Contacts of the helix formed by residues 1079 - 1089 (chain B) in PDB entry 2IUI
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 SER1079 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002B ASN* 6.3 0.9 - - - -
1003B ASN 5.7 4.7 - - - -
1006B SER* 4.9 5.4 - - - -
1069B TYR* 3.8 13.2 - - - -
1077B PHE* 3.4 3.3 - - - +
1078B SER* 1.3 80.5 - - - +
1080B VAL* 1.3 63.3 + - - +
1081B VAL* 3.2 15.9 - - - +
1082B GLU* 3.0 29.3 + - - +
1083B LEU* 3.1 22.0 + - - +
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Residues in contact with VAL1080 (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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1007B LEU* 4.1 28.0 - - + +
1012B TRP* 4.2 4.9 - - + -
1036B VAL* 4.4 7.0 - - + -
1047B TYR* 3.8 20.9 - - + -
1062B ILE* 4.2 23.1 - - + -
1069B TYR* 3.7 33.8 - - + -
1079B SER* 1.3 73.1 - - - +
1081B VAL* 1.3 57.9 + - - +
1083B LEU* 3.5 6.1 - - + +
1084B ILE* 2.9 41.2 + - + +
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Residues in contact with VAL1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006B SER* 3.5 37.7 - - - +
1007B LEU* 3.7 25.1 - - + +
1010B ALA* 4.5 2.2 - - + -
1012B TRP* 3.8 25.1 - - + -
1079B SER* 3.2 13.0 - - - +
1080B VAL* 1.3 72.6 - - - +
1082B GLU* 1.3 65.3 + - - +
1085B ASN* 2.9 45.5 + - - +
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Residues in contact with GLU1082 (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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1076B THR 4.4 2.4 - - - +
1077B PHE* 3.6 18.0 - - + -
1078B SER* 3.2 41.2 + - - -
1079B SER* 3.0 19.6 + - - +
1081B VAL* 1.3 85.1 - - + +
1083B LEU* 1.3 60.4 + - - +
1085B ASN* 3.9 4.9 - - - +
1086B HIS* 3.2 22.5 + - - +
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Residues in contact with LEU1083 (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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1062B ILE* 3.7 37.0 - - + -
1069B TYR* 4.1 7.0 - - + -
1070B GLY* 3.8 22.9 - - - +
1071B PHE* 4.0 20.6 - - + -
1077B PHE* 3.4 38.3 - - + -
1079B SER 3.1 11.5 + - - +
1080B VAL* 3.5 9.0 - - - +
1082B GLU* 1.3 72.8 - - - +
1084B ILE* 1.3 68.4 + - + +
1086B HIS* 3.1 14.7 + - - +
1087B TYR* 3.2 33.6 + - + -
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Residues in contact with ILE1084 (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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1012B TRP* 3.7 38.1 - - + +
1034B PHE* 3.6 29.6 - - + -
1036B VAL* 4.0 16.4 - - + -
1049B LEU* 4.1 13.9 - - + -
1062B ILE* 4.6 9.6 - - + -
1071B PHE* 5.1 2.5 - - + -
1080B VAL* 2.9 29.3 + - + +
1083B LEU* 1.3 76.7 - - + +
1085B ASN* 1.3 65.1 + - - +
1087B TYR* 3.2 4.0 + - - -
1088B ARG* 3.0 27.9 + - - +
1103B LEU* 3.6 22.0 - - + +
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Residues in contact with ASN1085 (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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1012B TRP* 4.8 12.8 + - - -
1081B VAL* 2.9 36.0 + - - +
1082B GLU* 3.9 6.3 - - - +
1084B ILE* 1.3 73.3 - - - +
1086B HIS* 1.3 70.4 + - - +
1088B ARG* 3.2 28.0 + - - +
1089B ASN* 3.9 8.5 + - - -
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Residues in contact with HIS1086 (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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1077B PHE* 3.7 20.5 - + + -
1082B GLU 3.2 11.9 + - - +
1083B LEU 3.1 11.3 + - - +
1085B ASN* 1.3 79.1 - - - +
1087B TYR* 1.3 84.7 + + - +
1089B ASN* 2.8 28.5 + - - +
1090B GLU* 2.7 34.3 + - + +
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Residues in contact with TYR1087 (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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1071B PHE* 3.8 17.9 - + + -
1077B PHE* 3.8 10.7 - + - -
1083B LEU* 3.2 32.4 + - + -
1084B ILE 3.2 5.0 + - - +
1086B HIS* 1.3 98.3 + + - +
1088B ARG* 1.3 61.0 + - - +
1089B ASN 3.2 0.7 - - - -
1090B GLU* 3.0 37.1 + - - +
1091B SER 4.0 11.4 - - - -
1092B LEU* 3.8 19.3 - - + -
1095B TYR* 2.6 39.3 + + - -
1102B LYS* 3.5 1.2 - - - +
1103B LEU* 3.0 40.3 + - + -
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Residues in contact with ARG1088 (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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1011B GLU* 4.7 3.8 + - - -
1012B TRP* 4.6 8.5 - - - +
1034B PHE* 3.7 19.7 - - - -
1084B ILE* 3.0 18.8 + - + +
1085B ASN* 3.3 23.8 + - - +
1086B HIS 3.0 0.6 + - - -
1087B TYR* 1.3 77.9 - - - +
1089B ASN* 1.3 65.8 + - - +
1090B GLU 3.6 0.2 - - - -
1102B LYS* 3.5 18.2 - - - +
1103B LEU* 3.0 30.4 + - - +
1104B LEU* 3.4 21.0 + - - +
1106B PRO* 3.1 31.8 - - - +
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Residues in contact with ASN1089 (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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1085B ASN 4.2 9.1 + - - -
1086B HIS 2.8 9.0 + - - +
1088B ARG* 1.3 86.9 - - - +
1090B GLU* 1.3 60.8 + - - +
1102B LYS* 3.8 17.4 + - - +
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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