Contacts of the helix formed by residues 1115 - 1132 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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965A GLU* 5.9 0.9 - - - -
1033A VAL* 6.1 2.0 - - - -
1037A VAL* 5.0 1.6 - - - -
1113A ARG 3.8 0.4 + - - -
1114A PRO* 1.3 77.0 - - - +
1116A PHE* 1.3 59.6 + - - +
1117A ARG* 3.8 8.5 + - - +
1118A ASP* 3.2 34.0 + - - +
1119A LEU* 3.0 28.5 + - - +
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Residues in contact with PHE1116 (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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961A CYS* 3.9 28.5 - - - +
964A MET* 3.7 47.3 - - + -
965A GLU* 4.0 16.9 + - + +
977A LEU* 4.3 0.2 - - + -
1033A VAL* 4.0 18.5 - - + +
1036A ASP* 3.8 23.1 - - + -
1037A VAL* 3.6 34.9 - - + +
1040A PHE* 3.8 26.9 - + + -
1115A SER* 1.3 72.6 - - - +
1117A ARG* 1.3 57.3 + - - +
1119A LEU* 3.4 13.2 + - + +
1120A ALA* 3.0 29.1 + - - +
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Residues in contact with ARG1117 (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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965A GLU* 3.9 42.2 + - - +
1115A SER* 3.2 9.5 + - - +
1116A PHE* 1.3 78.1 - - - +
1118A ASP* 1.3 61.0 + - - +
1120A ALA* 3.4 8.3 + - + +
1121A LEU* 3.1 36.8 + - + +
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Residues in contact with ASP1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114A PRO* 4.8 7.0 - - + +
1115A SER* 3.2 27.2 + - - +
1117A ARG* 1.3 76.9 - - - +
1119A LEU* 1.3 58.5 + - - +
1121A LEU* 3.3 20.8 + - - +
1122A ARG* 2.9 40.5 + - + +
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Residues in contact with LEU1119 (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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961A CYS* 3.9 11.0 - - - -
1037A VAL* 4.1 20.2 - - + -
1040A PHE* 3.8 25.4 - - + -
1101A ILE* 3.6 31.4 - - + -
1105A CYS* 3.8 4.9 - - - -
1114A PRO* 3.7 23.1 - - + +
1115A SER 3.0 21.5 + - - +
1116A PHE* 3.6 21.8 - - + +
1118A ASP* 1.3 76.2 - - - +
1120A ALA* 1.3 57.1 + - - +
1122A ARG* 3.3 10.4 + - - +
1123A VAL* 2.9 36.3 + - + +
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Residues in contact with ALA1120 (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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958A SER* 4.9 4.0 - - - +
961A CYS* 4.1 19.2 - - + -
962A LYS* 4.6 24.0 - - + +
1116A PHE 3.0 17.4 + - - +
1117A ARG* 3.6 7.4 - - - +
1119A LEU* 1.3 75.1 - - - +
1121A LEU* 1.3 58.0 + - + +
1123A VAL* 3.9 3.8 - - - +
1124A ASP* 2.9 38.9 + - - +
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Residues in contact with LEU1121 (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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1117A ARG* 3.1 22.4 + - + +
1118A ASP* 3.5 29.6 - - - +
1119A LEU 3.3 0.2 - - - -
1120A ALA* 1.3 76.9 - - + +
1122A ARG* 1.3 58.6 + - + +
1124A ASP* 3.9 4.6 - - + +
1125A GLN* 3.0 31.9 + - - +
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Residues in contact with ARG1122 (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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1097A GLU 5.0 0.4 + - - -
1100A MET* 4.4 7.5 - - - +
1101A ILE* 3.6 39.0 - - + +
1104A GLU* 2.6 48.8 + - - +
1114A PRO* 4.5 15.9 - - - +
1118A ASP* 2.9 27.3 + - + +
1119A LEU* 3.8 8.6 - - - +
1121A LEU* 1.3 76.7 - - + +
1123A VAL* 1.3 63.7 + - - +
1125A GLN* 3.4 11.7 + - - +
1126A ILE* 3.1 31.7 + - + +
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Residues in contact with VAL1123 (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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954A LEU* 3.4 41.7 - - + +
957A THR* 3.8 21.5 - - + -
958A SER* 4.1 13.0 - - - +
961A CYS* 5.3 0.7 - - - -
1040A PHE* 5.2 2.9 - - + -
1044A LEU* 5.7 0.9 - - + -
1101A ILE* 4.1 22.9 - - + -
1119A LEU 2.9 22.0 + - - +
1120A ALA* 3.9 4.9 - - - +
