Contacts of the helix formed by residues 112 - 121 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D GLU* 3.3 26.3 + - - -
110D GLU 3.2 3.6 - - - -
111D GLY* 1.3 79.1 - - - +
113D VAL* 1.3 62.0 + - - +
114D THR* 3.7 10.4 + - - +
115D ASN* 3.1 30.1 + - - +
116D MET 3.1 10.4 + - - -
144D TYR* 3.4 8.7 + - - -
148D PHE* 3.5 4.2 - - - -
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLY 4.0 0.4 + - - -
112D SER* 1.3 71.6 - - - +
114D THR* 1.3 63.5 + - - +
116D MET* 3.1 12.6 + - + +
117D PHE* 3.0 47.3 + - + +
148D PHE* 3.7 22.5 - - + -
274D PHE* 3.6 31.6 - - + -
278D THR* 5.5 5.0 + - - +
317D ALA* 3.6 27.4 - - + +
320D LEU* 4.1 6.7 - - + -
321D SER* 4.0 13.9 - - - +
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Residues in contact with THR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D SER* 3.7 8.3 - - - +
113D VAL* 1.3 81.0 - - - +
115D ASN* 1.3 60.8 + - - +
117D PHE* 3.6 3.9 + - - +
118D THR* 2.8 34.6 + - - +
274D PHE* 3.6 22.9 - - - +
275D THR* 3.2 27.0 + - - +
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Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU 3.8 7.1 + - - +
108D PHE* 3.4 12.5 - - - +
109D GLU* 2.9 39.2 + - + +
112D SER* 3.1 27.2 + - - +
114D THR* 1.3 75.4 - - - +
116D MET* 1.3 68.0 + - - +
118D THR* 3.3 19.4 + - - +
119D SER* 3.3 16.1 + - - -
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Residues in contact with MET 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ILE* 4.4 9.2 - - + -
108D PHE* 3.9 18.2 - - + -
112D SER 3.1 11.5 + - - +
113D VAL* 3.1 19.8 + - + +
115D ASN* 1.3 79.6 + - - +
117D PHE* 1.3 89.3 + - + +
119D SER* 3.6 1.7 + - - -
120D ILE* 3.3 39.3 + - + +
138D LEU* 4.1 16.8 - - + -
140D ILE* 4.7 15.3 - - + -
144D TYR* 4.0 27.5 + - - +
148D PHE* 5.7 0.2 - - - -
313D VAL 5.9 0.2 - - - +
317D ALA* 4.8 4.7 - - + +
320D LEU* 4.7 14.8 - - + -
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Residues in contact with PHE 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D VAL* 3.0 25.5 + - + +
114D THR* 4.2 3.1 - - - +
116D MET* 1.3 90.0 - - + +
118D THR* 1.3 61.9 + - - +
119D SER 3.1 2.2 - - - -
120D ILE* 4.9 2.2 - - + -
121D VAL* 2.8 52.3 + - + +
122D GLY 3.4 0.9 + - - -
135D LEU* 5.0 1.3 - - + -
138D LEU* 4.4 5.2 - - + -
274D PHE* 3.6 27.1 - + - -
309D MET* 3.6 32.5 - - + -
313D VAL* 3.7 19.3 - - + -
314D LEU* 4.7 4.7 - - + -
317D ALA* 3.5 34.1 - - + -
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Residues in contact with THR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D THR* 2.8 31.1 + - - +
115D ASN* 3.3 13.3 + - - +
117D PHE* 1.3 76.4 - - - +
119D SER* 1.3 58.6 + - - +
122D GLY* 3.1 27.6 - - - -
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Residues in contact with SER 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D GLU 4.9 0.2 - - - +
61D SER* 3.2 38.1 + - - -
62D SER* 5.6 1.2 - - - -
103D TYR* 5.9 0.2 - - - -
107D LEU* 4.7 14.0 + - - +
108D PHE* 4.3 15.0 - - - -
115D ASN* 3.3 12.4 + - - -
116D MET 4.0 6.1 - - - -
117D PHE 3.1 0.6 - - - -
118D THR* 1.3 83.8 - - - +
120D ILE* 1.3 66.6 + - - +
121D VAL 3.4 0.3 + - - -
122D GLY* 3.6 4.2 + - - -
123D ASN 5.1 1.2 + - - -
124D VAL* 5.5 0.5 - - - +
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ILE* 4.1 18.8 - - + -
40D PHE* 3.6 32.7 - - + -
61D SER* 4.2 1.6 - - - -
103D TYR* 4.0 28.0 - - + +
108D PHE* 4.3 12.1 - - + -
116D MET* 3.3 30.7 + - + +
117D PHE* 4.5 3.4 - - + +
119D SER* 1.3 76.0 - - - +
121D VAL* 1.3 61.6 + - + +
124D VAL* 3.7 11.4 - - - +
135D LEU* 4.1 21.3 - - + -
138D LEU* 3.8 27.4 - - + -
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 5.0 0.2 - - + -
117D PHE* 2.8 37.6 + - + +
120D ILE* 1.3 80.6 - - + +
122D GLY* 1.3 65.4 + - - +
123D ASN 3.8 0.7 - - - -
124D VAL* 4.6 1.1 - - - -
125D PHE* 3.5 40.7 - - + +
135D LEU* 3.7 29.6 - - + -
309D MET* 4.1 23.8 - - + -
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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