Contacts of the strand formed by residues 149 - 159 (chain A) in PDB entry 4A12
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 THR 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE* 3.4 31.7 - - + +
95A LEU 3.4 4.3 - - - +
96A ASP* 3.0 36.4 + - - +
147A ASN 4.1 4.7 + - - -
148A ASP* 1.3 73.5 - - - +
150A VAL* 1.3 61.9 - - - +
151A ARG* 3.6 4.2 + - - +
171A TYR 3.7 6.4 - - - +
172A VAL* 3.9 13.8 - - - +
173A LYS 4.8 1.7 + - - -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ILE* 3.4 3.6 - - - -
95A LEU* 2.8 39.7 + - + +
97A ILE* 3.8 19.1 - - + -
114A LEU* 3.7 15.0 - - + -
117A GLN* 3.1 28.9 + - - +
144A VAL* 3.7 30.5 - - + -
148A ASP 4.9 0.2 - - - +
149A THR* 1.3 71.0 - - - +
151A ARG* 1.3 60.6 + - - +
170A SER* 3.6 26.0 - - - -
171A TYR 3.5 7.9 - - - +
172A VAL* 3.9 7.6 - - + -
177A VAL* 4.5 3.6 - - + -
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Residues in contact with ARG 151 (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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83A ILE* 4.9 7.0 - - + -
92A GLN* 3.5 25.0 + - + +
93A SER 3.7 4.9 - - - +
94A ILE* 3.8 21.8 - - + -
149A THR 3.6 2.5 + - - +
150A VAL* 1.3 69.6 - - - +
152A ALA* 1.3 59.5 + - - +
153A GLU* 3.7 17.2 + - - -
169A LYS 3.7 2.3 - - - +
170A SER* 3.4 2.0 - - - -
171A TYR* 2.8 78.9 + - - +
173A LYS 3.5 23.0 + - - +
174A HIS* 4.8 10.6 - - - +
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Residues in contact with ALA 152 (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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92A GLN* 3.3 5.8 - - - +
93A SER* 2.9 32.8 + - - +
117A GLN* 3.5 29.4 - - + +
118A ALA* 5.3 0.7 - - - -
121A LEU* 3.4 16.3 - - + +
150A VAL 3.6 0.8 + - - -
151A ARG* 1.3 73.0 - - - +
153A GLU* 1.3 61.0 + - - +
168A VAL* 4.5 5.6 - - + -
169A LYS 3.7 0.4 - - - -
170A SER* 3.3 24.9 - - - +
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Residues in contact with GLU 153 (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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90A LYS* 4.2 14.1 + - - -
91A ALA 3.4 3.1 - - - +
92A GLN* 3.0 36.5 + - + +
121A LEU* 4.1 1.1 - - - -
151A ARG* 3.7 19.2 + - - +
152A ALA* 1.3 73.5 - - - +
154A ALA* 1.3 59.3 + - - +
155A ARG* 3.8 24.4 + - - +
167A GLU 3.7 1.7 - - - +
168A VAL* 3.4 2.9 - - - +
169A LYS* 2.9 46.9 + - + +
171A TYR* 3.3 24.3 + - + -
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Residues in contact with ALA 154 (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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90A LYS* 3.3 6.2 - - - +
91A ALA 2.8 35.2 + - - +
121A LEU* 3.6 26.8 - - + +
122A CYS* 4.6 2.9 - - - -
125A LEU* 3.8 11.1 - - + +
153A GLU* 1.3 72.6 - - - +
155A ARG* 1.3 61.5 + - - +
166A VAL* 3.8 18.4 - - + -
167A GLU 3.4 4.9 - - - -
168A VAL* 3.8 11.0 - - + -
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Residues in contact with ARG 155 (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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89A VAL 3.5 6.1 - - - +
90A LYS* 3.7 26.3 - - + +
125A LEU* 4.4 0.2 - - - -
153A GLU* 3.8 38.8 + - - +
154A ALA* 1.3 78.0 - - - +
156A VAL* 1.3 64.0 - - - +
157A VAL* 3.4 7.5 + - + +
166A VAL* 3.4 5.6 - - - -
167A GLU* 2.9 45.0 + - + +
169A LYS* 3.2 42.2 - - - +
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Residues in contact with VAL 156 (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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88A ASN* 3.4 37.0 - - - +
89A VAL* 2.9 12.5 + - - +
125A LEU* 3.8 22.0 - - + -
126A ILE* 4.8 0.9 - - + -
155A ARG* 1.3 70.7 - - - +
157A VAL* 1.3 60.7 + - - +
158A ASN* 3.5 26.0 - - - +
159A GLN* 4.8 2.9 - - + +
164A TYR* 3.7 25.6 - - + -
165A TYR 3.5 5.8 - - - +
166A VAL* 4.4 6.7 - - + +
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Residues in contact with VAL 157 (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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155A ARG* 3.5 18.6 - - + +
156A VAL* 1.3 73.8 - - - +
158A ASN* 1.3 59.9 + - + +
165A TYR* 2.7 15.8 + - + +
166A VAL 4.6 0.4 - - - -
167A GLU* 3.6 46.7 - - + +
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Residues in contact with ASN 158 (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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156A VAL* 3.5 9.4 - - - +
157A VAL* 1.3 78.9 - - + +
159A GLN* 1.3 69.1 + - - +
160A THR* 4.0 11.5 - - - +
165A TYR* 2.7 64.9 + - + +
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Residues in contact with GLN 159 (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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88A ASN* 5.3 0.7 - - - +
156A VAL* 4.8 3.1 - - + +
158A ASN* 1.3 85.4 + - - +
160A THR* 1.3 69.9 + - - +
163A HIS 3.4 10.8 - - - +
164A TYR* 3.0 45.8 + - + -
186A TYR* 3.2 23.8 + - - +
188A LYS* 5.8 2.4 - - - +
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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