Contacts of the helix formed by residues 1115 - 1131 (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 SER1115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1033B VAL* 5.9 3.8 - - - -
1037B VAL* 4.9 1.6 - - - -
1113B ARG 3.8 0.6 + - - -
1114B PRO* 1.3 76.5 - - - +
1116B PHE* 1.3 58.7 + - - +
1117B ARG* 3.6 10.5 + - - +
1118B ASP* 2.7 38.3 + - - +
1119B LEU* 2.9 28.9 + - - +
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Residues in contact with PHE1116 (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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961B CYS* 3.9 25.4 - - - +
964B MET* 3.7 55.2 - - + -
965B GLU* 4.1 14.0 - - + +
1033B VAL* 4.1 17.1 - - + +
1036B ASP* 3.8 28.9 - - + -
1037B VAL* 3.8 20.9 - - + -
1040B PHE* 3.8 26.9 - + + -
1114B PRO 4.1 0.4 + - - -
1115B SER* 1.3 71.2 - - - +
1117B ARG* 1.3 59.5 + - - +
1119B LEU* 3.6 14.3 - - + +
1120B ALA* 2.9 31.7 + - - +
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Residues in contact with ARG1117 (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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1097A GLU* 4.4 21.1 + - - -
1129A GLN* 4.4 34.8 + - - +
1130A MET* 5.4 6.3 - - - +
965B GLU* 3.7 33.2 - - + +
1115B SER* 3.6 9.8 + - - +
1116B PHE* 1.3 78.2 - - - +
1118B ASP* 1.3 64.2 + - - +
1120B ALA* 3.5 2.6 + - - +
1121B LEU* 3.2 40.1 + - + +
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Residues in contact with ASP1118 (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* 5.9 0.7 - - - +
1093A GLY 5.3 1.3 - - - +
1094A CYS 5.6 1.3 - - - +
1095A PRO* 3.4 44.2 - - + +
1096A ASP* 3.5 9.5 + - + +
1097A GLU* 5.2 1.9 + - - +
1114B PRO* 4.7 7.9 - - + -
1115B SER* 2.7 34.7 + - - +
1117B ARG* 1.3 77.3 - - - +
1119B LEU* 1.3 60.9 + - - +
1121B LEU* 3.3 15.0 + - - +
1122B ARG* 2.9 40.4 + - - +
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Residues in contact with LEU1119 (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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961B CYS* 3.8 13.0 - - - -
1037B VAL* 4.2 13.0 - - + -
1040B PHE* 3.7 26.2 - - + -
1101B ILE* 3.5 32.5 - - + -
1105B CYS* 3.9 11.0 - - - -
1114B PRO* 3.8 21.8 - - + +
1115B SER 2.9 21.2 + - - +
1116B PHE* 3.6 21.3 - - + +
1118B ASP* 1.3 77.0 - - - +
1120B ALA* 1.3 56.9 + - - +
1122B ARG* 3.3 10.5 + - - +
1123B VAL* 2.9 35.6 + - + +
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Residues in contact with ALA1120 (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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958B SER* 5.0 2.7 - - - +
961B CYS* 4.0 19.7 - - + -
962B LYS* 4.5 18.8 - - + -
965B GLU* 4.3 13.2 - - - +
1116B PHE 2.9 17.2 + - - +
1117B ARG 3.7 4.5 - - - +
1118B ASP 3.3 0.2 - - - -
1119B LEU* 1.3 76.4 - - - +
1121B LEU* 1.3 59.9 + - + +
1123B VAL* 4.0 3.0 - - - +
1124B ASP* 3.0 37.9 + - - +
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Residues in contact with LEU1121 (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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1096A ASP* 5.7 12.1 - - + +
1117B ARG* 3.2 35.4 + - + +
1118B ASP* 3.7 17.0 - - - +
1119B LEU 3.3 0.2 - - - -
1120B ALA* 1.3 78.0 - - + +
1122B ARG* 1.3 63.4 + - + +
1124B ASP* 3.6 5.5 + - + +
1125B GLN* 3.1 26.2 + - - +
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Residues in contact with ARG1122 (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* 3.1 26.4 - - - +
1096A ASP* 4.4 18.2 - - + +
1097B GLU 4.9 1.0 + - - -
1100B MET* 4.3 3.8 - - - +
1101B ILE* 3.5 40.7 - - + +
1104B GLU* 2.8 49.7 + - - +
1114B PRO* 4.3 12.1 - - - +
1118B ASP* 2.9 27.6 + - + +
1119B LEU* 3.7 11.6 - - + +
1121B LEU* 1.3 75.8 - - + +
1123B VAL* 1.3 64.3 + - - +
1125B GLN* 3.4 10.1 + - - +
1126B ILE* 3.1 32.8 + - + +
