Contacts of the strand formed by residues 167 - 173 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B GLY 5.4 1.7 - - - +
110B ILE* 3.5 47.6 - - + +
163B TYR* 3.6 4.0 - - - -
164B ILE* 2.9 30.4 + - - +
165B ALA 2.8 25.5 + - - -
166B GLY* 1.3 84.1 - - - +
168B PRO* 1.4 76.7 - - + +
169B ALA* 4.4 1.6 - - - +
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Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLY* 3.4 15.9 - - - +
161B GLN* 3.4 26.2 - - + +
162B ILE 3.3 8.5 - - - +
163B TYR* 3.5 22.8 - - + -
166B GLY 4.5 1.1 - - - +
167B HIS* 1.4 91.6 - - + +
169B ALA* 1.3 57.7 - - - +
170B PHE* 5.4 5.2 - - + -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.9 13.0 - - + -
107B ARG 3.4 13.2 - - - +
108B GLY 4.6 1.8 - - - +
109B LEU* 4.5 6.1 - - + -
157B ALA* 6.0 0.9 - - - +
161B GLN* 3.0 17.4 + - - +
162B ILE* 2.8 22.0 + - + +
164B ILE* 3.8 28.7 - - + -
167B HIS 4.4 1.3 - - - +
168B PRO* 1.3 73.5 - - - +
170B PHE* 1.3 69.8 + - - +
171B VAL* 4.4 1.0 + - - -
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Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B HIS 3.6 1.0 - - - +
106B ILE* 3.3 5.2 - - - +
107B ARG* 2.8 73.1 + - + +
108B GLY* 5.5 2.9 - - - -
157B ALA* 6.1 0.4 - - - -
161B GLN* 3.8 24.0 - - - -
168B PRO* 5.4 4.5 - - + -
169B ALA* 1.3 76.6 - - - +
171B VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B VAL* 4.0 21.3 - - + -
105B HIS 3.4 3.1 - - - +
106B ILE* 3.7 32.5 - - + -
107B ARG* 4.3 0.6 - - - +
122B LEU* 5.2 0.9 - - + -
153B ALA* 4.8 12.6 - - + +
154B VAL* 4.5 12.4 - - + +
157B ALA* 3.9 24.0 - - + +
162B ILE* 3.7 33.4 - - + -
169B ALA 4.7 0.4 - - - +
170B PHE* 1.3 84.3 - - - +
172B ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR* 5.4 10.1 - - + +
104B VAL* 3.4 1.9 - - - -
105B HIS* 2.7 47.2 + - - +
107B ARG* 3.1 29.1 + - - +
154B VAL* 4.0 16.4 - - + -
171B VAL* 1.3 75.2 + - - +
173B TYR* 1.3 70.9 + - + +
182B GOL 4.9 2.8 + - - -
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B THR* 3.7 38.6 - - + +
99B PRO 3.5 24.7 - - - +
100B ALA* 3.8 20.7 - - + +
101B SER 3.3 31.0 - - - +
103B VAL 3.6 4.3 - - - +
104B VAL* 4.2 1.8 - - + +
147B VAL 5.1 0.2 - - - -
150B ALA* 3.9 2.5 - - + -
151B CYS* 3.3 42.7 + - - +
154B VAL* 3.7 36.3 - - + +
155B ASN* 4.5 2.6 + - - -
172B ASN* 1.3 85.7 - - + +
174B SER* 1.3 65.2 + - - +
175B THR 4.0 0.3 + - - -
182B GOL 4.2 4.9 + - - -
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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