Contacts of the helix formed by residues 112 - 121 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C GLU* 3.4 29.6 + - - -
110C GLU 3.2 1.4 + - - -
111C GLY* 1.3 78.8 - - - +
113C VAL* 1.3 62.6 + - - +
114C THR* 3.6 9.9 + - - +
115C ASN* 3.0 30.4 + - - +
116C MET* 3.2 9.7 + - - +
144C TYR* 3.4 9.2 + - - -
148C PHE* 3.5 5.5 - - - -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLY 4.0 0.8 + - - -
112C SER* 1.3 72.3 - - - +
114C THR* 1.3 63.8 + - - +
116C MET* 3.2 13.2 + - + +
117C PHE* 3.1 33.3 + - + +
148C PHE* 3.7 22.8 - - + -
274C PHE* 3.6 36.3 - - + -
278C THR* 5.6 4.0 + - - +
317C ALA* 3.6 35.0 - - + +
320C LEU* 4.0 7.4 - - + -
321C SER* 4.0 14.1 - - - +
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Residues in contact with THR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C SER* 3.1 8.3 - - - +
113C VAL* 1.3 80.6 - - - +
115C ASN* 1.3 56.1 + - + +
117C PHE* 3.6 4.2 + - - +
118C THR* 2.6 39.0 + - - +
274C PHE* 3.5 23.0 - - - +
275C THR* 3.2 26.5 + - - +
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Residues in contact with ASN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU 3.8 6.2 + - - +
108C PHE* 3.4 12.3 - - - +
109C GLU* 2.9 39.3 + - + +
112C SER* 3.0 26.0 + - - +
114C THR* 1.3 75.5 - - - +
116C MET* 1.3 67.8 + - - +
118C THR* 3.2 19.2 + - - +
119C SER* 3.3 16.9 + - - -
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Residues in contact with MET 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.4 8.3 - - + -
108C PHE* 3.8 20.1 - - + -
112C SER 3.2 9.7 + - - +
113C VAL* 3.2 19.4 + - + +
115C ASN* 1.3 80.0 + - - +
117C PHE* 1.3 91.4 + - + +
119C SER* 3.5 2.1 + - - -
120C ILE* 3.3 38.9 + - + +
138C LEU* 4.1 17.0 - - + -
140C ILE* 4.4 20.4 - - + -
144C TYR* 4.1 26.4 + - - +
148C PHE* 5.7 0.2 - - - -
313C VAL 6.0 0.2 - - - +
317C ALA* 4.9 4.9 - - + -
320C LEU* 4.7 8.1 - - + -
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 3.1 19.4 + - + +
114C THR* 4.2 3.1 - - - +
116C MET* 1.3 92.5 - - + +
118C THR* 1.3 66.5 + - - +
120C ILE* 5.5 2.0 - - + -
121C VAL* 2.9 45.2 + - + +
122C GLY* 3.4 1.4 + - - -
135C LEU* 5.1 1.3 - - + -
138C LEU* 4.5 4.9 - - + -
274C PHE* 3.5 41.1 - + - -
309C MET* 3.6 32.5 - - + -
313C VAL* 3.8 17.7 - - + -
314C LEU* 4.5 6.1 - - + -
317C ALA* 3.6 23.1 - - + -
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C THR* 2.6 30.7 + - - +
115C ASN* 3.2 14.8 + - - +
117C PHE* 1.3 76.5 - - - +
119C SER* 1.3 59.1 + - - +
122C GLY* 3.1 27.5 - - - -
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C GLU 4.9 0.5 - - - +
61C SER* 3.3 37.7 + - - +
62C SER* 5.6 1.4 + - - -
103C TYR* 5.7 0.9 - - - -
107C LEU* 4.7 13.1 + - - +
108C PHE* 4.3 16.5 - - - -
115C ASN* 3.3 12.7 + - - -
116C MET 3.9 6.3 - - - -
117C PHE 3.1 0.6 - - - -
118C THR* 1.3 82.4 - - - +
120C ILE* 1.3 67.7 + - - +
121C VAL 3.4 0.3 + - - -
122C GLY* 3.6 4.0 + - - -
123C ASN 5.1 1.4 + - - -
124C VAL* 5.6 0.2 - - - +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.1 16.4 - - + -
40C PHE* 3.6 36.3 - - + -
61C SER* 4.2 2.3 - - - -
103C TYR* 4.1 26.5 - - + +
108C PHE* 4.3 11.0 - - + -
116C MET* 3.3 35.7 + - + +
117C PHE* 4.6 3.4 - - + +
119C SER* 1.3 76.5 - - - +
121C VAL* 1.3 58.7 + - + +
124C VAL* 3.7 10.9 - - - +
135C LEU* 3.9 20.6 - - + -
138C LEU* 3.9 26.2 - - + -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C PHE* 5.0 0.2 - - + -
117C PHE* 2.9 37.5 + - + +
120C ILE* 1.3 79.1 - - + +
122C GLY* 1.3 64.0 + - - +
123C ASN 3.8 1.1 - - - -
124C VAL* 4.6 0.9 - - - -
125C PHE* 3.6 40.5 - - + +
135C LEU* 3.7 28.3 - - + -
309C MET* 4.1 23.6 - - + -
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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