Contacts of the strand formed by residues 163 - 171 (chain A) in PDB entry 4A12
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 HIS 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS* 3.1 29.8 + + + -
159A GLN* 3.4 2.1 - - - -
160A THR* 2.8 47.0 + - - +
162A LYS* 1.4 97.3 - - + +
164A TYR* 1.3 58.8 + - - +
165A TYR* 4.1 18.0 + - + -
183A LYS* 3.6 40.6 - - + -
184A MSE 3.3 3.8 - - - +
185A PHE* 3.7 24.6 - + + +
186A TYR* 3.4 8.5 - - - -
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Residues in contact with TYR 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.4 42.7 + - + +
126A ILE* 3.7 42.4 - - + -
128A GLN* 4.0 10.1 + - + -
156A VAL* 3.7 26.0 - - + -
158A ASN 3.7 1.8 - - - -
159A GLN* 3.0 37.9 + - + -
163A HIS* 1.3 70.9 - - - +
165A TYR* 1.3 62.0 + - - +
166A VAL* 3.8 1.9 + - + -
182A PHE 3.5 1.9 - - - +
183A LYS* 3.8 1.2 - - - -
184A MSE 2.7 39.1 + - + +
186A TYR* 3.4 46.9 - + + -
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Residues in contact with TYR 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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156A VAL* 3.5 3.5 - - - -
157A VAL* 2.7 35.5 + - + -
158A ASN* 2.7 48.0 + - + +
159A GLN 4.4 0.7 - - - -
160A THR* 3.6 29.0 + - + +
163A HIS* 4.1 17.3 + - + +
164A TYR* 1.3 73.9 - - - +
166A VAL* 1.3 55.3 + - - +
182A PHE 3.4 6.7 - - - +
183A LYS* 3.6 46.6 + - + -
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Residues in contact with VAL 166 (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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122A CYS* 3.7 27.1 - - - -
125A LEU* 3.8 7.9 - - + -
126A ILE* 3.8 28.5 - - + -
154A ALA* 3.8 21.8 - - + -
155A ARG 3.4 11.0 - - - +
156A VAL* 4.4 11.4 - - + -
157A VAL* 4.6 0.4 - - - -
164A TYR 4.3 2.9 - - - +
165A TYR* 1.3 77.1 - - - +
167A GLU* 1.3 65.3 + - - +
180A GLY 3.9 0.3 - - - +
181A ASN* 3.4 3.8 - - - +
182A PHE* 2.7 43.3 + - + +
184A MSE 4.0 11.2 - - + -
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Residues in contact with GLU 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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153A GLU 3.7 2.1 - - - +
154A ALA* 3.4 1.2 - - - -
155A ARG* 2.9 42.2 + - + +
157A VAL* 3.6 34.9 - - + +
166A VAL* 1.3 71.9 - - - +
168A VAL* 1.3 61.4 + - - +
169A LYS* 3.5 25.4 + - - +
179A LYS* 6.5 0.4 - - + -
180A GLY 3.4 3.6 - - - +
181A ASN* 3.3 27.0 - - - +
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Residues in contact with VAL 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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118A ALA* 3.9 25.6 - - + +
121A LEU* 4.7 2.2 - - + -
122A CYS* 3.7 30.1 - - - -
152A ALA* 4.5 6.7 - - + -
153A GLU 3.4 12.3 - - - +
154A ALA* 3.8 11.0 - - + -
166A VAL* 4.3 1.1 - - + -
167A GLU* 1.3 75.0 - - - +
169A LYS* 1.3 66.2 + - - +
170A SER* 4.1 14.8 - - - +
178A PHE* 4.5 2.7 - - + -
179A LYS* 3.4 6.3 - - - +
180A GLY 2.7 38.2 + - - +
182A PHE* 3.8 19.3 - - + -
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Residues in contact with LYS 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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153A GLU* 2.9 41.4 + - + +
155A ARG* 3.2 30.2 - - - +
167A GLU* 3.5 24.7 + - - +
168A VAL* 1.3 77.6 - - - +
170A SER* 1.3 62.4 + - - +
171A TYR* 3.4 32.4 - - + +
176A LEU* 3.8 14.6 - - + -
178A PHE 3.6 4.0 - - - -
179A LYS* 4.3 22.8 - - + +
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Residues in contact with SER 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 LEU* 4.8 3.7 + - - +
117A GLN* 4.4 2.1 + - - -
118A ALA* 5.3 0.9 - - - +
150A VAL* 3.6 22.2 - - - +
151A ARG 3.4 4.5 - - - -
152A ALA* 3.3 20.1 - - - +
168A VAL* 4.1 3.5 - - - +
169A LYS* 1.3 72.7 - - - +
171A TYR* 1.3 61.0 + - - +
176A LEU* 3.6 5.5 - - - +
177A VAL* 3.0 24.9 + - - -
178A PHE* 2.9 41.8 + - - +
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Residues in contact with TYR 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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149A THR 3.7 0.7 - - - +
150A VAL* 3.5 4.7 - - - -
151A ARG* 2.8 76.0 + - - +
153A GLU* 3.3 25.6 + - + -
169A LYS* 3.4 43.9 - - + +
170A SER* 1.3 73.8 - - - +
172A VAL* 1.3 64.5 + - - +
173A LYS 4.0 5.8 - - - +
174A HIS* 4.7 3.1 - - - -
175A THR 3.3 12.8 - - - +
176A LEU* 3.5 40.0 - - + +
177A VAL* 4.1 0.7 - - - -
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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