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Residues in contact with VAL1123 (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* 3.3 44.1 - - + +
957B THR* 3.9 20.0 - - + -
958B SER* 4.0 15.7 - - - +
961B CYS* 4.9 3.8 - - - -
1040B PHE* 5.3 1.1 - - + -
1044B LEU* 5.8 0.9 - - + -
1101B ILE* 4.2 22.2 - - + -
1119B LEU* 2.9 23.4 + - - +
1120B ALA* 4.0 4.7 - - - +
1122B ARG* 1.3 76.3 - - - +
1124B ASP* 1.3 57.8 + - - +
1126B ILE* 3.3 9.5 + - - +
1127B ARG* 2.9 28.1 + - - +
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Residues in contact with ASP1124 (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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958B SER* 2.6 22.7 + - - -
962B LYS* 3.4 23.1 + - - -
1120B ALA 3.0 22.4 + - - +
1121B LEU* 4.1 6.5 - - + +
1123B VAL* 1.3 75.4 - - - +
1125B GLN* 1.3 56.8 + - - +
1127B ARG* 2.8 26.1 + - - +
1128B ASP* 2.9 40.1 + - - +
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Residues in contact with GLN1125 (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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1096A ASP* 4.3 18.6 + - - +
1097B GLU* 5.2 5.7 + - - -
1121B LEU 3.1 18.6 + - - +
1122B ARG* 3.6 9.3 + - - +
1123B VAL 3.2 0.2 - - - -
1124B ASP* 1.3 75.1 - - - +
1126B ILE* 1.3 61.6 + - - +
1128B ASP* 3.3 10.5 + - + +
1129B GLN* 3.0 55.9 + - + +
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Residues in contact with ILE1126 (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* 3.8 17.9 - - + -
1097B GLU* 3.8 43.7 - - + +
1098B ILE* 3.9 15.3 - - + -
1101B ILE* 3.7 27.6 - - + -
1122B ARG* 3.1 20.3 + - + +
1123B VAL* 3.7 7.2 - - - +
1125B GLN* 1.3 75.5 - - + +
1127B ARG* 1.3 59.7 + - - +
1129B GLN* 3.2 10.6 + - + +
1130B MET* 2.9 40.6 + - + +
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Residues in contact with ARG1127 (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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951B ILE* 3.5 22.6 + - + +
954B LEU* 3.6 38.6 - - + +
955B GLN* 3.7 41.2 - - - +
958B SER* 3.6 10.5 + - - -
962B LYS* 4.8 4.4 - - - +
1123B VAL* 2.9 15.4 + - - +
1124B ASP* 2.8 45.8 + - - +
1126B ILE* 1.3 76.9 - - - +
1128B ASP* 1.3 63.8 + - - +
1130B MET* 3.4 2.2 + - - -
1131B ALA* 3.1 24.8 + - - +
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Residues in contact with ASP1128 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124B ASP* 2.9 24.7 + - - +
1125B GLN* 3.3 12.2 + - + +
1127B ARG* 1.3 77.7 - - - +
1129B GLN* 1.3 62.4 + - + +
1131B ALA* 3.5 6.2 + - - +
1132B GLY* 3.3 18.4 + - - -
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Residues in contact with GLN1129 (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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1097B GLU* 4.1 19.7 + - - +
1125B GLN* 3.0 40.6 + - + +
1126B ILE* 3.2 17.4 + - + +
1128B ASP* 1.3 76.2 - - + +
1130B MET* 1.3 63.7 + - + +
1132B GLY* 3.4 12.9 + - - +
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Residues in contact with MET1130 (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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949B ASP* 6.3 0.2 - - - -
950B HIS* 3.8 30.5 - - + +
951B ILE* 3.8 27.4 - - + +
954B LEU* 3.7 28.5 - - - -
1098B ILE* 5.6 2.0 - - - -
1126B ILE* 2.9 26.2 + - + +
1127B ARG 3.8 4.3 - - - +
1129B GLN* 1.3 77.9 - - + +
1131B ALA* 1.3 58.1 + - - +
1132B GLY* 3.2 5.7 + - - +
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Residues in contact with ALA1131 (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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951B ILE* 3.9 13.7 - - + -
1127B ARG 3.1 16.1 + - - +
1128B ASP* 3.5 6.9 + - - +
1129B GLN 3.3 0.2 - - - -
1130B MET* 1.3 76.0 - - - +
1132B GLY* 1.3 64.9 + - - +
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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