Contacts of the strand formed by residues 140 - 146 (chain A) in PDB entry 2WIN
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 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ARG* 1.3 74.8 - - - +
141A VAL* 1.3 64.2 + - - +
142A MET* 4.8 0.7 - - - -
157A SER* 4.1 20.4 - - - +
158A LEU 4.0 9.0 - - - +
159A SER* 4.3 9.7 + - - -
188A TYR* 3.6 5.2 - - - -
189A GLU* 2.9 62.1 + - + +
190A ASN* 6.1 0.8 - - - +
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Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 4.3 7.9 - - + -
127A ILE* 4.4 7.6 - - + -
129A THR* 3.6 30.1 - - + -
139A ARG 4.4 5.6 - - - +
140A THR* 1.3 79.0 - - - +
142A MET* 1.3 67.6 + - - +
143A VAL* 3.8 24.5 + - + +
157A SER* 3.5 6.4 - - - -
158A LEU 3.0 32.8 + - - +
167A LEU* 4.0 13.2 - - + -
186A ALA* 4.2 10.1 - - + -
187A TYR 3.8 10.3 - - - +
188A TYR* 4.3 14.8 - - + -
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Residues in contact with MET 142 (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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140A THR* 4.8 6.3 - - - -
141A VAL* 1.3 74.1 - - - +
143A VAL* 1.3 61.0 + - - +
144A ASN* 4.4 6.7 - - - +
155A GLN* 6.0 2.7 - - + -
156A ASP 3.6 11.9 - - - +
157A SER* 3.2 29.6 - - - -
186A ALA* 3.2 3.5 - - - -
187A TYR* 2.9 76.6 + - + +
189A GLU* 4.5 20.9 - - + +
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Residues in contact with VAL 143 (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 TYR* 4.0 30.7 - - + +
127A ILE* 4.2 16.8 - - + -
141A VAL* 3.8 15.7 + - + +
142A MET* 1.3 75.8 - - - +
144A ASN* 1.3 75.9 + - - +
145A ILE* 5.1 1.3 - - + -
154A LYS 3.8 1.0 - - - +
155A GLN* 3.1 1.7 - - - -
156A ASP* 2.8 43.6 + - + +
167A LEU* 5.9 1.8 - - + -
169A LEU* 4.4 11.4 - - + -
184A ILE* 4.1 10.5 - - + -
185A ARG 3.6 3.4 - - - +
186A ALA* 3.7 17.7 - - + -
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Residues in contact with ASN 144 (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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142A MET* 4.4 10.9 + - - +
143A VAL* 1.3 86.9 + - - +
145A ILE* 1.3 70.8 + - - +
146A GLU* 5.3 4.7 - - + +
152A PRO* 4.3 16.2 - - + +
154A LYS 3.3 4.9 - - - +
155A GLN* 3.3 29.4 + - - +
156A ASP 4.6 0.8 + - - +
184A ILE* 3.5 4.5 - - - +
185A ARG* 2.7 45.7 + - + +
187A TYR* 5.0 9.3 + - + -
1296B LEU* 5.0 11.4 - - - +
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Residues in contact with ILE 145 (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 TYR* 3.9 27.6 - - + +
143A VAL* 5.1 2.0 - - + -
144A ASN* 1.3 80.7 - - - +
146A GLU* 1.3 62.6 + - - +
152A PRO* 4.1 0.7 - - - -
153A VAL* 2.9 38.4 + - + +
154A LYS* 3.0 22.0 + - + +
171A TRP* 4.1 38.6 - - + -
182A TRP* 4.0 24.7 - - + -
183A LYS 3.6 9.6 - - - +
184A ILE* 4.2 20.4 - - + -
200A PHE* 4.6 3.8 - - + -
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Residues in contact with GLU 146 (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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144A ASN* 5.3 4.1 - - + +
145A ILE* 1.3 78.3 - - - +
147A ASN* 1.3 64.3 + - - +
150A GLY* 3.9 15.3 - - - -
151A ILE 3.6 10.5 - - - +
152A PRO* 3.8 29.3 - - + +
182A TRP* 3.2 12.9 - - - -
183A LYS* 2.9 46.4 + - + +
185A ARG* 3.4 44.9 + - + -
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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