + - - +
1098C ALA* 3.1 12.3 + - - +
1152C THR* 4.0 11.4 - - + +
1156C GLY* 3.3 34.8 - - - +
1157C THR* 3.8 6.5 - - - +
1158C TRP* 3.8 43.5 - - + +
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Residues in contact with ARG1095 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091C LEU* 3.5 37.1 - - + +
1092C ASP* 3.3 29.6 + - - +
1094C VAL* 1.3 76.0 - - - +
1096C ARG* 1.3 65.7 + - - +
1098C ALA* 3.4 6.9 + - - -
1099C LEU* 3.0 22.7 + - - +
1121C LEU* 6.1 0.4 - - - -
1124C LYS* 6.3 0.4 - - - +
1126C TRP* 3.1 45.8 - - - +
1152C THR 4.0 13.5 - - - +
1153C PHE* 3.0 35.9 + - + -
1154C ARG 3.1 12.3 + - - -
1155C THR 2.9 23.8 + - - -
1156C GLY* 3.7 14.2 - - - -
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Residues in contact with ARG1096 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C TYR* 3.5 61.7 + - + +
1089C ASP* 4.0 31.3 + - - +
1091C LEU* 3.2 18.2 + - + +
1092C ASP 2.9 27.0 + - - +
1093C ALA* 3.4 15.0 - - - +
1095C ARG* 1.3 77.2 - - - +
1097C ALA* 1.3 62.2 + - - +
1099C LEU* 3.3 4.4 + - - +
1100C ILE* 3.0 30.1 + - + +
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Residues in contact with ALA1097 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C ILE* 3.5 41.4 - - + +
1006C MET* 3.8 14.5 - - + +
1093C ALA 3.0 14.9 + - - +
1094C VAL 3.1 10.3 + - - +
1096C ARG* 1.3 75.5 - - - +
1098C ALA* 1.3 57.5 + - - +
1100C ILE* 3.2 5.8 + - - +
1101C ASN* 2.9 26.5 + - - +
1158C TRP* 4.2 7.6 - - + -
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Residues in contact with ALA1098 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C MET* 4.1 6.7 - - + +
1094C VAL 3.1 7.3 + - - +
1095C ARG* 3.8 2.2 - - - +
1096C ARG 3.3 0.2 - - - -
1097C ALA* 1.3 74.0 - - - +
1099C LEU* 1.3 66.1 + - - +
1101C ASN* 3.1 21.5 - - - +
1102C MET* 3.2 9.4 + - - +
1149C VAL* 4.3 7.3 - - + +
1152C THR* 3.8 29.2 - - + -
1153C PHE* 3.4 33.4 - - + -
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Residues in contact with LEU1099 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078C ILE* 4.4 9.0 - - + -
1084C LEU* 3.4 32.8 - - + -
1087C VAL* 4.3 20.9 - - + +
1088C TYR* 4.7 12.6 - - + +
1091C LEU* 4.2 20.9 - - + -
1095C ARG 3.0 16.3 + - - +
1096C ARG* 3.6 5.6 - - - +
1098C ALA* 1.3 73.1 - - - +
1100C ILE* 1.3 65.4 + - - +
1102C MET* 3.2 9.6 + - + +
1103C VAL* 3.1 22.9 + - + +
1111C VAL* 4.5 6.7 - - + -
1118C LEU* 4.4 12.8 - - + -
1121C LEU* 5.3 3.6 - - + -
1153C PHE* 3.4 13.2 - - + -
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Residues in contact with ILE1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C ILE* 3.3 32.5 - - + -
1007C LEU* 5.1 3.4 - - + -
1071C VAL* 4.7 5.2 - - + +
1074C ALA* 4.0 21.3 - - + +
1075C VAL* 3.8 25.1 - - + -
1078C ILE* 3.4 26.0 - - + -
1088C TYR* 3.8 20.4 - - + +
1096C ARG* 3.0 23.9 + - + +
1097C ALA* 3.2 2.4 + - - +
1099C LEU* 1.3 72.3 - - - +
