Contacts of the helix formed by residues 112 - 122 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H ASN* 4.8 0.2 + - - -
244H ALA* 3.8 2.1 - - - -
245H GLY* 3.3 31.1 + - - -
109R GLU* 3.3 25.5 + - - -
110R GLU 3.3 1.2 - - - -
111R GLY* 1.3 76.2 - - - +
113R VAL* 1.3 61.9 + - - +
114R THR* 3.7 3.3 - - - -
115R ASN* 3.0 32.6 + - - +
116R MET* 3.2 9.7 + - - +
144R TYR* 3.5 9.5 + - - -
148R PHE* 3.4 5.1 - - - -
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Residues in contact with VAL 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H GLY* 5.1 1.0 - - - -
111R GLY 4.0 1.0 + - - -
112R SER* 1.3 73.1 - - - +
114R THR* 1.3 62.8 + - - +
116R MET* 3.1 9.6 + - + +
117R PHE* 2.9 29.3 + - + +
148R PHE* 3.6 22.4 - - + -
274R PHE* 3.6 42.0 - - + -
278R THR* 5.4 3.9 + - - +
317R ALA* 3.4 33.9 - - + +
320R MET* 3.7 13.9 - - + -
321R SER* 3.7 12.3 - - - +
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Residues in contact with THR 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H THR* 3.4 32.1 - - + -
244H ALA 3.6 15.0 + - - +
245H GLY* 4.7 2.6 + - - -
271H THR* 2.9 39.5 + - - +
272H GLY* 3.7 3.8 - - - +
112R SER* 3.7 4.0 - - - +
113R VAL* 1.3 79.1 - - - +
115R ASN* 1.3 53.2 + - - +
117R PHE* 3.5 1.9 + - - -
118R THR* 2.7 36.4 + - - -
274R PHE* 3.5 13.7 - - - +
275R THR* 3.1 15.1 + - - -
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Residues in contact with ASN 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205H ASN* 3.0 32.7 + - - +
207H ASN* 3.1 27.9 + - - +
209H GLN* 3.6 5.9 + - - +
107R LEU 3.7 1.7 - - - +
108R PHE* 3.4 13.0 - - - +
109R GLU* 2.9 31.5 + - + +
112R SER* 3.0 26.8 + - - +
114R THR* 1.3 73.6 - - - +
116R MET* 1.3 67.0 + - - +
118R THR* 3.2 4.8 + - - -
119R SER* 3.2 22.0 + - - -
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Residues in contact with MET 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36R ILE* 4.9 4.0 - - - -
108R PHE* 3.8 22.4 - - + -
112R SER 3.2 9.9 + - - +
113R VAL* 3.1 14.0 + - + +
115R ASN* 1.3 79.5 + - - +
117R PHE* 1.3 81.9 + - + +
119R SER* 3.5 1.0 + - - -
120R ILE* 3.1 41.9 + - + +
138R LEU* 3.8 22.0 - - + -
140R ILE* 3.7 24.5 - - + -
144R TYR* 4.0 13.7 - - + +
317R ALA* 4.9 2.9 - - + -
320R MET* 3.9 28.9 - - + -
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Residues in contact with PHE 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271H THR* 4.2 11.0 - - + -
297H MET* 4.4 15.0 - - + -
113R VAL* 2.9 21.4 + - + +
114R THR* 3.9 4.5 - - - +
116R MET* 1.3 93.7 - - + +
118R THR* 1.3 58.8 + - - +
120R ILE* 5.1 1.8 - - + -
121R VAL* 2.8 54.2 + - + +
122R GLY* 3.3 1.6 + - - -
135R LEU* 5.8 2.2 - - + -
138R LEU* 4.9 2.7 - - + -
270R LEU* 5.9 0.2 - - + -
274R PHE* 3.8 22.4 - + + -
309R ILE* 4.2 10.8 - - + -
313R VAL* 4.1 20.0 - - + -
314R LEU* 4.0 26.5 - - + -
317R ALA* 3.7 31.6 - - + -
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Residues in contact with THR 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H GLU* 3.3 38.2 - - + +
205H ASN* 3.8 4.4 - - - +
207H ASN* 5.5 0.9 - - - -
243H THR* 4.8 0.5 - - - +
268H ASP* 3.2 23.6 + - - +
271H THR* 2.8 24.3 + - - +
296H ALA* 4.1 6.3 - - + -
114R THR* 2.7 26.7 + - - +
115R ASN* 3.2 9.7 + - - -
117R PHE* 1.3 76.5 - - - +
119R SER* 1.3 58.3 + - - +
122R GLY* 3.0 25.4 - - - -
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Residues in contact with SER 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178H LEU* 3.9 9.7 - - - +
204H GLU* 5.8 0.2 - - - -
205H ASN* 2.8 34.4 + - - +
60R GLU 4.8 0.5 - - - +
61R SER* 3.1 35.8 - - - -
103R TYR* 5.5 0.7 - - - -
107R LEU* 4.7 5.5 + - - -
108R PHE* 4.4 15.7 - - - -
115R ASN* 3.2 11.9 + - - -
116R MET 4.0 5.4 - - - -
118R THR* 1.3 79.2 - - - +
120R ILE* 1.3 65.1 + - - +
121R VAL 3.4 0.2 + - - -
122R GLY* 3.7 3.5 + - - -
123R ASN 5.1 1.6 + - - -
124R VAL* 5.4 0.3 - - - +
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Residues in contact with ILE 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36R ILE* 3.8 29.2 - - + -
38R ALA* 4.2 2.2 - - + -
40R PHE* 3.5 35.2 - - + -
61R SER* 4.2 6.8 - - - -
103R TYR* 3.9 22.2 - - + +
108R PHE* 4.0 11.9 - - + -
116R MET* 3.1 30.0 + - + +
117R PHE* 5.1 1.3 - - + -
119R SER* 1.3 76.6 - - - +
121R VAL* 1.3 59.9 + - + +
124R VAL* 3.7 11.3 - - - +
135R LEU* 4.1 20.6 - - + -
138R LEU* 3.8 19.1 - - + -
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Residues in contact with VAL 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H MET* 3.4 26.6 - - + -
300H VAL* 3.8 10.7 - - + +
117R PHE* 2.8 39.9 + - + +
120R ILE* 1.3 81.3 - - + +
122R GLY* 1.3 66.3 + - - +
123R ASN 3.7 1.3 - - - -
124R VAL* 4.7 0.7 - - - -
125R PHE* 3.5 30.3 - - + +
135R LEU* 3.7 28.9 - - + -
309R ILE* 3.9 23.6 - - + -
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Residues in contact with GLY 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204H GLU* 5.3 0.2 - - - -
295H ARG 4.6 0.3 - - - +
296H ALA* 3.4 11.2 - - - -
297H MET* 2.7 31.0 + - - -
298H HIS* 4.6 4.7 + - - -
299H ALA* 5.4 1.6 + - - +
117R PHE 3.3 1.5 + - - -
118R THR 3.0 26.4 + - - -
119R SER 3.7 1.8 + - - -
120R ILE 3.7 1.4 - - - -
121R VAL* 1.3 78.1 - - - +
123R ASN* 1.3 68.1 + - - +
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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