Contacts of the strand formed by residues 164 - 171 (chain A) in PDB entry 2UYC
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LYS* 3.2 54.7 + - + +
151A VAL* 4.4 7.4 - - + -
152A LEU 3.6 4.3 - - - -
153A ASN* 3.2 30.6 - - + +
162A LYS* 2.9 40.6 + - - +
163A ASN* 1.3 70.7 - - - +
165A ARG* 1.3 87.3 + - - +
250A THR* 4.7 1.4 + - - -
426D G 6.1 0.9 - - - +
427D C 4.6 1.3 + - - +
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Residues in contact with ARG 165 (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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119A GLU* 3.3 22.6 + - + +
120A ASN 3.4 11.4 - - - +
121A VAL* 3.6 14.9 - - - +
122A LYS 4.0 2.5 - - - +
151A VAL* 3.1 8.3 - - - +
152A LEU 2.8 32.4 + - - -
163A ASN* 3.3 33.1 - - - +
164A GLU* 1.3 103.0 + - - +
166A ILE* 1.3 59.8 + - - +
167A TYR* 3.4 27.1 - - + +
250A THR* 3.2 24.9 - - - +
251A LEU 4.5 1.6 + - - -
303A GLY 5.0 0.6 + - - -
305A SER 5.1 0.4 + - - -
306A VAL* 6.4 1.6 - - + -
427D C 2.8 66.3 + - - -
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 3.5 5.5 - - - +
120A ASN* 2.9 47.4 + - + +
121A VAL 3.6 15.9 - - - +
122A LYS* 4.5 0.2 - - - +
124A PHE* 4.0 9.9 - - + -
125A ALA* 4.4 15.0 - - + -
133A LEU* 4.8 6.7 - - + -
149A ALA* 3.9 9.6 - - + -
150A LYS* 3.3 39.5 - - - +
151A VAL* 3.6 16.4 - - + +
165A ARG* 1.3 72.7 - - - +
167A TYR* 1.3 60.6 + - - +
168A MET* 4.1 23.6 + - + +
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Residues in contact with TYR 167 (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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117A PHE* 4.2 9.2 - + + -
118A MET 3.6 2.2 - - - +
119A GLU* 3.9 20.3 - - + +
148A HIS 3.5 1.4 - - - +
149A ALA* 3.1 4.7 - - - -
150A LYS 2.9 32.8 + - - +
152A LEU* 3.6 37.4 + - + -
163A ASN* 4.1 7.6 + - - -
165A ARG* 3.4 39.2 - - + +
166A ILE* 1.3 72.3 - - - +
168A MET* 1.3 61.5 + - - +
169A ILE* 4.1 1.1 - - + -
182A PHE* 3.6 12.0 - - + -
306A VAL* 5.6 1.4 - - + +
307A VAL* 5.1 6.4 + - - +
310A VAL* 3.6 22.8 - - + +
311A LEU* 3.6 27.3 - - + +
314A ILE* 3.5 25.4 - - + -
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Residues in contact with MET 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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79A PHE* 3.9 33.0 - - + -
116A VAL 3.4 4.7 - - - +
117A PHE* 3.5 1.4 - - - -
118A MET* 2.9 58.4 + - + +
119A GLU 4.3 1.6 - - - +
120A ASN* 4.4 2.0 - - + -
124A PHE* 4.2 7.2 - - + -
133A LEU* 4.0 13.7 - - - -
136A VAL* 4.1 13.2 - - - -
147A PHE* 3.7 38.1 - - + -
148A HIS 3.2 3.8 - - - -
149A ALA* 3.9 7.9 - - + -
166A ILE* 4.1 24.2 - - + +
167A TYR* 1.3 77.6 - - - +
169A ILE* 1.3 63.8 + - - +
170A CYS* 4.1 2.0 - - - -
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Residues in contact with ILE 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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115A VAL* 4.0 6.5 - - + -
116A VAL 3.5 1.6 - - - -
117A PHE* 3.2 40.4 - - + -
148A HIS* 2.8 39.2 + - + +
167A TYR* 4.7 2.0 - - + -
168A MET* 1.3 77.7 - - - +
170A CYS* 1.3 63.2 + - - +
171A PHE* 3.7 24.7 - - + -
180A PHE* 3.4 32.1 - - + -
182A PHE* 4.2 10.3 - - + -
314A ILE* 3.6 11.7 - - + -
318A ILE* 3.7 23.6 - - + -
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Residues in contact with CYS 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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114A LYS 3.7 0.3 - - - +
115A VAL* 3.2 9.1 - - - +
116A VAL* 2.8 48.2 + - + +
118A MET* 4.1 10.5 - - - -
140A MET* 3.8 19.3 - - + -
145A TYR* 3.9 15.6 - - + -
146A SER 3.2 12.8 - - - +
147A PHE* 3.6 31.9 - - - -
168A MET 4.4 1.1 - - - -
169A ILE* 1.3 80.6 - - - +
171A PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 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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114A LYS 3.6 2.0 - - - -
115A VAL* 3.7 28.0 - - + -
145A TYR* 3.2 2.9 - - - -
146A SER* 2.8 47.6 + - - +
148A HIS* 3.9 11.9 - + - -
169A ILE* 3.7 16.8 - - + -
170A CYS* 1.3 74.1 - - - +
172A ARG* 1.3 67.7 + - - +
173A ASN* 3.1 1.0 + - - +
175A LEU* 4.9 1.1 - - + -
177A ILE* 3.5 43.5 - - + +
180A PHE* 3.5 45.3 - + + -
318A ILE* 4.1 13.9 - - + -
321A SER* 4.4 1.8 - - - -
322A LEU* 3.8 16.2 - - + -
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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