Contacts of the helix formed by residues 112 - 122 (chain V) in PDB entry 1UW9
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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244O ALA* 3.8 2.1 - - - -
245O GLY* 3.3 31.9 + - - -
109V GLU* 3.2 23.9 + - - -
110V GLU 3.2 1.6 - - - -
111V GLY* 1.3 76.8 - - - +
113V VAL* 1.3 61.8 + - - +
114V THR* 3.7 3.1 - - - -
115V ASN* 2.9 27.2 + - - +
116V MET* 3.2 15.9 + - - +
144V TYR* 3.4 8.8 + - - -
148V PHE* 3.5 5.2 - - - -
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Residues in contact with VAL 113 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245O GLY* 5.1 1.0 + - - -
111V GLY 3.9 1.0 + - - -
112V SER* 1.3 68.1 - - - +
114V THR* 1.3 65.6 + - - +
116V MET* 3.1 9.9 + - + +
117V PHE* 2.9 28.6 + - + +
148V PHE* 3.6 23.1 - - + -
274V PHE* 3.6 41.7 - - + -
278V THR* 5.3 3.7 + - - +
317V ALA* 3.5 33.2 - - + +
320V MET* 3.7 14.8 - - + -
321V SER* 3.7 12.8 - - - +
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Residues in contact with THR 114 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207O ASN* 5.0 0.2 - - - +
243O THR* 3.4 32.8 - - + -
244O ALA 3.6 15.9 + - - +
245O GLY* 4.7 2.0 + - - -
271O THR* 2.9 39.4 + - - +
272O GLY* 3.7 3.8 - - - +
112V SER* 3.7 3.4 - - - +
113V VAL* 1.3 79.2 - - - +
115V ASN* 1.3 53.2 + - - +
117V PHE* 3.5 2.1 + - - +
118V THR* 2.7 35.6 + - - +
274V PHE* 3.5 13.9 - - - +
275V THR* 3.1 14.6 + - - -
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Residues in contact with ASN 115 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205O ASN* 3.0 32.9 + - - +
207O ASN* 3.1 27.4 + - - +
209O GLN* 3.6 6.5 + - - +
107V LEU 3.7 1.6 - - - +
108V PHE* 3.4 12.3 - - - +
109V GLU* 2.9 31.7 + - + +
112V SER* 2.9 27.9 + - - +
114V THR* 1.3 73.9 - - - +
116V MET* 1.3 65.2 + - - +
118V THR* 3.2 5.0 + - - -
119V SER* 3.2 23.1 + - - -
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Residues in contact with MET 116 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36V ILE* 4.9 4.0 - - - -
108V PHE* 3.8 22.4 - - + -
112V SER 3.2 11.1 + - - +
113V VAL* 3.1 13.6 + - + +
115V ASN* 1.3 78.3 + - - +
117V PHE* 1.3 82.5 + - + +
119V SER* 3.5 1.2 + - - -
120V ILE* 3.1 41.7 + - + +
138V LEU* 3.7 23.3 - - + -
140V ILE* 3.7 22.9 - - + -
144V TYR* 4.1 13.0 + - + +
316V LYS* 6.5 0.2 - - + -
317V ALA* 4.9 3.4 - - + +
320V MET* 3.9 29.2 - - + -
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Residues in contact with PHE 117 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271O THR* 4.3 11.4 - - + -
297O MET* 4.4 15.0 - - + -
113V VAL* 2.9 21.0 + - + +
114V THR* 3.9 4.7 - - - +
116V MET* 1.3 94.7 - - + +
118V THR* 1.3 58.1 + - - +
120V ILE* 5.0 1.8 - - + -
121V VAL* 2.8 55.6 + - + +
122V GLY* 3.3 1.4 + - - -
135V LEU* 5.8 1.6 - - + -
138V LEU* 4.8 2.7 - - + -
270V LEU* 5.9 0.2 - - + -
274V PHE* 3.9 21.8 - + + -
309V ILE* 4.2 11.0 - - + -
313V VAL* 4.1 19.7 - - + -
314V LEU* 4.0 25.8 - - + -
317V ALA* 3.6 32.3 - - + -
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Residues in contact with THR 118 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204O GLU* 3.3 39.0 - - + +
205O ASN* 3.7 5.1 - - - +
207O ASN* 5.5 0.4 - - - -
243O THR* 4.8 0.7 - - - +
268O ASP* 3.2 24.1 + - - +
271O THR* 2.8 24.5 + - - -
296O ALA* 4.2 4.7 - - + -
114V THR* 2.7 24.6 + - - +
115V ASN* 3.2 10.4 + - - -
117V PHE* 1.3 76.6 - - - +
119V SER* 1.3 58.0 + - - +
122V GLY* 3.1 25.2 - - - -
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Residues in contact with SER 119 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178O LEU* 3.9 8.8 - - - +
204O GLU* 5.7 0.2 - - - -
205O ASN* 2.8 34.3 + - - +
60V GLU 4.8 0.7 - - - +
61V SER* 3.1 35.8 + - - -
103V TYR* 5.5 0.4 - - - -
107V LEU* 4.7 5.4 + - - +
108V PHE* 4.3 15.0 - - - -
115V ASN* 3.2 11.8 + - - -
116V MET 4.0 5.8 - - - -
118V THR* 1.3 81.0 - - - +
120V ILE* 1.3 65.3 + - - +
121V VAL 3.4 0.7 + - - -
122V GLY* 3.6 3.8 + - - -
123V ASN 5.0 1.2 + - - -
124V VAL* 5.4 0.3 - - - +
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Residues in contact with ILE 120 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36V ILE* 3.8 29.2 - - + -
38V ALA* 4.2 2.9 - - + -
40V PHE* 3.4 34.7 - - + -
61V SER* 4.2 6.5 - - - -
103V TYR* 4.0 22.9 - - + +
108V PHE* 4.1 11.0 - - + -
116V MET* 3.1 30.4 + - + +
117V PHE* 5.0 1.3 - - + -
119V SER* 1.3 76.9 - - - +
121V VAL* 1.3 60.0 + - + +
124V VAL* 3.7 10.4 - - - +
135V LEU* 4.1 21.3 - - + -
138V LEU* 3.8 19.1 - - + -
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Residues in contact with VAL 121 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297O MET* 3.4 25.4 - - + -
300O VAL* 3.8 10.7 - - + +
117V PHE* 2.8 50.8 + - + +
120V ILE* 1.3 81.1 - - + +
122V GLY* 1.3 67.4 - - - +
123V ASN 3.7 1.1 - - - -
124V VAL 4.9 0.9 - - - -
125V PHE* 3.6 33.7 - - + +
135V LEU* 3.7 28.5 - - + -
309V ILE* 3.9 14.8 - - + -
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Residues in contact with GLY 122 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204O GLU* 5.3 0.2 - - - -
295O ARG 4.6 0.2 - - - +
296O ALA* 3.4 10.6 - - - -
297O MET* 2.7 30.2 + - - -
298O HIS* 4.6 4.7 + - - -
299O ALA* 5.4 2.1 + - - +
117V PHE 3.3 1.9 + - - -
118V THR* 3.1 26.9 + - - -
119V SER 3.6 3.2 + - - -
121V VAL* 1.3 77.9 - - - +
123V ASN* 1.3 69.1 + - - +
124V VAL 4.8 0.2 - - - +
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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