Contacts of the strand formed by residues 167 - 173 (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 LYS 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B ASN* 3.9 38.0 - - + +
133B LEU 5.0 5.2 + - - +
134B PHE* 3.6 24.5 - - + +
162B GLU* 6.2 0.2 - - - +
165B GLY 3.9 2.9 + - - +
166B TRP* 1.3 76.3 - - - +
168B ILE* 1.3 62.7 + - - +
182B VAL* 3.4 5.4 - - - -
183B ASN* 2.7 49.6 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B SER* 4.9 7.1 + - - -
132B ASN* 4.7 6.3 + - - +
133B LEU* 4.7 5.0 - - - +
134B PHE* 4.2 4.2 - - - -
153B LEU* 4.4 6.1 - - + -
158B LYS* 5.9 3.8 - - + +
161B LEU* 3.7 38.4 - - + -
162B GLU 5.9 0.2 - - - +
166B TRP* 3.9 13.4 + - + +
167B LYS* 1.3 85.1 - - - +
169B ALA* 1.3 74.5 + - - +
170B LYS* 3.7 22.6 + - + +
179B ILE* 4.0 19.5 - - + -
181B ALA 3.6 2.7 - - - +
182B VAL* 3.6 24.9 - - + -
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Residues in contact with ALA 169 (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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127B CYS* 4.3 9.6 - - - -
133B LEU* 3.9 20.2 - - + -
134B PHE* 3.9 5.0 - - + -
137B LEU* 3.7 18.2 - - + -
168B ILE* 1.3 75.6 - - - +
170B LYS* 1.3 59.8 + - - +
180B ALA* 2.8 26.4 + - - -
181B ALA* 2.8 35.9 + - + +
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Residues in contact with LYS 170 (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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127B CYS* 3.1 6.9 - - - -
128B ILE* 2.6 63.5 + - + +
129B PRO 5.0 1.4 + - - -
130B SER* 4.9 14.5 - - - -
133B LEU* 5.2 0.4 - - - +
153B LEU* 4.2 4.9 - - + -
158B LYS* 3.6 21.8 - - + +
168B ILE* 3.7 22.6 + - + +
169B ALA* 1.3 75.1 - - - +
171B ALA* 1.3 58.0 + - - +
177B GLU* 3.5 28.0 - - - +
178B PHE 3.6 7.6 - - - +
180B ALA* 4.3 0.7 - - - -
803B SO4 2.9 24.6 + - - +
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Residues in contact with ALA 171 (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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125B ASN* 4.7 3.4 - - - -
126B SER 3.3 21.5 - - - +
128B ILE* 4.1 5.8 - - - -
145B PHE* 4.5 4.9 - - + -
170B LYS* 1.3 73.8 - - - +
172B LYS* 1.3 61.9 + - - +
177B GLU* 3.4 5.5 - - - +
178B PHE* 2.9 55.5 + - + -
180B ALA* 3.7 17.3 - - + -
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Residues in contact with LYS 172 (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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125B ASN* 3.0 17.4 + - - +
128B ILE* 4.3 9.4 - - + -
171B ALA* 1.3 77.2 - - - +
173B TYR* 1.3 60.6 + - - +
174B GLY 3.5 22.0 - - - +
175B SER* 4.2 13.7 - - - +
176B GLU 3.2 17.3 - - - +
177B GLU* 4.3 14.6 - - + +
178B PHE* 3.9 0.2 - - - -
231B TYR* 3.2 58.6 + - + +
234B TYR 3.6 2.6 - - - +
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Residues in contact with TYR 173 (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* 4.1 16.4 - + + -
117B LYS* 3.1 42.6 - - + -
118B PRO* 2.4 49.6 + - - +
119B VAL* 4.8 0.4 - - + -
120B PRO 4.3 0.5 + - - -
121B GLU* 3.4 52.5 - - + +
122B ILE 5.2 0.2 + - - -
125B ASN* 4.0 0.4 - - - +
172B LYS* 1.3 71.9 - - - +
174B GLY* 1.3 64.3 + - - +
176B GLU* 2.9 18.8 + - - +
178B PHE* 3.7 12.2 - - + -
234B TYR* 3.5 30.6 - + + -
236B LEU* 3.6 24.2 - - + +
495B PRO* 5.8 0.3 - - - +
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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
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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