Contacts of the helix formed by residues 160 - 178 (chain V) in PDB entry 4UJ3
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 ASN 160 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151V ILE* 3.4 27.8 - - + +
152V GLU 3.2 22.9 + - - +
153V THR* 3.7 3.4 - - + +
158V SER 3.2 2.2 + - - -
159V THR* 1.3 83.4 - - - +
161V VAL* 1.3 63.8 + - - +
162V GLU* 3.3 3.3 - - - +
163V ALA* 3.6 15.3 - - - +
164V ALA* 2.9 26.2 + - - +
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Residues in contact with VAL 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27V LEU* 4.1 24.7 - - + +
30V ARG* 3.5 35.7 - - + -
31V PHE* 4.1 13.0 - - + +
153V THR* 4.5 6.3 - - - -
154V SER 3.4 31.0 - - - +
155V ALA* 4.0 4.5 - - - -
158V SER* 3.2 14.2 + - - +
159V THR 2.8 6.8 + - - +
160V ASN* 1.3 79.5 - - - +
162V GLU* 1.3 65.6 + - - +
164V ALA* 3.4 5.9 + - - +
165V PHE* 3.3 21.7 + - + -
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Residues in contact with GLU 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31V PHE* 4.3 11.8 - - - -
51V ARG* 2.9 44.9 + - - -
53V ILE* 4.3 8.7 - - - +
158V SER 4.4 2.9 + - - +
160V ASN* 3.3 0.9 - - - -
161V VAL* 1.3 82.4 - - - +
163V ALA* 1.3 63.1 + - - +
164V ALA 3.3 0.3 + - - -
165V PHE* 3.3 3.3 + - - +
166V GLN* 3.1 37.2 + - + +
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Residues in contact with ALA 163 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151V ILE* 4.1 10.1 - - + -
160V ASN* 3.3 23.1 + - - +
162V GLU* 1.3 80.3 - - - +
164V ALA* 1.3 60.7 + - - +
166V GLN* 3.4 7.8 + - - +
167V THR* 2.9 32.3 + - - +
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Residues in contact with ALA 164 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88V LEU* 5.5 1.6 - - + -
120V MET* 3.4 35.5 - - + +
122V VAL* 5.2 1.8 - - + -
151V ILE* 3.9 17.7 - - + +
153V THR* 4.1 8.7 - - + -
160V ASN 2.9 17.8 + - - +
161V VAL 3.8 5.2 - - - +
162V GLU 3.3 0.4 - - - -
163V ALA* 1.3 76.1 - - - +
165V PHE* 1.3 68.0 + - + +
167V THR* 3.5 2.7 - - - -
168V ILE* 3.1 19.4 + - - +
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Residues in contact with PHE 165 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V VAL* 5.6 0.2 - - + -
16V LEU* 4.8 2.5 - - + -
27V LEU* 3.9 22.2 - - + -
28V LEU* 5.1 0.2 - - - -
31V PHE* 3.3 69.1 - + + -
53V ILE* 5.3 0.2 - - - -
64V ILE* 3.5 38.6 - - + -
88V LEU* 3.3 33.2 - - + -
161V VAL* 3.3 22.0 - - + -
162V GLU 3.3 2.3 + - - +
163V ALA 3.3 0.4 - - - -
164V ALA* 1.3 79.1 - - + +
166V GLN* 1.3 67.0 + - - +
168V ILE* 4.0 8.7 - - + -
169V LEU* 3.0 35.2 + - + +
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Residues in contact with GLN 166 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53V ILE* 3.0 39.4 - - + +
54V GLN 3.8 15.4 + - - +
55V VAL* 4.7 4.8 - - - +
162V GLU* 3.1 34.3 + - + +
163V ALA* 3.7 7.6 - - - +
165V PHE* 1.3 76.0 - - - +
167V THR* 1.3 59.1 + - - +
169V LEU* 4.1 2.6 - - - +
170V THR* 2.9 38.0 + - - +
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Residues in contact with THR 167 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120V MET* 4.6 11.9 - - - -
149V SER* 5.0 3.1 - - - -
151V ILE* 5.8 1.4 - - - +
163V ALA* 2.9 22.6 + - - +
164V ALA* 3.5 6.5 - - - -
165V PHE 3.1 0.2 - - - -
166V GLN* 1.3 76.1 - - - +
168V ILE* 1.3 67.1 + - - +
170V THR* 2.8 21.2 + - - +
171V GLU* 3.0 36.1 + - + +
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Residues in contact with ILE 168 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V VAL* 4.2 9.6 - - + -
86V GLY* 4.4 2.0 - - - -
87V ALA 3.6 29.8 - - - +
88V LEU* 3.5 33.2 - - + -
118V VAL* 3.9 20.2 - - + +
120V MET* 4.2 13.2 - - + -
149V SER* 5.5 0.2 - - - +
164V ALA 3.1 10.8 + - - +
165V PHE* 3.5 21.8 - - + +
167V THR* 1.3 80.7 - - - +
169V LEU* 1.3 70.8 + - + +
171V GLU* 4.0 7.0 - - - +
172V ILE* 3.1 36.3 + - + +
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Residues in contact with LEU 169 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V PHE* 3.9 32.4 - - + -