1122A ARG* 1.3 76.6 - - - +
1124A ASP* 1.3 57.6 + - - +
1126A ILE* 3.1 9.9 + - + +
1127A ARG* 2.8 32.3 + - - +
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Residues in contact with ASP1124 (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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958A SER* 2.6 31.2 + - - -
962A LYS* 3.7 18.7 + - - -
1120A ALA* 2.9 24.8 + - - +
1121A LEU* 4.0 5.1 - - + +
1123A VAL* 1.3 71.9 - - - +
1125A GLN* 1.3 56.9 + - - +
1127A ARG* 3.1 23.9 + - - +
1128A ASP* 3.1 38.2 + - - +
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Residues in contact with GLN1125 (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 LEU 3.0 19.2 + - - +
1122A ARG* 3.5 12.2 - - - +
1124A ASP* 1.3 76.1 - - - +
1126A ILE* 1.3 63.2 + - + +
1128A ASP* 3.4 8.4 + - + +
1129A GLN* 3.1 49.4 + - + +
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Residues in contact with ILE1126 (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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954A LEU* 3.8 19.1 - - + -
1097A GLU* 3.5 45.3 - - + +
1098A ILE* 3.8 24.2 - - + -
1101A ILE* 3.8 18.8 - - + -
1122A ARG* 3.1 19.4 + - + +
1123A VAL* 3.1 6.9 + - - +
1125A GLN* 1.3 73.3 - - + +
1127A ARG* 1.3 67.1 + - - +
1129A GLN* 3.3 11.3 + - + +
1130A MET* 3.0 30.4 + - + +
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Residues in contact with ARG1127 (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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951A ILE* 4.8 15.4 + - + +
954A LEU* 3.6 40.2 - - + -
955A GLN* 3.7 35.6 + - - +
958A SER* 3.6 12.3 + - - -
962A LYS* 5.1 3.4 - - - +
1123A VAL* 2.8 16.5 + - - +
1124A ASP* 3.1 40.9 + - - +
1125A GLN 3.3 0.2 - - - -
1126A ILE* 1.3 76.9 - - - +
1128A ASP* 1.3 60.9 + - - +
1130A MET* 3.3 6.6 + - - +
1131A ALA* 3.1 27.1 + - - +
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Residues in contact with ASP1128 (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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1124A ASP* 3.1 21.1 + - - +
1125A GLN* 3.7 7.5 - - - +
1126A ILE 3.3 0.4 - - - -
1127A ARG* 1.3 80.3 - - - +
1129A GLN* 1.3 61.8 + - + +
1131A ALA* 3.3 14.7 + - - +
1132A GLY* 3.3 13.7 + - - -
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Residues in contact with GLN1129 (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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1097A GLU* 4.4 12.5 - - - +
1125A GLN* 3.1 39.0 + - + +
1126A ILE* 3.3 14.8 + - + +
1128A ASP* 1.3 77.6 - - + +
1130A MET* 1.3 61.3 + - + +
1131A ALA 3.4 0.4 + - - -
1132A GLY* 4.6 9.4 + - - +
1117B ARG* 4.4 27.4 + - - +
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Residues in contact with MET1130 (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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950A HIS* 4.0 25.4 - - + +
951A ILE* 3.9 38.8 - - + +
954A LEU* 3.7 28.9 - - - -
1095A PRO* 5.5 10.3 - - + -
1097A GLU* 5.1 4.9 - - - +
1126A ILE* 3.0 24.8 + - + +
1127A ARG* 3.7 6.1 - - - +
1128A ASP 3.2 0.2 - - - -
1129A GLN* 1.3 77.3 - - - +
1131A ALA* 1.3 63.1 + - - +
1132A GLY* 4.5 2.7 - - - +
1117B ARG* 5.4 6.7 - - - +
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Residues in contact with ALA1131 (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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951A ILE* 5.5 7.0 - - + -
1127A ARG 3.1 15.1 + - - +
1128A ASP* 3.3 10.9 + - - +
1130A MET* 1.3 79.3 - - - +
1132A GLY* 1.3 67.2 + - - +
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Residues in contact with GLY1132 (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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1128A ASP 3.3 10.6 + - - -
1129A GLN 4.6 8.5 - - - +
1130A MET 4.5 3.3 - - - +
1131A ALA* 1.3 85.0 - - - +
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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