Contacts of the strand formed by residues 123 - 130 (chain A) in PDB entry 4WB7
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ILE* 5.2 3.6 - - + +
114A LEU* 4.0 29.6 - - + +
115A VAL 3.3 14.1 - - - +
116A LYS* 3.9 24.5 - - + +
121A GLY 3.7 12.7 + - - -
122A ASN* 1.3 72.6 - - - +
124A TYR* 1.3 75.4 + - - +
177A TYR* 4.0 18.2 + - + +
376A PRO* 3.6 24.0 + - + -
377A GLY* 4.3 6.4 - - - -
507A ZN 2.3 38.1 - - - -
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Residues in contact with TYR 124 (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 PHE* 4.2 15.7 - + - -
114A LEU* 3.6 7.4 - - - +
115A VAL* 2.9 36.8 + - + +
117A HIS* 4.0 14.0 - + + -
120A THR* 4.8 1.0 + - - +
122A ASN* 3.7 44.1 + - + +
123A HIS* 1.3 79.4 - - - +
125A ALA* 1.3 59.8 + - - +
162A GLU* 4.0 30.3 - - + -
163A PHE* 3.8 23.3 - + - -
174A VAL* 3.5 19.7 - - + -
175A MET 3.4 15.9 - - - +
176A GLU* 4.4 4.3 - - + -
177A TYR* 3.7 8.7 - - - -
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Residues in contact with ALA 125 (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 LEU* 4.1 5.6 - - + -
112A VAL* 3.9 13.0 - - + -
113A MET 3.5 4.7 - - - -
124A TYR* 1.3 70.1 - - - +
126A MET* 1.3 61.5 + - - +
173A MET 3.5 2.4 - - - +
174A VAL* 4.5 0.7 - - - -
175A MET* 2.8 40.4 + - - +
177A TYR* 3.9 6.9 - - - +
501A ATP 3.4 44.4 - - + +
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Residues in contact with MET 126 (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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95A LEU* 3.9 19.5 - - + -
98A PHE* 4.7 8.7 - - - -
100A ARG* 3.9 23.6 - - + -
111A ARG 3.4 1.9 - - - +
112A VAL* 3.3 3.4 - - - -
113A MET* 2.8 35.2 + - + +
115A VAL* 4.0 28.9 - - + -
124A TYR 4.0 0.6 - - - -
125A ALA* 1.3 71.9 - - - +
127A LYS* 1.3 68.9 + - - +
128A ILE* 3.6 33.1 + - + +
165A PHE* 4.2 5.8 - - - -
172A TYR* 4.0 14.6 - - + -
173A MET 3.5 4.0 - - - +
174A VAL* 3.9 25.4 - - + +
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Residues in contact with LYS 127 (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 PHE* 5.6 0.4 - - - -
110A GLY* 4.6 1.8 - - - -
111A ARG 3.4 6.1 - - - +
112A VAL* 3.9 13.5 - - + -
125A ALA 3.7 1.4 + - - -
126A MET* 1.3 72.5 - - - +
128A ILE* 1.3 63.3 + - - +
129A LEU* 4.1 28.2 + - + -
146A GLU* 2.8 33.3 + - - +
171A LEU 3.6 1.0 - - - +
172A TYR* 3.3 6.8 - - - -
173A MET* 2.7 52.2 + - + +
175A MET* 3.7 19.2 - - + +
239A ASP* 3.4 4.9 + - - +
501A ATP 2.6 55.8 + - - +
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Residues in contact with ILE 128 (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 PHE 4.6 0.2 - - - +
110A GLY* 3.5 5.2 - - - -
111A ARG* 2.8 40.1 + - + +
113A MET* 3.8 22.2 - - + -
126A MET* 3.7 36.1 - - + +
127A LYS* 1.3 74.8 - - - +
129A LEU* 1.3 65.1 + - - +
130A ASP 4.3 1.0 + - - +
170A ASN* 4.0 20.2 - - + +
171A LEU 3.5 2.5 - - - -
172A TYR* 4.0 21.3 - - + -
390A ILE* 3.8 33.7 - - + -
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Residues in contact with LEU 129 (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 PHE* 3.4 42.0 - - + +
110A GLY* 3.6 7.9 - - - +
127A LYS* 4.3 12.1 - - + -
128A ILE* 1.3 75.0 - - - +
130A ASP* 1.3 63.6 + - - +
131A LYS 3.4 0.3 + - - -
134A VAL* 4.0 17.7 - - + -
143A THR* 3.6 25.4 - - + +
146A GLU* 4.3 6.1 - - - +
170A ASN* 3.2 6.1 - - - -
171A LEU* 2.8 49.7 + - + +
173A MET* 3.6 30.7 - - + -
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Residues in contact with ASP 130 (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 PHE 5.1 2.8 + - - -
128A ILE* 4.3 1.6 + - - +
129A LEU* 1.3 69.3 - - - +
131A LYS* 1.3 65.5 + - - +
132A GLN* 2.8 40.0 + - - +
133A LYS* 3.1 24.3 + - + +
134A VAL* 3.0 23.0 + - - +
169A SER* 4.1 6.0 - - - +
170A ASN* 3.5 16.9 + - - +
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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