Contacts of the strand formed by residues 176 - 187 (chain A) in PDB entry 1OXD
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 VAL 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ILE* 5.2 0.7 - - + -
168A ARG* 3.3 44.9 - - + +
169A HIS 3.4 13.5 - - - +
170A ASN* 4.7 7.0 - - - +
171A ILE* 3.4 10.6 - - - +
175A SER* 1.3 89.0 + - - +
177A GLN* 1.3 64.8 + - - +
178A LEU* 3.9 4.7 + - + +
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Residues in contact with GLN 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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100A PHE* 3.6 18.7 - - + +
101A LYS* 2.9 32.4 + - - +
103A ASP* 4.7 3.5 - - - +
135A ASN* 2.9 28.6 + - - +
136A ILE* 4.0 17.6 - - + +
141A LEU* 3.8 23.8 - - + -
168A ARG* 3.7 0.2 - - - -
169A HIS* 2.8 46.6 + - + +
171A ILE* 3.6 5.5 - - + +
176A VAL* 1.3 71.8 - - - +
178A LEU* 1.3 86.8 + - - +
179A ALA 3.7 0.7 + - - -
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Residues in contact with LEU 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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100A PHE* 3.4 1.9 - - - -
101A LYS* 2.9 57.0 + - + +
166A LYS* 3.8 29.8 - - + -
167A ILE 3.6 10.8 - - - +
168A ARG* 3.3 33.2 - - + +
176A VAL* 3.9 6.9 + - + +
177A GLN* 1.3 82.9 + - - +
179A ALA* 1.3 64.6 + - - +
180A ASP* 3.4 28.5 - - - +
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Residues in contact with ALA 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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98A ILE* 3.8 4.0 - - + -
99A PHE 3.4 6.5 - - - -
100A PHE* 3.7 27.1 - - + -
167A ILE* 2.8 36.9 + - + +
169A HIS* 4.0 12.3 - - + +
178A LEU* 1.3 74.2 - - - +
180A ASP* 1.3 61.3 + - - +
181A HIS* 3.0 27.1 + - + -
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Residues in contact with ASP 180 (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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97A THR 3.6 2.4 - - - +
98A ILE* 3.3 2.8 - - - -
99A PHE* 2.9 47.8 + - + +
101A LYS* 5.4 2.6 - - - +
165A PHE 3.9 2.9 - - - +
166A LYS* 3.2 37.7 + - - +
178A LEU* 3.4 22.8 - - - +
179A ALA* 1.3 69.3 - - - +
181A HIS* 1.3 61.9 + - - +
182A TYR* 3.8 25.6 + - + +
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Residues in contact with HIS 181 (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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59A THR 6.1 0.2 - - - -
62A THR* 2.7 30.4 + - - -
96A ARG* 3.8 9.6 - - - -
97A THR 3.8 2.9 - - - -
98A ILE* 3.4 37.8 - - + +
100A PHE* 6.0 0.2 - + - -
164A ASN* 3.2 7.0 - - - +
165A PHE* 2.8 71.1 + + + +
167A ILE* 3.3 26.9 - - + +
169A HIS* 5.5 1.6 - - - -
179A ALA* 3.0 25.4 + - + -
180A ASP* 1.3 75.0 - - - +
182A TYR* 1.3 65.6 + - - +
183A GLN 4.2 0.2 - - - -
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Residues in contact with TYR 182 (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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96A ARG* 3.0 8.1 - - - +
97A THR* 3.0 41.8 + - - +
99A PHE* 3.7 37.2 - + + -
163A ALA 3.6 3.1 - - - -
164A ASN* 4.2 19.3 - - + -
180A ASP* 3.8 27.0 + - + +
181A HIS* 1.3 75.2 - - - +
183A GLN* 1.3 60.9 + - - +
184A GLN* 6.0 3.6 - - - +
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A GLN* 2.9 29.4 + - - +
84A PHE* 4.5 4.0 - - - -
94A GLN* 3.3 7.4 + - + -
95A GLU 3.3 9.6 - - - +
96A ARG* 2.9 39.5 + - + +
150A VAL* 4.4 0.6 - - - +
152A ILE* 6.2 0.2 - - - +
161A ILE* 5.1 2.0 - - - +
162A LYS* 3.2 6.4 - - - +
163A ALA* 2.7 50.9 + - + +
165A PHE* 3.5 14.0 - - + -
182A TYR* 1.3 75.1 - - - +
184A GLN* 1.3 72.7 + - - +
185A ASN* 2.9 24.0 + - - +
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Residues in contact with GLN 184 (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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93A VAL 3.8 0.7 - - - +
94A GLN* 3.6 0.2 - - - -
95A GLU* 2.8 50.5 + - + +
155A ASP* 4.8 9.6 - - - +
161A ILE 3.5 6.7 - - - +
162A LYS* 4.4 11.0 - - + -
182A TYR* 6.0 3.6 - - - +
183A GLN* 1.3 80.5 - - - +
185A ASN* 1.3 64.6 + - - +
186A THR* 5.4 4.7 - - + -
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Residues in contact with ASN 185 (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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83A PHE* 3.8 12.1 - - + -
84A PHE* 3.8 9.9 - - - -
92A TYR* 3.4 24.4 - - + -
93A VAL 3.1 6.1 - - - +
94A GLN* 2.9 26.7 + - - +
155A ASP* 5.6 0.2 - - - +
160A GLY* 3.3 4.5 - - - -
161A ILE* 2.9 52.7 + - + +
162A LYS* 5.8 0.2 - - - -
183A GLN* 2.9 26.2 + - - +
184A GLN* 1.3 81.2 - - - +
186A THR* 1.3 67.3 + - - +
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Residues in contact with THR 186 (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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83A PHE* 4.1 1.1 - - - -
92A TYR* 3.2 4.8 - - - -
93A VAL* 2.8 47.0 + - - +
95A GLU* 4.9 7.0 + - - +
158A LYS* 3.7 34.1 - - + +
184A GLN* 5.4 4.0 - - + -
185A ASN* 1.3 81.7 - - - +
187A PRO* 1.3 73.7 + - - +
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Residues in contact with PRO 187 (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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83A PHE* 3.9 5.1 - - + -
87A ALA* 4.5 4.9 - - + -
91A GLY 3.7 8.1 - - - +
92A TYR* 4.2 3.8 - - + -
93A VAL* 5.5 0.7 - - - +
158A LYS 3.9 2.9 - - - +
159A ASN* 3.0 50.5 - - + +
186A THR* 1.3 92.0 + - - +
188A ILE* 1.3 63.1 + - - +
189A GLY* 4.0 16.0 - - - +
193A VAL* 3.9 20.9 - - + -
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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