1101C ASN* 1.3 55.1 + - - +
1103C VAL* 3.2 2.7 + - - +
1104C PHE* 2.8 33.0 + - + +
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Residues in contact with ASN1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C ILE* 4.7 0.2 - - - +
1006C MET* 3.3 20.6 - - - +
1007C LEU* 3.1 22.2 - - + +
1010C ASP* 2.8 27.1 + - - -
1097C ALA 2.9 13.2 + - - +
1098C ALA* 3.1 17.0 - - - +
1100C ILE* 1.3 75.1 - - - +
1102C MET* 1.3 63.6 + - - +
1104C PHE* 3.1 1.4 + - - +
1105C GLN* 3.0 22.2 + - - +
1145C ARG* 2.7 31.1 + - - +
1149C VAL* 3.8 18.6 - - + +
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Residues in contact with MET1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098C ALA 3.2 10.1 + - - +
1099C LEU* 3.2 12.1 + - - +
1101C ASN* 1.3 78.1 - - - +
1103C VAL* 1.3 57.8 + - - +
1105C GLN* 3.9 5.0 - - - +
1106C MET* 3.0 44.9 + - - +
1111C VAL* 4.0 34.7 - - + +
1133C LEU* 4.8 14.4 - - + -
1138C TRP* 3.8 48.7 - - + +
1149C VAL* 4.4 3.6 - - + +
1153C PHE* 4.1 21.5 - - - -
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Residues in contact with VAL1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074C ALA* 4.1 28.5 - - + +
1077C GLY* 5.8 0.4 - - - -
1078C ILE* 4.0 9.9 - - + +
1084C LEU* 4.0 11.0 - - + -
1099C LEU* 3.1 28.8 + - + +
1100C ILE* 3.6 9.0 - - - +
1101C ASN 3.2 0.2 - - - -
1102C MET* 1.3 75.6 - - - +
1104C PHE* 1.3 57.1 + - - +
1106C MET 2.7 21.1 - - - +
1107C GLY 3.7 15.6 - - - +
1108C GLU* 4.2 17.0 - - + -
1111C VAL* 3.8 16.6 - - + -
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Residues in contact with PHE1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C LEU* 3.9 25.4 - - + -
1011C GLU* 4.1 15.7 - - + -
1029C ILE 3.5 21.1 - - - -
1030C GLY* 3.5 29.3 - - - +
1067C PHE* 4.1 13.7 - + - -
1070C ASP* 3.4 39.9 - - + -
1071C VAL* 3.8 28.5 - - + -
1074C ALA* 4.6 6.9 - - + +
1100C ILE* 2.8 18.1 + - + +
1101C ASN 3.1 4.9 + - - +
1103C VAL* 1.3 77.5 - - - +
1105C GLN* 1.3 66.0 + - - +
1106C MET 3.8 1.9 - - - +
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Residues in contact with GLN1105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011C GLU* 4.1 7.9 - - - +
1101C ASN 3.0 11.7 + - - +
1102C MET* 3.9 4.9 - - - +
1104C PHE* 1.3 82.4 - - - +
1106C MET* 1.3 66.3 + - + +
1138C TRP* 3.8 24.0 + - - +
1142C THR* 3.5 31.3 + - - +
1145C ARG* 2.8 48.7 + - - +
1149C VAL* 6.1 0.2 - - - +
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Residues in contact with MET1106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102C MET* 3.0 25.9 + - - +
1103C VAL 2.7 19.9 - - - +
1104C PHE 3.8 2.4 - - - +
1105C GLN* 1.3 90.9 - - + +
1107C GLY* 1.3 63.8 + - - +
1110C GLY* 4.4 22.2 - - - +
1111C VAL* 5.2 5.4 - - + -
1137C ARG* 3.7 26.0 - - - +
1138C TRP* 4.0 29.8 - - + +
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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