Contacts of the helix formed by residues 107 - 117 (chain B) in PDB entry 2WP9
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 MET 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 3.5 28.5 - - - +
52B ARG* 4.3 13.3 - - - +
61B GLY 5.3 1.6 - - - +
94B LEU* 4.7 3.4 - - - -
97B LEU* 4.0 17.0 - - - -
105B VAL* 3.4 20.6 + - + +
106B ASP* 1.3 72.0 + - - +
108B GLY* 1.3 66.8 + - - +
109B GLN 3.2 2.7 - - - -
110B PHE* 2.9 15.3 + - + +
111B TYR* 2.9 48.4 + - + +
151B LEU 3.7 11.7 - - - +
152B CYS* 3.9 7.4 - - - +
153B ALA* 3.8 28.0 - - + -
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASP* 2.9 18.3 + - - -
107B MET* 1.3 76.6 - - - +
109B GLN* 1.3 56.8 + - - +
111B TYR* 3.1 11.6 + - - +
112B ALA* 2.8 30.6 + - - +
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 5.0 10.1 - - + -
98B PRO* 6.1 2.9 - - + -
106B ASP* 4.7 3.2 + - - -
107B MET 3.2 0.6 - - - -
108B GLY* 1.3 75.1 - - - +
110B PHE* 1.3 62.4 + - - +
112B ALA* 3.9 9.7 - - - +
113B GLN* 2.9 44.4 + - - +
116B LYS* 4.1 3.3 + - - +
162B PHE* 4.8 2.5 - - + -
166B PRO* 2.8 49.8 - - + +
167B ASP* 3.5 15.4 - - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 4.8 9.3 - - + +
107B MET* 2.9 21.8 + - + +
109B GLN* 1.3 80.0 - - - +
111B TYR* 1.3 79.0 + + - +
113B GLN* 3.4 4.5 + - + +
114B TYR* 3.3 20.7 + - + +
151B LEU* 3.8 39.5 - - + -
153B ALA* 3.6 36.1 - - + -
156B SER* 3.4 32.3 - - - -
157B THR* 5.7 0.9 - - + -
162B PHE* 4.4 15.0 - + + -
173B ALA* 3.5 23.8 - - + -
174B GLY 5.3 0.9 - - - -
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 3.5 57.9 - + + +
43A ARG* 2.9 29.6 + - - -
150A TYR* 5.2 2.9 - - - +
52B ARG* 6.1 0.5 - - - -
107B MET* 2.9 46.2 + - + +
108B GLY* 3.7 7.9 - - - +
110B PHE* 1.3 94.2 - + - +
112B ALA* 1.3 67.5 + - - +
114B TYR* 3.1 13.4 + + + +
115B GLU* 3.0 35.4 + - - +
151B LEU* 4.8 6.3 - - + -
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLY 2.8 17.0 + - - +
109B GLN* 3.7 22.0 - - - +
111B TYR* 1.3 77.4 - - - +
113B GLN* 1.3 64.1 + - - +
115B GLU* 3.2 12.0 + - - +
116B LYS* 3.0 30.7 + - - +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN* 2.9 33.5 + - - +
110B PHE* 4.0 4.9 - - + +
111B TYR 3.3 0.4 - - - -
112B ALA* 1.3 75.1 - - - +
114B TYR* 1.3 64.3 + - - +
116B LYS* 3.0 38.9 + - - +
117B ILE* 3.6 7.8 + - - +
162B PHE* 4.0 7.9 - - + -
166B PRO 3.2 18.9 + - - +
167B ASP 3.3 18.8 + - - -
168B LYS 3.7 2.4 + - - +
169B PHE 2.9 24.5 + - - +
170B ILE* 3.3 43.6 - - - +
174B GLY* 5.2 0.9 - - - -
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A HIS* 4.8 5.9 - - - -
150A TYR* 4.4 10.8 - + - -
151A GLN* 3.2 31.7 + - + +
154A LEU* 4.0 17.5 - - + -
110B PHE* 3.3 13.1 + - + +
111B TYR* 3.1 18.8 + + + +
113B GLN* 1.3 79.8 - - - +
115B GLU* 1.3 62.0 + - + +
117B ILE* 3.3 26.7 - - - +
119B PRO* 3.4 28.2 - - + +
151B LEU* 4.0 41.4 - - + +
173B ALA 5.4 0.4 - - - -
174B GLY* 4.7 11.5 - - - -
177B ALA* 3.6 31.6 - - + -
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TYR* 4.7 3.2 + - - +
154A LEU* 4.0 38.9 - - + +
111B TYR* 3.0 26.5 + - + +
112B ALA* 3.2 10.9 + - - +
114B TYR* 1.3 74.4 - - + +
116B LYS* 1.3 67.0 + - - +
118B LYS* 3.0 18.2 + - - +
119B PRO* 3.9 8.5 - - - +
120B TYR* 5.0 2.5 + - + -
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN* 4.1 6.1 + - - +
112B ALA* 3.0 17.6 + - - +
113B GLN* 3.0 40.5 + - - +
115B GLU* 1.3 76.7 - - + +
117B ILE* 1.3 58.0 + - - +
118B LYS* 3.2 11.1 + - - +
167B ASP* 3.1 25.6 + - - +
168B LYS 6.1 0.2 - - - +
170B ILE* 4.1 13.0 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLN 3.6 4.7 + - - +
114B TYR* 3.3 19.5 - - - +
116B LYS* 1.3 77.1 - - - +
118B LYS* 1.3 72.5 + - - +
119B PRO* 3.9 19.5 - - + -
170B ILE* 3.8 35.0 - - + -
174B GLY 3.8 15.0 - - - +
175B LEU* 5.0 0.2 - - + -
177B ALA* 4.1 4.9 - - + -
178B ALA* 3.7 36.5 - - + +
181B PHE* 5.2 0.2 - - + -
193B ARG* 3.2 13.2 + - - +
197B LEU* 3.9 22.4 - - + -
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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