14V VAL* 4.3 16.4 - - + -
31V PHE* 4.6 10.1 - - + -
53V ILE* 3.8 26.5 - - + -
55V VAL* 4.6 10.7 - - + +
60V ILE* 4.6 5.6 - - + +
62V ALA* 3.7 33.7 - - + -
64V ILE* 5.7 0.2 - - + -
165V PHE* 3.0 30.2 + - + +
166V GLN* 4.1 3.4 - - - +
168V ILE* 1.3 81.9 - - + +
170V THR* 1.3 58.8 + - - +
172V ILE* 3.3 6.5 + - + +
173V TYR* 2.9 24.9 + - - +
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Residues in contact with THR 170 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55V VAL* 3.2 40.6 - - + -
56V ASP 5.6 0.2 - - - +
166V GLN* 2.9 25.8 + - + +
167V THR* 2.8 21.7 + - - +
169V LEU* 1.3 75.6 - - - +
171V GLU* 1.3 64.9 + - - +
173V TYR* 3.2 5.9 + - - +
174V ARG* 3.1 21.0 + - - +
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Residues in contact with GLU 171 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118V VAL* 3.6 26.0 - - + +
149V SER* 3.6 23.0 + - - -
167V THR* 3.0 37.2 + - + +
168V ILE* 4.0 5.8 - - - +
170V THR* 1.3 79.3 - - - +
172V ILE* 1.3 60.6 + - - +
174V ARG* 3.5 14.9 + - - +
175V ILE* 3.5 17.8 + - - +
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Residues in contact with ILE 172 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V PHE* 3.5 34.8 - - + -
14V VAL* 4.3 10.1 - - + -
85V VAL* 3.3 34.5 - - + +
86V GLY* 3.5 17.3 - - - +
118V VAL* 3.2 25.1 - - + -
168V ILE* 3.1 24.1 + - + +
169V LEU* 3.5 7.2 - - + +
170V THR 3.2 0.6 - - - -
171V GLU* 1.3 76.2 - - - +
173V TYR* 1.3 63.7 + - - +
175V ILE* 3.4 5.2 + - + +
176V VAL* 3.1 21.3 + - + +
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Residues in contact with TYR 173 (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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10V TYR* 4.6 27.4 - + - -
12V PHE* 3.8 11.6 - - + -
55V VAL* 3.3 29.2 - - + -
56V ASP* 3.1 40.9 + - + -
58V LYS* 3.5 25.8 - - + +
60V ILE* 5.2 7.6 - - + -
169V LEU 2.9 13.0 + - - +
170V THR* 3.2 13.0 - - - +
172V ILE* 1.3 77.1 - - - +
174V ARG* 1.3 54.1 + - - +
176V VAL* 3.1 1.7 + - - -
177V SER* 2.8 54.9 + - - -
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Residues in contact with ARG 174 (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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170V THR 3.1 8.6 + - - +
171V GLU* 3.6 11.9 - - - +
172V ILE 3.3 0.4 - - - -
173V TYR* 1.3 81.2 - - - +
175V ILE* 1.3 62.4 + - + +
177V SER* 3.5 7.1 + - - -
178V GLN* 3.3 22.0 + - - +
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Residues in contact with ILE 175 (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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116V ASN* 3.8 31.2 - - + +
118V VAL* 4.2 14.8 - - + -
171V GLU 3.5 11.2 + - - +
172V ILE* 3.4 9.0 + - - +
173V TYR 3.3 0.4 - - - -
174V ARG* 1.3 78.3 - - + +
176V VAL* 1.3 62.4 + - - +
178V GLN* 3.6 19.4 + - - +
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Residues in contact with VAL 176 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V TYR* 3.9 26.4 + - + -
12V PHE* 4.1 15.5 - - + -
172V ILE* 3.1 17.1 + - + +
173V TYR 3.7 3.6 - - - +
175V ILE* 1.3 77.1 - - - +
177V SER* 1.3 65.2 + - - +
178V GLN 3.5 6.9 - - - +
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Residues in contact with SER 177 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V TYR* 4.7 7.9 - - - -
173V TYR* 2.8 51.0 + - - -
174V ARG* 3.7 8.5 - - - -
175V ILE 3.4 0.2 - - - -
176V VAL* 1.3 74.7 - - - +
178V GLN* 1.3 66.5 + - - +
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Residues in contact with GLN 178 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174V ARG 3.3 13.6 + - - +
175V ILE* 3.9 11.4 - - - +
176V VAL 3.3 9.7 - - - +
177V SER* 1.3 86.2 - - - +
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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
------------------------------------------------------------
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