Contacts of the helix formed by residues 161 - 179 (chain A) in PDB entry 2OIL
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A LEU* 4.2 17.4 - - + +
153A GLU* 2.8 27.6 + - - +
154A THR* 4.0 4.5 - - + -
159A SER 3.0 3.0 + - - -
160A THR* 1.3 84.0 - - - +
162A VAL* 1.3 58.2 + - - +
163A GLU 3.5 1.8 - - - +
164A LEU* 3.5 29.0 - - - +
165A ALA* 2.7 32.1 + - - +
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.6 26.0 - - + +
31A ARG* 3.6 25.4 - - + -
32A PHE* 4.0 23.6 - - + +
154A THR* 4.3 2.0 - - - -
155A SER 3.5 26.5 - - - +
156A ALA* 4.0 5.2 - - - -
159A SER 3.1 12.0 + - - +
160A THR 3.8 4.0 - - - +
161A ASN* 1.3 76.0 - - - +
163A GLU* 1.3 68.6 + - + +
165A ALA* 3.4 4.8 + - - +
166A PHE* 3.2 38.0 + - + -
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG 6.0 0.4 - - - +
32A PHE* 4.0 11.9 - - + -
52A ARG* 2.6 45.0 + - - +
159A SER 4.7 1.4 + - - -
162A VAL* 1.3 81.1 - - + +
164A LEU* 1.3 52.5 + - - +
166A PHE* 3.3 1.7 + - - +
167A GLU* 2.8 57.7 + - - +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 3.8 23.1 - - + -
161A ASN* 3.5 32.3 - - - +
162A VAL 3.2 0.4 - - - -
163A GLU* 1.3 75.3 - - - +
165A ALA* 1.3 63.7 + - - +
167A GLU* 4.5 9.8 + - + +
168A THR* 2.7 42.7 + - - +
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Residues in contact with ALA 165 (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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28A LEU* 6.0 0.4 - - + -
89A LEU* 4.6 15.3 - - + -
121A MET* 3.6 25.5 - - - +
123A VAL* 5.0 0.4 - - + -
152A LEU* 3.5 12.9 - - + +
154A THR* 3.9 17.9 - - + -
161A ASN 2.7 23.4 + - - +
162A VAL* 3.5 6.1 - - - +
164A LEU* 1.3 75.2 - - - +
166A PHE* 1.3 64.3 + - + +
168A THR 3.4 0.2 + - - -
169A VAL* 3.2 19.8 + - - +
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 4.8 2.5 - - + -
17A LEU* 4.2 8.3 - - + -
28A LEU* 3.5 37.2 - - + -
29A LEU 4.4 0.2 - - - -
32A PHE* 3.4 40.8 - + + -
65A ILE* 3.5 46.0 - - + -
89A LEU* 3.8 39.3 - - + -
162A VAL* 3.2 28.5 + - + -
163A GLU 3.9 0.7 - - - +
165A ALA* 1.3 79.2 - - + +
167A GLU* 1.3 58.4 + - - +
169A VAL* 3.3 6.7 + - + +
170A LEU* 3.0 36.3 + - + +
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Residues in contact with GLU 167 (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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32A PHE* 4.8 7.0 - - + -
52A ARG* 4.4 4.5 + - - -
54A VAL* 3.9 29.9 - - + +
55A MET 5.9 0.2 - - - -
56A LEU* 4.5 2.6 - - + +
163A GLU* 2.8 51.1 + - - +
164A LEU* 4.1 8.6 + - + +
166A PHE* 1.3 72.7 - - - +
168A THR* 1.3 57.1 + - - +
170A LEU* 3.5 6.4 + - - +
171A LYS* 2.9 40.5 + - + +
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Residues in contact with THR 168 (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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121A MET* 3.8 19.5 - - + -
150A LEU* 4.0 16.6 - - + -
152A LEU* 4.8 2.1 - - + +
164A LEU* 2.7 40.1 + - - +
165A ALA 3.7 3.1 - - - -
167A GLU* 1.3 72.5 - - - +
169A VAL* 1.3 68.0 + - - +
171A LYS* 3.5 7.9 + - - +
172A GLU* 3.1 23.7 + - + +
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Residues in contact with VAL 169 (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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15A VAL* 4.5 15.0 - - + -
87A GLY* 4.1 14.8 - - - -
88A ALA 4.5 0.9 - - - +
89A LEU* 4.2 13.9 - - + -
119A VAL* 4.2 13.2 - - + +
121A MET* 3.6 37.9 - - + +
150A LEU* 4.3 6.3 - - + -
165A ALA 3.2 11.5 + - - +
166A PHE* 3.8 7.0 - - - +
168A THR* 1.3 78.1 - - - +
170A LEU* 1.3 59.5 + - + +
172A GLU* 3.0 5.2 + - - +
173A ILE* 2.9 50.6 + - + +
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Residues in contact with LEU 170 (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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13A PHE* 3.8 22.9 - - + -
15A VAL* 3.8 24.7 - - + -
32A PHE* 4.3 5.6 - - + -
54A VAL* 4.0 24.9 - - + -
56A LEU* 3.7 15.4 - - + +
61A VAL* 4.6 4.7 - - + -
63A ALA* 3.8 34.3 - - + -
65A ILE* 5.5 0.4 - - + -
