Contacts of the strand formed by residues 167 - 173 (chain A) in PDB entry 3R27
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLY 5.6 1.8 - - - +
110A ILE* 3.4 46.3 - - + +
163A TYR* 3.7 3.4 - - - -
164A ILE* 2.9 31.8 + - - +
165A ALA 2.7 24.5 + - - -
166A GLY* 1.3 85.4 + - - +
168A PRO* 1.4 75.6 - - + +
169A ALA* 3.6 1.0 + - - +
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Residues in contact with PRO 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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108A GLY* 3.4 16.6 - - - +
161A GLN* 3.6 28.9 - - + +
162A ILE 3.4 7.9 - - - +
163A TYR* 3.6 16.8 - - + -
166A GLY 4.5 1.3 - - - +
167A HIS* 1.4 91.7 - - + +
169A ALA* 1.3 58.0 + - - +
170A PHE* 5.4 4.7 - - + -
124B GLU 5.7 0.3 - - - +
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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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106A ILE* 3.8 21.8 - - + -
107A ARG 3.5 13.0 - - - +
108A GLY 4.7 1.3 - - - +
109A LEU* 4.4 7.0 - - + -
157A ALA* 6.0 0.9 - - - +
161A GLN* 2.8 18.9 + - - -
162A ILE* 2.8 21.5 + - + +
164A ILE* 3.9 19.5 - - + -
167A HIS 4.5 0.9 - - - +
168A PRO* 1.3 75.4 - - - +
170A PHE* 1.3 69.0 + - - +
171A VAL* 4.7 1.7 - - - +
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Residues in contact with PHE 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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105A HIS 3.6 1.1 - - - +
106A ILE* 3.3 5.4 - - - +
107A ARG* 2.8 64.9 + - - +
108A GLY* 5.5 0.2 - - - -
157A ALA* 6.0 0.4 - - - -
161A GLN* 4.9 15.0 - - - -
168A PRO* 5.4 3.4 - - + -
169A ALA* 1.3 79.2 - - - +
171A VAL* 1.3 65.4 + - - +
123B GLN* 3.3 61.2 - - + -
124B GLU* 3.7 19.1 - - - -
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Residues in contact with VAL 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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104A VAL* 3.9 22.4 - - + -
105A HIS 3.4 3.4 - - - +
106A ILE* 3.7 33.7 - - + -
107A ARG* 4.4 2.4 + - - +
122A LEU* 5.1 0.9 - - + -
153A ALA* 4.7 12.3 - - + +
154A VAL* 4.6 13.0 - - + +
157A ALA* 3.9 25.6 - - + +
162A ILE* 3.7 35.0 - - + -
169A ALA 4.7 0.4 - - - +
170A PHE* 1.3 83.3 - - - +
172A ASN* 1.3 64.1 + - - +
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Residues in contact with ASN 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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98A THR* 3.1 31.2 + - - +
104A VAL* 3.5 2.3 - - - -
105A HIS* 2.7 37.9 + - + +
107A ARG* 4.4 15.7 - - - +
154A VAL* 4.0 16.9 - - - +
171A VAL* 1.3 75.4 - - - +
173A TYR* 1.3 91.9 + - - +
120B GLU* 6.0 0.4 + - - -
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Residues in contact with TYR 173 (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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98A THR* 3.7 28.4 - - + +
99A PRO 3.4 25.6 - - - +
100A ALA* 3.8 19.4 - - + +
101A SER 3.4 26.9 - - - +
103A VAL 3.7 4.0 - - - +
104A VAL* 4.2 2.0 - - + +
105A HIS* 4.8 1.0 - - - +
147A VAL 5.1 0.4 - - - -
150A ALA* 3.8 16.6 - - + -
151A CYS* 3.3 31.0 + - - +
154A VAL* 3.6 36.9 - - + +
155A ASN* 4.7 1.9 + - - -
172A ASN* 1.3 98.6 + - - +
174A SER* 1.3 65.3 + - - +
175A THR* 4.1 0.5 + - - +
182A GOL 4.2 4.7 + - - -
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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