Contacts of the strand formed by residues 167 - 172 (chain A) in PDB entry 1UXI
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 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ARG* 2.7 61.4 + - + +
156A ILE* 3.7 25.6 - - + -
157A ALA* 4.0 22.4 - - + +
162A VAL* 4.1 13.9 - - + -
163A SER 3.8 13.9 - - - +
164A VAL* 3.2 9.0 + - - +
165A LYS 3.5 0.7 - - - -
166A ASP* 1.3 81.8 - - - +
168A GLN* 1.3 64.9 - - - +
187A THR 3.6 4.9 - - - +
188A ILE* 4.2 9.4 - - + -
193A VAL* 5.2 0.2 - - + -
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Residues in contact with GLN 168 (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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153A ARG* 4.0 7.6 - - - +
166A ASP 5.1 4.3 - - - +
167A VAL* 1.3 80.5 - - - +
169A ALA* 1.3 65.3 + - - +
185A PHE 4.9 0.4 - - - +
186A SER* 3.3 1.6 - - - -
187A THR* 2.8 50.0 + - - +
189A SER 6.2 0.4 - - - +
190A GLY* 5.6 1.7 + - - -
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Residues in contact with ALA 169 (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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149A ALA* 3.4 20.2 - - - +
152A TYR* 3.2 40.6 - - + -
153A ARG* 3.7 18.4 - - + +
156A ILE* 4.8 2.2 - - + -
168A GLN* 1.3 78.5 - - - +
170A MET* 1.3 62.6 + - - +
185A PHE 3.8 2.7 - - - -
186A SER* 3.5 7.9 - - - -
249A PRO* 5.4 2.3 - - - +
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Residues in contact with MET 170 (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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152A TYR* 4.8 1.6 - - - -
169A ALA* 1.3 76.6 - - - +
171A LEU* 1.3 68.2 + - - +
172A MET* 4.5 2.9 - - + -
181A PRO* 4.4 0.2 - - - +
182A LEU* 3.2 33.1 + - + +
185A PHE* 3.2 29.2 + - + +
247A VAL* 4.5 16.6 - - + +
248A MET* 4.4 4.0 - - - -
249A PRO* 3.7 35.2 - - + -
268A PRO* 3.4 29.2 - - + -
282A LEU* 4.2 23.3 - - + -
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Residues in contact with LEU 171 (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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145A GLY* 4.6 5.5 - - - +
148A ASP* 3.6 24.7 - - + +
149A ALA* 4.0 18.8 - - + +
152A TYR* 5.0 2.9 - - + -
169A ALA 3.9 0.6 + - - -
170A MET* 1.3 79.5 - - - +
172A MET* 1.3 74.0 - - - +
173A GLY 5.6 1.8 - - - +
179A MET* 3.5 25.1 - - + -
180A VAL 3.7 4.5 - - - +
181A PRO* 3.1 43.5 - - + -
182A LEU* 4.8 0.4 - - - -
209A THR* 4.0 17.0 - - + -
249A PRO* 3.2 26.2 - - + +
266A GLY* 5.0 0.7 - - - -
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Residues in contact with MET 172 (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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170A MET* 4.5 3.6 - - + -
171A LEU* 1.3 85.1 - - - +
173A GLY* 1.3 63.4 + - - +
179A MET* 3.9 0.5 - - - -
180A VAL* 2.8 40.8 + - + +
182A LEU* 3.9 25.7 - - + +
258A TYR* 3.4 39.9 - - + +
266A GLY* 3.4 14.4 - - - +
267A VAL* 4.1 4.3 - - + -
268A PRO* 3.8 24.7 - - + -
282A LEU* 4.0 13.0 - - - -
284A LEU* 4.2 10.5 - - - -
292A LEU* 3.9 26.2 - - + -
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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