Contacts of the strand formed by residues 176 - 184 (chain B) in PDB entry 1OX4
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 GLU 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG 4.7 0.5 - - - +
112B PHE* 3.6 11.1 - - + -
113B ASP* 2.8 29.7 + - + +
116B GLU* 4.2 3.4 - - - +
117B LYS* 2.5 32.5 + - - +
152B ILE* 3.4 36.6 - - + +
172B LYS* 3.2 5.0 - - - -
173B TYR 2.9 35.0 + - - +
174B GLY 3.4 0.4 - - - -
175B SER* 1.3 84.0 - - - +
177B GLU* 1.3 61.0 + - - +
178B PHE* 3.8 3.1 - - - -
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 4.2 20.4 - - + +
152B ILE* 3.5 7.7 - - - +
153B LEU* 2.8 39.2 + - + +
158B LYS* 3.3 29.0 + - - +
170B LYS* 3.5 19.7 - - + +
171B ALA 3.4 10.5 - - - +
172B LYS* 4.3 14.1 - - + +
175B SER 3.9 2.4 + - - +
176B GLU* 1.3 74.0 - - - +
178B PHE* 1.3 62.9 + - - +
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.8 15.0 - + + -
121B GLU* 3.4 20.0 - - - -
125B ASN* 4.5 1.3 - - - -
145B PHE* 3.9 20.2 - + - -
147B HIS* 3.9 15.0 - + - -
150B ALA* 4.0 18.6 - - + -
151B ALA 3.2 19.3 - - - +
152B ILE* 4.0 5.2 - - + -
153B LEU* 3.7 8.9 - - - +
170B LYS* 3.6 3.6 - - - -
171B ALA* 2.9 59.2 + - + +
172B LYS 3.9 0.9 - - - -
173B TYR* 3.7 28.0 - - + -
176B GLU 3.8 7.4 - - - -
177B GLU* 1.3 77.1 - - - +
179B ILE* 1.3 76.0 + - - +
180B ALA 3.3 0.5 + - - -
191B GLN* 4.5 0.7 - - + -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 4.7 8.6 - - + +
90B PHE* 3.9 18.2 - - + -
105B ILE* 5.1 0.2 - - + -
107B PHE* 4.2 1.8 - - + -
151B ALA* 3.0 34.9 + - + +
153B LEU* 3.7 24.0 - - + -
161B LEU* 3.9 26.5 - - + -
168B ILE* 4.0 13.0 - - + -
169B ALA 3.9 3.6 - - - -
178B PHE* 1.3 78.7 - - - +
180B ALA* 1.3 58.0 + - - +
181B ALA* 3.5 16.4 - - - +
182B VAL* 3.3 26.0 - - + -
191B GLN* 3.5 17.8 - - - +
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 4.6 0.2 - - - -
127B CYS* 4.5 13.9 - - - -
145B PHE* 3.8 18.2 - - + -
169B ALA 2.8 16.3 + - - +
170B LYS 4.3 0.9 - - - -
171B ALA* 3.7 27.1 - - + +
178B PHE* 3.3 3.5 + - - -
179B ILE* 1.3 73.7 - - - +
181B ALA* 1.3 63.3 + - - +
190B THR* 3.5 1.4 - - - -
191B GLN* 2.8 30.9 + - - +
192B PHE* 3.7 7.3 - - + -
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 4.2 1.6 - - - -
134B PHE* 3.9 5.6 - - + -
137B LEU* 3.8 17.0 - - + -
168B ILE* 3.6 1.0 - - - -
169B ALA* 2.8 43.7 + - + -
179B ILE* 3.4 10.5 - - - +
180B ALA* 1.3 83.6 - - - +
182B VAL* 1.3 64.8 + - - +
188B PHE* 4.5 0.2 - - + -
189B ALA 3.1 15.5 - - - +
190B THR* 4.3 9.0 - - + -
192B PHE* 4.6 2.2 - - + -
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 4.7 4.3 - - + -
89B LEU* 4.2 10.5 - - + -
90B PHE* 4.7 3.8 - - + -
105B ILE* 4.2 16.4 - - + -
134B PHE* 3.7 1.8 - - - -
166B TRP* 3.9 23.8 - - + -
167B LYS 3.4 6.5 - - - +
168B ILE* 3.6 14.6 - - + -
179B ILE* 3.3 28.5 - - + -
181B ALA* 1.3 72.2 - - - +
183B ASN* 1.3 65.1 + - - +
187B ILE* 4.9 0.4 - - + -
188B PHE* 3.3 9.1 - - - -
189B ALA* 2.9 46.6 + - + +
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Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 3.7 35.6 - - + +
135B PHE* 3.6 30.3 - - - -
165B GLY 4.4 0.3 - - - +
166B TRP* 4.1 1.8 - - - -
167B LYS* 2.7 47.7 + - + +
182B VAL* 1.3 78.9 - - - +
184B LYS* 1.3 63.9 + - - +
185B ASN 3.7 14.8 + - - -
186B ASN 5.0 0.2 - - - -
187B ILE 2.7 29.3 + - - -
188B PHE* 4.2 0.6 - - + +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ASP* 3.0 38.2 + - - +
165B GLY* 3.4 17.5 - - - +
166B TRP* 3.4 44.4 - - + +
183B ASN* 1.3 75.6 - - - +
185B ASN* 1.3 91.7 + - - +
186B ASN 3.0 0.9 + - - -
187B ILE* 2.9 27.0 + - + +
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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