Contacts of the helix formed by residues 112 - 121 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLU* 3.3 28.9 + - - -
110A GLU 3.2 1.9 + - - -
111A GLY* 1.3 79.1 - - - +
113A VAL* 1.3 61.5 + - - +
114A THR* 3.6 10.4 + - - +
115A ASN* 3.1 26.5 + - - +
116A MET* 3.2 15.4 + - - +
144A TYR* 3.4 9.7 + - - -
148A PHE* 3.5 4.4 - - - -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY 4.1 0.6 + - - -
112A SER* 1.3 69.6 - - - +
114A THR* 1.3 66.0 + - - +
116A MET* 3.2 13.2 + - + +
117A PHE* 3.0 49.9 + - + +
148A PHE* 3.7 22.7 - - + -
274A PHE* 3.8 25.6 - - + -
278A THR* 5.6 3.7 + - - +
317A ALA* 3.5 29.8 - - + +
320A LEU* 4.1 7.4 - - + -
321A SER* 4.1 12.6 - - - +
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.7 8.3 - - - +
113A VAL* 1.3 80.0 - - - +
115A ASN* 1.3 61.7 + - - +
117A PHE* 3.6 3.7 + - - +
118A THR* 2.7 34.5 + - - +
274A PHE* 3.5 23.1 - - - +
275A THR* 3.2 26.5 + - - +
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Residues in contact with ASN 115 (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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107A LEU 3.8 6.8 + - - +
108A PHE* 3.3 13.0 - - - +
109A GLU* 2.9 39.8 + - + +
112A SER* 3.1 26.4 + - - +
114A THR* 1.3 75.9 - - - +
116A MET* 1.3 67.8 + - - +
118A THR* 3.2 19.7 + - - +
119A SER* 3.3 16.9 + - - -
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Residues in contact with MET 116 (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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36A ILE* 5.4 3.4 - - + -
108A PHE* 3.8 20.4 - - + -
112A SER 3.2 9.6 + - - +
113A VAL* 3.2 20.9 + - + +
115A ASN* 1.3 80.4 + - - +
117A PHE* 1.3 90.7 + - + +
119A SER* 3.6 1.7 + - - -
120A ILE* 3.3 38.1 + - + +
138A LEU* 4.1 12.3 - - + -
140A ILE* 3.8 26.0 - - + -
144A TYR* 4.0 24.9 + - + +
313A VAL 6.0 0.2 - - - +
317A ALA* 4.8 7.0 - - + +
320A LEU* 4.9 11.0 - - + -
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Residues in contact with PHE 117 (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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113A VAL* 3.0 19.7 + - + +
114A THR* 4.1 3.1 - - - +
116A MET* 1.3 92.4 - - + +
118A THR* 1.3 66.2 + - - +
119A SER 3.1 0.4 - - - -
120A ILE* 4.6 1.8 - - + +
121A VAL* 2.9 46.9 + - + +
122A GLY* 3.4 1.2 + - - -
135A LEU* 5.0 0.9 - - + -
138A LEU* 4.4 5.6 - - + -
274A PHE* 3.4 42.6 - + - -
309A MET* 3.7 32.3 - - + -
313A VAL* 3.7 19.5 - - + -
314A LEU* 4.6 5.2 - - + -
317A ALA* 3.5 22.9 - - + -
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Residues in contact with THR 118 (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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114A THR* 2.7 30.2 + - - +
115A ASN* 3.2 13.7 + - - +
117A PHE* 1.3 76.7 - - - +
119A SER* 1.3 59.1 + - - +
122A GLY* 3.1 27.9 - - - -
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Residues in contact with SER 119 (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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60A GLU 4.9 0.3 - - - +
61A SER* 3.3 39.1 + - - +
62A SER* 5.5 1.7 + - - -
103A TYR* 5.7 0.2 - - - -
107A LEU* 4.8 12.5 + - - +
108A PHE* 4.4 16.5 - - - -
115A ASN* 3.3 12.1 + - - -
116A MET 4.0 6.1 - - - -
117A PHE 3.1 0.4 - - - -
118A THR* 1.3 81.6 - - - +
120A ILE* 1.3 66.8 + - - +
121A VAL 3.3 0.7 + - - -
122A GLY* 3.7 3.6 + - - -
123A ASN 5.1 1.6 + - - -
124A VAL* 5.5 0.3 - - - +
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Residues in contact with ILE 120 (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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36A ILE* 3.9 20.6 - - + -
40A PHE* 3.7 33.4 - - + -
61A SER* 4.2 7.6 - - - -
103A TYR* 4.1 19.7 - - + +
108A PHE* 4.3 12.1 - - + -
116A MET* 3.3 31.4 + - + +
117A PHE* 4.5 3.6 - - + +
119A SER* 1.3 76.2 - - - +
121A VAL* 1.3 68.6 + - + +
124A VAL* 3.8 11.3 - - - +
135A LEU* 4.2 12.8 - - + -
138A LEU* 3.9 27.1 - - + -
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Residues in contact with VAL 121 (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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40A PHE* 5.0 0.2 - - + -
117A PHE* 2.9 36.1 + - + +
120A ILE* 1.3 80.2 - - + +
122A GLY* 1.3 66.0 + - - +
123A ASN 3.7 1.3 - - - -
124A VAL* 4.6 1.1 - - - -
125A PHE* 3.6 39.9 - - + +
135A LEU* 3.8 28.9 - - + -
309A MET* 4.1 21.3 - - + -
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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