Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 1BQS
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A THR* 3.1 1.8 - - - -
114A ALA* 2.8 35.3 + - + -
117A VAL* 4.2 9.6 - - + -
120A VAL* 3.6 38.8 - - + +
125A LEU* 4.3 14.8 - - + -
127A PHE* 3.8 21.2 - - + -
143A GLY* 5.0 3.8 - - - +
144A PRO 3.4 13.9 - - - +
145A GLU* 4.3 13.9 - - + -
161A PHE* 4.1 0.4 - - + -
162A ARG* 1.3 76.0 - - - +
164A THR* 1.3 71.0 + - - +
165A GLU* 5.9 0.2 - - + -
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Residues in contact with THR 164 (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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111A ALA* 4.0 24.2 - - + -
112A CYS 3.4 9.6 - - - +
113A THR* 2.8 26.8 + - + +
127A PHE* 5.1 0.2 - - - -
143A GLY* 3.3 4.2 - - - -
144A PRO* 2.4 51.2 + - + +
146A VAL* 5.5 3.3 - - - +
162A ARG* 4.0 4.9 + - - +
163A VAL* 1.3 78.6 - - - +
165A GLU* 1.3 65.7 + - - +
166A ARG* 4.3 8.1 - - + -
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Residues in contact with GLU 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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111A ALA* 3.3 1.2 - - - -
112A CYS 2.8 30.5 + - - -
127A PHE* 3.7 36.1 + - + +
141A ALA* 4.1 11.1 - - - +
142A LEU 2.9 47.3 + - - +
143A GLY* 4.1 5.9 + - - -
164A THR* 1.3 76.0 - - - +
166A ARG* 1.3 66.5 + - - +
167A TRP* 3.5 35.0 + - + -
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Residues in contact with ARG 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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109A GLU* 2.5 45.9 + - - +
110A VAL 3.4 5.6 - - - +
111A ALA* 4.2 7.0 - - + +
141A ALA* 3.2 26.7 + - - -
142A LEU* 3.5 37.7 + - + +
144A PRO* 5.0 8.5 - - + -
164A THR* 4.3 14.1 - - + -
165A GLU* 1.3 85.1 + - - +
167A TRP* 1.3 65.9 + - - +
168A ARG* 5.4 11.5 - - - +
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Residues in contact with TRP 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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109A GLU* 2.8 29.4 + - - +
110A VAL* 2.9 35.5 + - + +
112A CYS* 3.7 17.7 - - + -
127A PHE* 3.6 26.0 - + + -
128A SER* 3.8 29.6 - - - +
129A LEU* 3.8 29.1 - - + +
139A ALA* 3.8 19.4 - - + +
140A GLN 3.0 32.2 + - - -
141A ALA* 4.6 3.2 - - - +
165A GLU* 3.5 46.2 - - + +
166A ARG* 1.3 76.8 - - - +
168A ARG* 1.3 62.6 + - - +
169A LEU* 3.4 2.1 + - + +
182A CYS* 4.4 4.3 - - + -
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Residues in contact with ARG 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 PRO 4.7 4.0 - - - +
109A GLU* 3.8 23.5 + - + +
138A GLY 3.9 2.6 - - - +
139A ALA* 3.7 6.2 - - - -
140A GLN* 3.4 52.9 + - + +
141A ALA 4.8 0.6 - - - +
166A ARG* 5.4 10.3 - - - +
167A TRP* 1.3 69.8 - - - +
169A LEU* 1.3 63.4 + - - +
170A PRO 3.8 0.2 - - - -
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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