Contacts of the helix formed by residues 1095 - 1106 (chain B) in PDB entry 2B7A
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 PRO1095 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950B HIS* 4.0 23.8 - - + +
1048B PHE* 4.0 10.5 - - + -
1093B GLY 3.5 7.1 - - - +
1094B CYS* 1.3 93.5 - - - +
1096B ASP* 1.3 65.3 + - - +
1097B GLU* 4.4 6.7 - - + +
1098B ILE* 3.0 28.0 + - + -
1099B TYR* 3.0 11.0 + - - +
1130B MET* 5.8 5.6 - - + -
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Residues in contact with ASP1096 (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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1090B ARG* 3.7 22.3 + - - +
1094B CYS 3.6 2.0 + - - -
1095B PRO* 1.3 70.7 - - - +
1097B GLU* 1.3 54.0 + - - +
1099B TYR* 3.2 11.3 + - - +
1100B MET* 2.8 50.9 + - + +
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Residues in contact with GLU1097 (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 PRO* 3.2 5.2 - - + +
1096B ASP* 1.3 77.1 - - - +
1098B ILE* 1.3 63.6 + - + +
1100B MET* 3.6 20.1 + - + +
1101B ILE* 3.4 22.7 + - + +
1122B ARG* 4.9 1.7 + - - +
1125B GLN* 5.2 4.9 + - - -
1126B ILE* 3.8 38.9 - - + +
1129B GLN* 4.1 13.5 + - - +
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Residues in contact with ILE1098 (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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950B HIS* 6.5 0.2 - - + -
954B LEU* 3.7 33.9 - - + -
1044B LEU* 4.0 18.8 - - + +
1048B PHE* 3.6 34.1 - - + -
1094B CYS* 3.8 10.1 - - - -
1095B PRO* 3.0 30.8 + - + +
1097B GLU* 1.3 76.8 - - + +
1099B TYR* 1.3 63.0 + - - +
1100B MET 3.2 0.2 - - - -
1101B ILE* 3.1 19.1 + - + +
1102B MET* 3.3 10.1 + - - +
1126B ILE* 3.9 26.0 - - + -
1130B MET* 5.6 1.3 - - - -
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Residues in contact with TYR1099 (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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1087B ARG* 4.9 4.7 + - - +
1088B LEU 2.8 22.5 + - - -
1089B PRO* 3.8 2.1 - - - +
1090B ARG* 3.4 59.5 + - + -
1091B PRO* 4.2 0.2 - - + -
1094B CYS* 3.9 3.5 - - - -
1095B PRO 3.0 10.0 + - - +
1096B ASP* 3.6 12.1 - - - +
1098B ILE* 1.3 76.7 - - - +
1100B MET* 1.3 59.6 + - + +
1102B MET* 3.2 39.0 + - + +
1103B THR* 3.0 51.1 + - + +
1106B TRP* 4.2 1.7 - + - -
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Residues in contact with MET1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096B ASP* 2.8 39.6 + - + +
1097B GLU* 3.7 23.3 - - + +
1098B ILE 3.2 0.2 - - - -
1099B TYR* 1.3 73.8 - - + +
1101B ILE* 1.3 61.6 + - - +
1103B THR* 3.0 20.5 + - - +
1104B GLU* 3.1 27.0 + - + +
1122B ARG* 4.3 4.7 - - - +
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Residues in contact with ILE1101 (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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954B LEU* 5.9 0.7 - - + -
1040B PHE* 4.7 2.2 - - + -
1044B LEU* 3.7 19.7 - - + -
1097B GLU* 3.4 12.1 - - + +
1098B ILE* 3.1 16.3 + - + +
1100B MET* 1.3 74.0 - - - +
1102B MET* 1.3 63.0 + - - +
1104B GLU* 3.5 2.8 + - - +
1105B CYS* 3.1 25.5 + - - -
1119B LEU* 3.5 28.6 - - + +
1122B ARG* 3.5 32.3 - - + +
1123B VAL* 4.2 21.3 - - + -
1126B ILE* 3.7 28.7 - - + -
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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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1041B GLY* 3.5 21.1 - - - +
1044B LEU* 3.9 21.3 - - + +
1045B TYR* 3.4 37.2 - - + -
1048B PHE* 5.5 0.2 - - - -
1091B PRO* 4.0 10.3 - - + -
1094B CYS* 4.9 4.3 - - - -
1098B ILE* 3.3 4.4 + - - +
1099B TYR* 3.2 42.3 + - + +
1101B ILE* 1.3 78.5 - - - +
1103B THR* 1.3 63.1 + - - +
1105B CYS* 3.2 8.9 + - - +
1106B TRP* 3.1 61.5 + - + -
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Residues in contact with THR1103 (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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1092A ASP* 5.7 0.8 - - - +
1087B ARG* 5.2 7.2 + - + +
1099B TYR* 3.0 51.0 + - + +
1100B MET* 3.0 24.1 + - - +
1102B MET* 1.3 76.2 - - - +
1104B GLU* 1.3 60.4 + - - +
1106B TRP* 3.1 33.5 + - + +
1107B ASN* 3.7 2.1 + - - +
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Residues in contact with GLU1104 (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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1090A ARG* 2.8 29.2 + - - -
1092A ASP* 4.0 31.5 - - + +
1093A GLY* 3.0 12.6 + - - +
1100B MET* 3.1 21.8 + - - +
1101B ILE 3.8 4.3 - - - +
1103B THR* 1.3 74.2 + - - +
1105B CYS* 1.3 64.7 + - - +
1106B TRP 3.4 0.3 + - - -
1107B ASN* 3.5 19.0 + - - +
1112B GLN 4.1 1.7 - - - +
1113B ARG* 3.9 1.9 - - - -
1114B PRO* 3.5 17.8 - - + +
1122B ARG* 2.8 45.0 + - - +
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Residues in contact with CYS1105 (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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1037B VAL* 3.4 35.9 - - - +
1038B TRP* 3.6 9.5 - - - -
1040B PHE* 3.9 21.1 - - - -
1041B GLY* 3.8 12.8 - - - -
1101B ILE* 3.1 23.7 + - - -
1102B MET 3.4 9.0 - - - +
1104B GLU* 1.3 76.3 - - - +
1106B TRP* 1.3 59.3 + - + +
1107B ASN 3.2 4.2 + - - -
1113B ARG* 3.4 21.5 + - - -
1114B PRO* 4.1 8.3 - - - -
1119B LEU* 3.9 15.7 - - - -
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Residues in contact with TRP1106 (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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1038B TRP* 3.3 45.5 + + + -
1041B GLY 3.3 22.2 - - - -
1042B VAL* 3.3 31.5 - - + +
1045B TYR* 4.0 2.0 - - + -
1087B ARG* 2.8 52.7 + - + +
1088B LEU* 3.7 43.1 - - + -
1099B TYR* 4.2 4.7 - + - -
1102B MET* 3.1 54.8 + - + -
1103B THR* 3.1 18.8 + - + +
1105B CYS* 1.3 77.2 - - + +
1107B ASN* 1.3 57.9 + - - +
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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