Contacts of the helix formed by residues 1083 - 1091 (chain A) in PDB entry 1I44
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 ASP1083 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A ACP 4.0 23.6 + - - +
1081A HIS 4.0 0.2 - - - +
1082A GLY* 1.3 76.1 - - - +
1084A LEU* 1.3 63.7 + - - +
1085A LYS* 3.1 14.4 + - - +
1086A SER* 2.6 48.4 + - - -
1087A TYR* 3.1 17.2 + - - +
1136A ARG* 3.4 27.3 - - - +
1138A CYS 3.1 7.2 - - - +
1139A MET* 3.4 9.1 - - + +
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Residues in contact with LEU1084 (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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1082A GLY 3.6 0.6 + - - -
1083A ASP* 1.3 69.7 - - - +
1085A LYS* 1.3 60.7 + - - +
1087A TYR* 3.1 8.0 + - + +
1088A LEU* 2.8 54.0 + - + +
1112A MET* 4.1 19.1 - - - -
1116A ILE* 4.0 22.0 - - + -
1135A ALA* 3.2 22.9 + - + +
1138A CYS* 2.6 34.0 + - + +
1140A VAL* 4.0 22.9 - - + -
1146A VAL* 4.2 6.1 - - + -
1198A VAL* 4.3 6.5 - - + -
1202A ILE* 4.3 9.6 - - + -
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Residues in contact with LYS1085 (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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1083A ASP* 3.1 8.8 + - - +
1084A LEU* 1.3 76.2 - - - +
1086A SER* 1.3 66.7 + - - +
1088A LEU* 3.0 5.4 + - - +
1089A ARG* 3.0 60.6 + - - +
1135A ALA* 3.4 15.0 + - + +
1136A ARG* 3.8 31.0 - - + +
1175A TRP* 6.4 1.3 - - + -
1201A GLU* 4.9 7.7 + - - +
1206A ALA* 3.6 19.4 + - + +
1207A GLU 5.5 1.8 + - - -
1208A GLN* 5.8 2.2 - - - +
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Residues in contact with SER1086 (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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1081A HIS 5.6 1.6 - - - -
1082A GLY* 6.0 0.4 - - - -
1083A ASP* 2.6 40.1 + - - -
1085A LYS* 1.3 75.8 - - - +
1087A TYR* 1.3 62.7 + - - +
1089A ARG* 3.3 8.8 + - - +
1090A SER* 3.2 21.7 + - - -
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Residues in contact with TYR1087 (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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1081A HIS* 4.0 32.7 + + + +
1083A ASP 3.1 13.0 + - - +
1084A LEU* 3.1 18.7 + - + +
1086A SER* 1.3 78.3 - - - +
1088A LEU* 1.3 66.5 + - + +
1090A SER* 2.7 28.4 + - - -
1091A LEU* 3.6 31.1 + - + +
1099A PRO* 5.6 1.6 - - + -
1101A ARG* 3.3 19.4 + - - -
1104A PRO* 6.3 1.3 - - + -
1112A MET* 5.7 7.2 - - + -
1140A VAL* 4.1 22.2 - - + -
1144A PHE* 3.3 38.6 - + + -
1146A VAL* 6.5 0.2 - - + -
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Residues in contact with LEU1088 (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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1084A LEU* 2.8 48.2 + - + +
1085A LYS 3.4 4.9 - - - +
1087A TYR* 1.3 80.1 - - + +
1089A ARG* 1.3 61.9 + - - +
1091A LEU* 3.1 21.6 + - + +
1092A ARG* 3.8 6.1 - - - +
1104A PRO* 4.6 10.1 - - + -
1112A MET* 4.9 3.6 - - + -
1135A ALA* 4.4 7.0 - - + -
1201A GLU 3.9 8.1 - - - +
1202A ILE* 3.7 50.7 - - + +
1205A LEU* 4.0 22.2 - - + +
1206A ALA* 3.8 14.6 - - + +
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Residues in contact with ARG1089 (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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1085A LYS* 3.0 45.7 + - - +
1086A SER* 3.3 7.5 + - - +
1088A LEU* 1.3 75.9 - - - +
1090A SER* 1.3 58.7 + - - +
1091A LEU 3.1 0.2 - - - -
1092A ARG* 2.9 47.6 + - - +
1095A ALA* 3.5 9.0 - - - +
1097A ASN* 4.6 0.9 + - - -
1205A LEU 3.6 10.1 - - - +
1206A ALA* 3.0 37.3 + - - -
1207A GLU* 4.5 3.4 - - - +
1208A GLN 5.2 0.8 - - - +
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Residues in contact with SER1090 (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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1086A SER 3.2 12.0 + - - -
1087A TYR* 2.7 29.1 + - - -
1089A ARG* 1.3 76.4 - - - +
1091A LEU* 1.3 58.7 + - - +
1092A ARG 3.2 1.8 - - - -
1095A ALA* 3.4 4.7 - - - +
1097A ASN* 3.6 35.9 - - - +
1098A ASN* 3.2 13.5 - - - +
1099A PRO* 3.1 25.5 - - - +
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Residues in contact with LEU1091 (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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1087A TYR* 3.8 41.1 - - + +
1088A LEU* 3.1 13.2 + - + +
1090A SER* 1.3 80.4 - - - +
1092A ARG* 1.3 61.6 + - - +
1093A PRO* 3.7 5.2 - - - +
1098A ASN* 3.7 7.7 - - - +
1099A PRO* 3.4 28.3 - - + -
1101A ARG* 3.9 27.2 - - + +
1102A PRO 4.0 8.3 - - - +
1103A PRO* 4.3 19.2 - - + +
1104A PRO* 3.8 28.3 - - + -
1205A LEU* 3.9 9.0 - - + +
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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