Contacts of the helix formed by residues 112 - 121 (chain B) in PDB entry 1IR1
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 SER 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B GLU* 3.3 26.8 + - - -
110B GLU 3.3 1.2 - - - -
111B GLY* 1.3 79.5 - - - +
113B VAL* 1.3 61.4 + - - +
114B THR* 3.5 11.0 + - - +
115B ASN* 3.0 27.3 + - - +
116B MET 3.2 14.6 + - - -
144B TYR* 3.4 10.6 + - - -
148B PHE* 3.5 5.8 - - - -
278B THR* 6.2 0.2 - - - -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B GLY 4.1 0.4 + - - -
112B SER* 1.3 69.8 - - - +
114B THR* 1.3 66.3 + - - +
116B MET* 3.1 15.1 + - + +
117B PHE* 3.0 50.4 + - + +
148B PHE* 3.7 22.7 - - + -
274B PHE* 3.8 24.0 - - + -
278B THR* 5.6 5.0 + - - +
317B ALA* 3.6 29.4 - - + +
320B LEU* 4.2 4.0 - - + -
321B SER* 4.0 14.6 - - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER* 3.6 8.1 - - - +
113B VAL* 1.3 81.8 - - - +
115B ASN* 1.3 56.8 + - - +
117B PHE* 3.6 3.3 + - - +
118B THR* 2.7 39.5 + - - +
274B PHE* 3.5 22.9 - - - +
275B THR* 3.2 27.3 + - - +
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Residues in contact with ASN 115 (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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107B LEU 3.8 6.5 + - - +
108B PHE* 3.4 12.0 - - - +
109B GLU* 2.9 40.5 + - + +
112B SER* 3.0 26.5 + - - +
114B THR* 1.3 75.3 - - - +
116B MET* 1.3 67.6 + - - +
118B THR* 3.3 18.4 + - - +
119B SER* 3.3 16.8 + - - -
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Residues in contact with MET 116 (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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36B ILE* 5.4 6.5 - - + -
108B PHE* 3.8 19.4 - - + -
112B SER 3.2 10.6 + - - +
113B VAL* 3.1 25.0 + - + +
115B ASN* 1.3 79.8 + - - +
117B PHE* 1.3 83.8 + - + +
119B SER 3.6 0.2 + - - -
120B ILE* 3.3 39.2 + - + +
138B LEU* 4.3 16.8 - - + -
140B ILE* 4.7 13.9 - - + -
144B TYR* 4.1 27.8 + - + +
148B PHE* 5.7 0.2 - - + -
317B ALA* 4.8 4.7 - - + -
320B LEU* 4.5 17.5 - - + -
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Residues in contact with PHE 117 (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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113B VAL* 3.0 20.8 + - + +
114B THR* 4.2 3.8 - - - +
116B MET* 1.3 83.0 - - + +
118B THR* 1.3 61.1 + - - +
119B SER 3.1 2.2 - - - -
120B ILE* 4.5 2.9 - - + +
121B VAL* 2.8 51.3 + - + +
122B GLY 3.4 0.9 + - - -
135B LEU* 4.9 1.6 - - + -
138B LEU* 4.2 14.6 - - + -
274B PHE* 3.6 34.8 - + - -
309B MET* 3.5 33.0 - - + -
313B VAL* 3.7 19.1 - - + -
314B LEU* 4.6 6.1 - - + -
317B ALA* 3.6 28.3 - - + -
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Residues in contact with THR 118 (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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114B THR* 2.7 31.2 + - - +
115B ASN* 3.3 12.7 + - - +
117B PHE* 1.3 77.2 - - - +
119B SER* 1.3 58.3 + - - +
122B GLY* 3.0 28.2 - - - -
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Residues in contact with SER 119 (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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60B GLU 4.9 0.3 - - - +
61B SER* 3.2 37.8 + - - -
62B SER* 5.6 1.2 + - - -
103B TYR* 5.8 0.4 - - - -
107B LEU* 4.6 14.2 + - - +
108B PHE* 4.3 14.5 - - - -
115B ASN* 3.3 12.4 + - - -
116B MET 4.0 6.5 - - - -
117B PHE 3.1 0.6 - - - -
118B THR* 1.3 82.2 - - - +
120B ILE* 1.3 65.1 + - - +
121B VAL 3.5 0.2 + - - -
122B GLY* 3.7 3.8 + - - -
123B ASN 5.2 1.2 + - - -
124B VAL* 5.5 0.3 - - - +
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Residues in contact with ILE 120 (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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36B ILE* 4.0 18.2 - - + -
40B PHE* 3.6 33.3 - - + -
61B SER* 4.3 1.6 - - - -
103B TYR* 4.0 25.4 - - + +
108B PHE* 4.1 13.2 - - + -
116B MET* 3.3 31.4 + - + +
117B PHE* 4.5 3.6 - - + +
119B SER* 1.3 77.2 - - - +
121B VAL* 1.3 59.8 + - + +
124B VAL* 3.8 11.8 - - - +
135B LEU* 4.1 21.3 - - + -
138B LEU* 3.7 27.6 - - + -
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Residues in contact with VAL 121 (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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117B PHE* 2.8 37.2 + - + +
120B ILE* 1.3 79.2 - - + +
122B GLY* 1.3 65.4 + - - +
123B ASN 3.7 1.8 - - - -
124B VAL* 4.8 0.7 - - - -
125B PHE* 3.6 41.4 - - + +
135B LEU* 3.8 27.4 - - + -
309B MET* 4.0 24.5 - - + -
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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