Contacts of the strand formed by residues 166 - 177 (chain C) in PDB entry 1OPT
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 LYS 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LYS* 5.2 7.1 - - - +
3C VAL* 3.8 40.5 - - + +
5C LEU* 3.5 21.1 - - + +
162C LEU* 3.1 8.2 - - - +
163C GLN 2.9 33.5 + - - +
164C ASN* 3.0 21.6 + - + +
165C GLN* 1.3 86.9 - - - +
167C LYS* 1.3 64.2 + - - +
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Residues in contact with LYS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.7 2.3 - - - +
160C THR* 3.9 19.3 - - + -
161C VAL 3.1 13.0 - - - +
162C LEU* 4.7 3.6 - - + -
165C GLN 5.7 0.7 - - - +
166C LYS* 1.3 80.2 - - - +
168C VAL* 1.3 73.0 + - - +
169C GLU* 5.9 2.4 + - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.4 42.8 - - + +
6C GLY* 4.6 5.4 - - - +
7C LYS* 4.8 9.0 - - + -
98C PHE* 4.6 8.5 - - + -
160C THR* 3.4 7.4 - - - -
161C VAL* 3.2 37.2 + - + +
167C LYS* 1.3 86.2 - - - +
169C GLU* 1.3 64.5 + - - +
170C PHE* 4.0 22.2 - - + -
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LYS* 3.3 25.9 - - - +
158C THR* 3.9 19.6 - - + +
159C CYS 3.3 9.2 - - - +
160C THR* 4.4 9.4 - - + +
167C LYS* 5.9 2.6 + - - +
168C VAL* 1.3 75.2 - - - +
170C PHE* 1.3 72.8 + - - +
171C LYS* 4.4 13.3 - - + +
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Residues in contact with PHE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LYS* 3.8 35.9 - - + +
8C LYS 4.9 0.9 - - - -
98C PHE* 3.5 36.8 - - + -
99C GLY* 4.1 2.9 - - - -
100C LEU* 4.0 35.2 - - + -
118C LEU* 4.6 0.2 - - + -
157C TRP 3.1 4.7 - - - +
158C THR* 3.6 1.4 - - - +
159C CYS* 2.8 50.3 + - + +
161C VAL* 3.6 32.1 - - + -
168C VAL* 4.0 17.7 - - + -
169C GLU* 1.3 85.3 - - - +
171C LYS* 1.3 62.0 + - - +
172C ILE* 3.8 7.1 + - + -
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Residues in contact with LYS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 5.1 6.2 - - - +
156C THR* 3.4 28.9 + - + +
157C TRP 3.3 4.9 - - - +
158C THR* 5.1 8.0 + - - +
169C GLU* 4.8 15.3 - - + +
170C PHE* 1.3 73.2 - - - +
172C ILE* 1.3 69.1 + - - +
173C ASP* 4.1 2.4 + - - +
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LEU* 3.8 27.1 - - + +
101C THR* 5.2 1.6 - - - -
102C ALA* 4.7 16.4 - - + +
106C THR* 6.1 0.2 - - + -
116C LEU* 4.7 11.7 - - + -
155C GLY 3.9 0.2 - - - +
156C THR* 3.6 0.4 - - - +
157C TRP* 2.8 47.0 + - + +
159C CYS* 4.7 13.2 - - - -
170C PHE* 4.4 16.4 - - + +
171C LYS* 1.3 87.5 - - - +
173C ASP* 1.3 67.7 + - - +
174C ILE* 3.7 21.0 + - + -
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C THR* 3.1 24.8 - - + +
155C GLY* 4.0 3.1 - - - -
156C THR* 2.7 34.1 + - - +
171C LYS* 4.1 2.6 + - - +
172C ILE* 1.3 76.8 - - - +
174C ILE* 1.3 66.2 - - - +
175C VAL* 5.4 2.7 - - + -
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ALA* 4.7 6.3 - - + -
106C THR* 4.1 18.8 - - + +
108C LEU* 5.1 0.7 - - + -
114C LEU* 4.0 28.9 - - + -
116C LEU* 5.3 0.7 - - + -
149C LEU* 4.6 13.0 - - + -
153C ASP 4.5 2.2 - - - +
154C SER* 3.7 1.1 + - - -
155C GLY* 3.0 34.6 + - - +
157C TRP* 3.6 36.8 - - + +
172C ILE* 4.0 18.8 - - + +
173C ASP* 1.3 84.2 - - - +
175C VAL* 1.3 78.3 + - - +
176C VAL* 4.4 12.1 - - + -
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Residues in contact with VAL 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C THR* 2.6 46.9 + - + +
107C HIS* 4.3 22.2 - - + +
108C LEU* 2.9 12.1 + - - +
154C SER* 3.3 8.7 - - - +
173C ASP* 5.4 2.2 - - + -
174C ILE* 1.3 84.4 - - - +
176C VAL* 1.3 74.3 + - - +
177C LEU* 4.9 6.1 - - + -
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C LEU 3.3 3.1 - - - +
109C LEU 3.7 6.7 - - - +
110C GLN* 3.5 40.8 - - + +
149C LEU* 4.0 28.9 - - + +
150C GLU 4.0 13.0 - - - +
151C LEU* 3.5 15.8 - - - +
153C ASP 4.5 0.2 - - - -
154C SER* 3.1 35.4 + - - +
174C ILE* 4.4 5.2 - - + -
175C VAL* 1.3 84.4 - - - +
177C LEU* 1.3 67.2 + - - +
178C ALA 3.7 0.5 + - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C HIS* 4.1 30.1 - - + +
108C LEU 3.1 22.3 + - - +
109C LEU* 3.9 24.6 - - + +
110C GLN* 3.1 26.8 + - - +
151C LEU* 4.1 0.7 - - - -
175C VAL* 4.9 5.2 - - + -
176C VAL* 1.3 78.4 - - - +
178C ALA* 1.3 60.0 + - - +
179C PHE* 3.5 9.1 + - + +
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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