166A PHE* 3.0 30.5 + - + +
167A GLU* 3.9 6.7 - - - +
169A VAL* 1.3 77.2 - - + +
171A LYS* 1.3 56.9 + - - +
173A ILE* 3.5 7.2 + - + +
174A PHE* 3.0 28.9 + - - +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.8 28.0 - - + -
167A GLU* 2.9 28.3 + - + +
168A THR* 4.0 6.3 - - - +
169A VAL 3.3 0.2 - - - -
170A LEU* 1.3 73.1 - - - +
172A GLU* 1.3 59.6 + - - +
174A PHE* 3.4 3.0 + - - +
175A ALA* 2.9 30.4 + - - +
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Residues in contact with GLU 172 (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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119A VAL* 3.8 28.0 - - + -
150A LEU* 4.2 19.5 - - + +
168A THR* 3.1 13.2 + - - +
169A VAL 3.0 8.6 + - - +
171A LYS* 1.3 75.3 - - - +
173A ILE* 1.3 64.9 + - - +
175A ALA* 3.4 9.4 + - - +
176A LYS* 2.9 31.8 + - - +
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Residues in contact with ILE 173 (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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13A PHE* 3.6 33.2 - - + -
15A VAL* 4.3 8.7 - - + -
86A VAL* 3.4 47.3 - - + +
87A GLY* 3.7 3.1 - - - +
119A VAL* 3.7 14.3 - - + +
169A VAL* 2.9 41.5 + - + +
170A LEU* 3.7 7.0 - - - +
172A GLU* 1.3 70.3 - - - +
174A PHE* 1.3 55.8 + - - +
176A LYS* 3.1 5.5 + - + +
177A VAL* 2.7 46.7 + - + +
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Residues in contact with PHE 174 (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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11A PHE* 3.3 42.6 - + - -
13A PHE* 3.7 12.8 - + + -
56A LEU* 3.7 20.0 - - + -
59A ALA* 3.6 23.1 - - + -
61A VAL* 4.1 14.6 - - + -
170A LEU 3.0 17.8 + - - +
171A LYS* 3.7 3.8 - - - +
172A GLU 3.3 0.2 - - - -
173A ILE* 1.3 72.1 - - - +
175A ALA* 1.3 72.2 + - - +
177A VAL* 3.6 1.5 - - - +
178A SER* 2.9 44.0 + - - -
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Residues in contact with ALA 175 (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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171A LYS 2.9 17.8 + - - +
172A GLU* 3.5 13.7 - - - +
174A PHE* 1.3 82.0 - - - +
176A LYS* 1.3 65.7 + - - +
178A SER* 3.4 14.6 + - - -
179A LYS* 3.7 13.6 + - - +
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Residues in contact with LYS 176 (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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116A ALA 5.3 0.6 + - - -
117A THR* 3.2 45.3 + - + +
118A ILE 4.5 3.0 + - - -
119A VAL* 3.7 21.7 - - + +
172A GLU* 2.9 20.2 + - - +
173A ILE* 3.3 10.1 - - + +
175A ALA* 1.3 76.0 - - - +
177A VAL* 1.3 58.1 + - + +
179A LYS* 3.0 28.8 + - - +
180A GLN* 3.5 20.8 + - + +
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Residues in contact with VAL 177 (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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11A PHE* 4.4 17.9 - - + -
13A PHE* 3.8 25.6 - - + -
86A VAL* 5.1 10.8 - - + -
173A ILE* 2.7 41.2 + - + +
174A PHE* 3.6 6.3 - - - +
176A LYS* 1.3 72.5 - - + +
178A SER* 1.3 62.7 + - - +
180A GLN* 3.3 44.7 + - - +
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Residues in contact with SER 178 (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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11A PHE* 5.5 4.1 - - - -
174A PHE* 2.9 46.7 + - - -
175A ALA* 3.4 9.2 - - - -
176A LYS 3.2 0.2 - - - -
177A VAL* 1.3 77.7 - - - +
179A LYS* 1.3 60.5 + - - +
180A GLN 3.4 3.4 - - - +
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Residues in contact with LYS 179 (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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175A ALA 4.1 12.8 - - - +
176A LYS* 3.0 14.7 + - - +
178A SER* 1.3 80.3 - - - +
180A GLN* 1.3 63.3 + - - +
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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
------------------------------------------------------------
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