Contacts of the strand formed by residues 167 - 176 (chain A) in PDB entry 1BZH
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 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.4 18.6 - - + -
161A GLU* 3.3 4.0 - - - +
162A ASN* 2.8 28.8 + - - -
165A THR* 3.1 24.3 + - - +
166A GLN* 1.3 80.0 - - - +
168A THR* 1.3 68.4 + - - +
169A ARG* 3.1 31.0 + - + +
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Residues in contact with THR 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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100A TRP* 4.3 0.9 - - - -
159A GLU* 4.0 25.6 + - - +
160A LEU 3.3 5.6 - - - -
161A GLU* 3.5 32.8 - - + +
166A GLN 5.0 2.2 - - - +
167A GLU* 1.3 84.1 - - - +
169A ARG* 1.3 66.2 + - - +
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Residues in contact with ARG 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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99A VAL 4.5 0.4 + - - -
100A TRP* 2.5 71.2 + - + +
103A LYS* 3.8 40.1 - - - +
104A SER 5.4 4.0 + - - -
159A GLU* 3.4 7.3 - - - +
160A LEU* 2.8 30.6 + - - +
167A GLU* 3.1 26.7 + - + +
168A THR* 1.3 78.0 - - - +
170A GLU* 1.3 61.7 + - - +
171A ILE* 4.4 17.3 - - + -
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Residues in contact with GLU 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 ARG* 2.6 60.1 + - - +
157A GLN* 2.4 38.8 - - + +
158A LEU 3.3 11.0 - - - +
159A GLU* 4.7 1.3 - - + +
169A ARG* 1.3 75.3 - - - +
171A ILE* 1.3 68.1 + - - +
172A LEU* 3.3 16.1 - - + +
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Residues in contact with ILE 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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96A TRP* 4.1 13.0 - - + -
99A VAL* 3.7 15.5 - - + -
100A TRP* 6.2 0.2 - - - -
104A SER 3.5 23.1 - - - +
105A ARG 3.5 10.1 - - - +
107A VAL* 3.9 24.2 - - + -
156A ARG 3.7 0.3 - - - +
157A GLN* 3.9 1.0 - - - -
158A LEU* 2.7 46.6 + - + +
160A LEU* 3.9 31.6 - - + +
169A ARG* 4.4 14.4 - - + +
170A GLU* 1.3 80.4 - - - +
172A LEU* 1.3 75.1 + - - +
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Residues in contact with LEU 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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105A ARG* 2.8 38.4 + - - +
106A GLY* 3.2 3.1 - - - -
107A VAL 3.0 25.5 + - - +
155A VAL* 4.7 7.6 - - + -
156A ARG 3.4 9.0 - - - +
157A GLN* 4.5 7.9 - - + +
170A GLU* 3.3 32.5 - - + +
171A ILE* 1.3 75.5 - - - +
173A HIS* 1.3 61.7 + - - +
174A PHE* 3.6 18.9 + - + -
201A SER* 3.7 31.2 - - - +
203A SER* 4.0 5.6 - - - +
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Residues in contact with HIS 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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96A TRP* 4.9 0.2 - + - -
107A VAL* 3.5 27.5 - - + +
109A MET* 4.0 19.2 - - + +
124A TYR* 2.6 31.8 + + - -
125A TRP* 3.9 19.6 - + - -
154A THR 3.3 2.8 - - - +
155A VAL* 3.3 6.3 - - - -
156A ARG* 2.7 81.3 + - + +
158A LEU* 3.8 21.8 - - + -
171A ILE 3.7 0.6 + - - -
172A LEU* 1.3 73.1 - - - +
174A PHE* 1.3 60.1 + - - +
175A HIS* 4.3 3.3 - - + +
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Residues in contact with PHE 174 (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 GLY* 4.8 1.8 - - - -
107A VAL 2.7 18.3 + - - +
108A VAL* 3.3 5.6 - - + -
109A MET* 2.7 34.6 + - - +
153A TYR* 5.0 0.7 - + - -
154A THR 3.7 2.0 - - - -
155A VAL* 3.7 33.2 - - + -
172A LEU* 3.6 23.1 - - + -
173A HIS* 1.3 72.5 - - - +
175A HIS* 1.3 54.2 + - - +
194A PHE* 3.6 24.0 - + + -
197A LYS* 3.9 24.0 - - + -
198A VAL* 3.7 28.5 - - + -
201A SER* 3.2 27.4 - - - -
203A SER* 3.5 24.5 - - - -
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Residues in contact with HIS 175 (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 MET* 3.4 27.7 - - + -
111A ASN 2.4 31.5 + - - -
112A ARG* 4.1 10.5 - - + +
113A VAL 5.2 0.4 - - - -
125A TRP* 3.8 13.7 - + - -
154A THR* 2.9 35.6 + - - +
156A ARG* 3.3 40.0 + - - +
173A HIS* 3.8 3.6 + - + +
174A PHE* 1.3 71.6 - - - +
176A TYR* 1.3 73.0 + - - +
177A THR* 3.0 23.8 + - + +
194A PHE* 3.8 4.6 - - - -
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Residues in contact with TYR 176 (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 MET 2.9 13.4 + - - +
110A LEU* 3.9 20.9 - - + +
111A ASN 3.9 2.6 - - - +
112A ARG* 5.3 0.2 + - - -
152A TYR* 3.4 15.5 - + - -
153A TYR* 3.9 0.2 - - - -
175A HIS* 1.3 78.5 - - - +
177A THR* 1.3 59.8 + - - +
178A THR* 3.5 17.2 + - - -
179A TRP* 3.2 59.7 + + + +
185A PRO* 3.7 20.3 - - - +
190A SER* 3.6 19.8 - - - -
191A PHE* 3.7 28.7 + + + -
194A PHE* 3.4 43.5 - + + -
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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