Contacts of the helix formed by residues 1113 - 1123 (chain A) in PDB entry 5JQE
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 SER1113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1112A VAL* 1.3 74.9 - - - +
1114A ARG* 1.3 58.1 + - - +
1115A SER* 3.1 8.3 + - - -
1116A GLU* 3.2 32.3 + - - +
1117A LEU* 2.6 38.3 + - - +
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Residues in contact with ARG1114 (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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1113A SER* 1.3 75.2 - - - +
1115A SER* 1.3 57.8 + - - +
1117A LEU* 3.3 10.9 + - + +
1118A ARG* 3.1 55.5 + - + +
1121A LYS* 5.7 0.2 - - - -
1135A ASP* 5.5 7.3 + - - +
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Residues in contact with SER1115 (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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1113A SER* 3.1 7.9 + - - -
1114A ARG* 1.3 76.3 - - - +
1116A GLU* 1.3 68.5 + - - +
1117A LEU 3.0 2.3 + - - -
1118A ARG* 3.3 42.0 + - - +
1119A SER* 3.3 13.7 + - - -
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Residues in contact with GLU1116 (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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1111A GLU 2.8 24.1 - - - +
1112A VAL* 4.0 9.0 - - + +
1113A SER* 3.2 31.8 + - - +
1115A SER* 1.3 84.3 + - - +
1117A LEU* 1.3 58.2 + - - +
1119A SER* 3.4 10.9 - - - -
1120A PHE* 3.3 14.4 + - - +
1167A ILE* 3.5 26.9 - - + +
1168A ASN* 3.4 31.4 + - - +
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Residues in contact with LEU1117 (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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1112A VAL* 4.0 8.1 - - + -
1113A SER 2.6 20.9 + - - +
1114A ARG* 3.5 11.7 - - + +
1115A SER 3.0 0.2 - - - -
1116A GLU* 1.3 72.0 - - - +
1118A ARG* 1.3 52.1 + - - +
1119A SER 3.0 4.9 - - - -
1120A PHE* 2.8 14.4 + - + +
1121A LYS* 2.7 51.8 + - + +
1137A MET 3.7 16.8 - - - +
1138A ASN* 3.9 4.9 - - + -
1139A LEU* 3.6 37.5 - - + +
1142A ILE* 3.8 24.9 - - + -
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Residues in contact with ARG1118 (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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1114A ARG* 3.1 49.1 + - + +
1115A SER* 3.3 34.3 + - - +
1117A LEU* 1.3 74.1 - - - +
1119A SER* 1.3 61.6 + - - +
1121A LYS* 4.0 21.6 - - + +
1122A GLY* 3.7 13.5 + - - -
1135A ASP* 5.5 7.6 - - - +
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Residues in contact with SER1119 (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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1115A SER 3.3 11.7 + - - -
1116A GLU* 3.4 13.3 - - - -
1117A LEU 3.0 0.6 - - - -
1118A ARG* 1.3 75.2 - - - +
1120A PHE* 1.3 60.8 + - - +
1121A LYS 3.3 0.2 + - - -
1122A GLY 3.3 1.6 + - - -
1123A GLY* 2.8 29.6 + - - -
1163A VAL* 5.4 0.2 - - - +
1166A GLN 6.0 0.2 - - - -
1167A ILE* 3.6 22.6 - - - +
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Residues in contact with PHE1120 (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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1108A ILE* 6.0 0.4 - - + -
1112A VAL* 5.5 4.5 - - + -
1116A GLU 3.3 3.9 + - - +
1117A LEU* 2.8 20.0 + - + +
1119A SER* 1.3 75.1 - - - +
1121A LYS* 1.3 66.2 + - - +
1123A GLY 3.8 0.5 - - - -
1124A LEU* 3.3 35.1 + - + +
1139A LEU* 3.9 30.3 - - + -
1142A ILE* 3.6 32.1 - - + -
1143A PHE* 4.1 12.6 - + - -
1146A MET* 4.4 9.0 - - + -
1160A LEU* 4.5 9.6 - - + -
1163A VAL* 3.4 31.6 - - + +
1164A CYS* 4.5 18.8 - - - -
1167A ILE* 3.2 19.9 - - + +
1171A LEU* 6.4 1.3 - - + -
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Residues in contact with LYS1121 (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 LEU* 2.7 55.8 + - + +
1118A ARG* 4.1 19.3 - - + +
1120A PHE* 1.3 77.8 - - - +
1122A GLY* 1.3 57.4 + - - +
1124A LEU* 4.2 0.7 - - - +
1125A GLN* 3.3 30.2 + - - +
1133A LEU* 3.9 19.4 - - + +
1134A ASP 3.4 10.6 + - - +
1135A ASP* 3.4 44.3 + - - +
1137A MET 3.9 12.4 + - - -
1142A ILE* 4.3 9.6 - - + -
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Residues in contact with GLY1122 (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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1118A ARG 3.7 7.8 + - - -
1119A SER 3.3 3.9 + - - -
1121A LYS* 1.3 78.3 - - - +
1123A GLY* 1.3 56.4 + - - +
1124A LEU 3.3 4.9 - - - -
1125A GLN* 4.0 16.7 - - - +
1126A GLU* 2.9 29.3 + - - +
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Residues in contact with GLY1123 (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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1119A SER 2.8 18.5 + - - -
1120A PHE 3.8 2.5 - - - -
1122A GLY* 1.3 75.6 - - - +
1124A LEU* 1.3 57.7 + - - +
1126A GLU* 3.9 22.6 - - - +
1127A GLU* 4.7 4.2 + - - +
1163A VAL* 3.4 21.7 - - - +
1166A GLN* 4.0 15.6 + - - -
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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