Contacts of the strand formed by residues 170 - 176 (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 ASN 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ILE* 4.0 12.3 - - + +
129A LEU 3.2 7.2 - - - +
130A ASP* 3.5 20.3 + - - +
131A LYS* 3.9 2.6 - - - -
166A LYS* 3.5 6.1 - - - +
167A ASP* 2.8 34.4 + - - +
169A SER* 1.3 86.5 - - - +
171A LEU* 1.3 63.3 + - - +
172A TYR* 2.8 37.6 + - + +
390A ILE* 3.7 20.8 - - - +
391A ARG 3.7 14.6 + - - +
392A VAL* 4.4 0.4 - - - +
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Residues in contact with LEU 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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127A LYS 3.6 0.9 - - - +
128A ILE* 3.5 4.7 - - - -
129A LEU* 2.8 47.0 + - + +
131A LYS* 3.7 25.1 - - + -
134A VAL* 4.8 3.4 - - + -
143A THR* 3.6 29.6 - - + -
165A PHE 3.9 3.1 - - - -
166A LYS* 3.9 20.0 - - + -
170A ASN* 1.3 71.7 - - - +
172A TYR* 1.3 66.2 + - - +
173A MET* 6.1 0.4 - - - -
402A PHE* 3.6 34.5 - - + -
405A PHE* 3.9 30.3 - - + -
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Residues in contact with TYR 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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95A LEU* 3.6 26.3 - - + +
126A MET* 4.0 21.3 - - + -
127A LYS 3.3 4.3 - - - +
128A ILE* 4.0 24.7 - - + -
164A SER* 3.3 8.3 - - - -
165A PHE* 2.9 77.5 + + + +
166A LYS* 4.0 0.9 - - - -
167A ASP* 2.5 40.2 + - - -
170A ASN* 2.8 34.6 + - + -
171A LEU* 1.3 77.4 - - - +
173A MET* 1.3 64.2 + - - +
174A VAL* 4.1 0.9 - - - -
390A ILE* 4.0 5.3 - - + +
392A VAL* 4.1 0.3 - - - +
405A PHE* 3.8 1.8 - - - -
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Residues in contact with MET 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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125A ALA 3.5 3.3 - - - +
126A MET* 3.5 0.5 - - - -
127A LYS* 2.7 52.7 + - + +
129A LEU* 3.6 31.6 - - + -
143A THR* 4.7 2.5 - - + -
146A GLU* 3.6 35.4 - - + +
147A LYS* 4.0 24.7 - - + -
150A LEU* 5.7 3.8 - - + -
161A LEU* 3.7 22.2 - - + -
163A PHE 3.9 3.6 - - - -
164A SER* 4.7 0.7 - - - -
171A LEU* 5.8 0.7 - - + +
172A TYR* 1.3 77.8 - - - +
174A VAL* 1.3 61.9 + - - +
175A MET* 3.7 5.9 + - + +
405A PHE* 3.8 19.1 - - + -
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Residues in contact with VAL 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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98A PHE* 4.2 14.1 - - + -
115A VAL* 4.8 3.6 - - + -
124A TYR* 3.5 31.9 - - + -
125A ALA 3.7 4.0 - - - +
126A MET* 3.9 20.4 - - + +
161A LEU* 3.5 2.7 - - - +
162A GLU* 2.8 31.5 + - - +
163A PHE* 2.9 42.0 + - + +
165A PHE* 3.8 29.4 - - + -
173A MET* 1.3 73.0 - - - +
175A MET* 1.3 51.7 + - - +
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Residues in contact with MET 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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112A VAL* 4.6 1.3 - - + -
124A TYR* 3.4 8.2 - - - +
125A ALA 2.8 38.9 + - - +
127A LYS* 3.7 37.2 - - + +
150A LEU* 4.5 10.3 - - + -
159A VAL* 4.1 13.2 - - + -
160A LYS 3.2 14.4 - - - +
161A LEU* 4.2 14.1 - - + -
162A GLU* 4.2 3.8 - - - -
173A MET* 4.0 4.5 - - + +
174A VAL* 1.3 76.1 - - - +
176A GLU* 1.3 73.9 + - - +
177A TYR 3.3 0.2 + - - -
238A THR* 3.5 22.2 - - - +
239A ASP 5.3 0.9 - - - -
501A ATP 3.6 25.6 - - + +
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Residues in contact with GLU 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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123A HIS 5.3 0.2 - - - -
124A TYR* 4.4 9.4 - - + -
159A VAL* 3.5 11.8 - - + +
160A LYS* 2.9 42.3 + - + +
162A GLU* 3.8 19.2 - - - +
175A MET* 1.3 69.7 - - - +
177A TYR* 1.3 62.2 + - - +
178A VAL* 3.6 7.6 + - + -
236A GLN* 3.0 7.4 - - - +
501A ATP 3.0 23.6 + - - -
506A ZN 2.2 35.0 - - - -
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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