Contacts of the strand formed by residues 176 - 180 (chain B) in PDB entry 3UXA
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 ILE 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 5.0 12.1 - - + -
34B ARG* 3.5 39.0 - - + +
37B ILE* 4.9 4.0 - - + -
129B THR* 5.7 0.2 - - + -
155B GLU* 3.3 29.4 - - + +
156B PRO 3.6 15.9 + - - +
157B ALA* 3.6 12.7 - - + +
158B ILE* 2.8 31.9 + - - +
175B ARG* 1.3 79.4 - - - +
177B ILE* 1.3 66.6 + - - +
178B ILE* 5.7 0.2 - - + -
206B VAL* 3.3 27.8 - - + +
208B VAL* 4.6 12.8 - - + -
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 3.3 11.2 - - + +
160B ILE* 3.7 34.5 - - + -
166B LEU* 4.4 11.4 - - + -
169B ALA* 4.1 13.7 - - + -
170B LEU* 5.1 5.2 - - + -
174B ALA* 3.6 23.1 - - + -
176B ILE* 1.3 81.4 - - - +
178B ILE* 1.3 66.0 + - - +
179B ILE* 3.8 9.3 - - + +
201B ILE* 4.2 15.9 - - + -
205B VAL* 3.6 22.9 - - + -
206B VAL 2.8 9.5 + - - +
207B LYS* 3.4 4.1 - - - -
208B VAL* 2.9 27.0 + - - +
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Residues in contact with ILE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 6.3 0.7 - - + -
49B ILE* 6.2 2.5 - - + -
81B VAL* 5.7 3.4 - - + -
108B LEU* 4.3 11.9 - - + -
110B TRP* 5.1 7.6 - - + +
131B GLY* 5.7 0.2 - - - -
157B ALA* 3.6 27.1 - - + -
158B ILE 2.7 11.8 + - - +
159B VAL* 3.4 23.4 - - + +
160B ILE 2.8 33.1 + - - +
176B ILE* 4.2 0.8 - - + -
177B ILE* 1.3 73.7 - - - +
179B ILE* 1.3 57.8 + - - +
180B SER* 3.6 1.9 + - - +
208B VAL* 3.4 25.1 - - + +
210B ALA* 3.4 33.0 - - + -
231B GLU* 3.6 15.7 - - + +
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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
----------------------------------------------------------
160B ILE* 3.6 12.8 - - + -
177B ILE* 3.8 6.7 - - + +
178B ILE* 1.3 70.3 - - - +
180B SER* 1.3 60.4 + - - +
194B GLN* 2.9 40.8 - - + +
197B LEU* 3.9 33.4 - - + -
198B ILE* 4.0 15.7 - - + -
201B ILE* 3.7 25.6 - - + -
207B LYS* 3.5 31.9 - - + -
208B VAL 3.0 17.6 + - - +
209B ALA* 3.7 1.9 - - - +
210B ALA 2.9 16.6 + - - -
227B VAL* 6.0 0.2 - - + -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B VAL* 5.0 11.2 - - - -
160B ILE 2.9 13.9 + - - -
161B ASN* 3.1 29.6 - - - +
178B ILE* 3.6 2.5 + - - -
179B ILE* 1.3 76.5 - - - +
181B SER* 1.3 57.3 + - - +
182B ARG* 3.0 20.5 + - - +
193B ASN* 5.0 0.9 + - - -
194B GLN* 3.7 3.6 - - - +
210B ALA* 3.6 13.0 - - - -
211B SER* 2.5 25.0 + - - -
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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