Contacts of the helix formed by residues 136 - 142 (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 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 4.5 0.2 - - - -
110A ASP 3.6 19.7 - - - +
111A ASP* 3.8 20.0 - - - +
112A GLY* 4.2 1.3 - - - -
134B LEU* 5.1 11.4 - - + -
135B GLN* 1.3 74.1 - - - +
137B PRO* 1.3 76.3 - - + +
138B GLU* 4.2 8.7 - - + +
139B GLN* 2.9 30.7 + - + +
140B ARG* 2.8 19.6 + - - +
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Residues in contact with PRO 137 (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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108A ARG* 4.3 12.6 - - + +
109A LEU 3.4 26.0 - - - +
110A ASP* 3.7 28.7 - - + +
135B GLN 3.8 0.4 - - - -
136B MET* 1.3 87.6 - - + +
138B GLU* 1.3 57.0 + - - +
140B ARG* 3.1 8.4 + - + +
141B GLU* 2.9 44.2 + - - +
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Residues in contact with GLU 138 (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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136B MET* 3.2 7.0 - - + +
137B PRO* 1.3 81.1 - - - +
139B GLN* 1.3 65.0 + - + +
141B GLU* 3.8 17.4 + - - +
142B LYS* 3.8 28.3 + - - +
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Residues in contact with GLN 139 (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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134B LEU 4.3 3.7 + - - +
135B GLN* 3.7 20.2 + - + -
136B MET* 2.9 44.6 + - + +
138B GLU* 1.3 79.6 - - + +
140B ARG* 1.3 64.9 + - - +
142B LYS* 3.4 35.0 + - - +
143B LEU* 4.3 3.8 + - - +
183B ILE 5.0 2.8 - - - +
184B ASP* 6.0 0.2 - - - -
185B SER* 3.5 31.2 + - - +
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Residues in contact with ARG 140 (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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105A PRO* 2.9 29.9 + - - +
106A PHE 2.9 26.7 + - - +
107A SER* 4.5 12.8 + - - +
108A ARG* 3.8 15.3 - - + +
137A ALA* 4.7 1.6 - - - +
138A ALA 5.2 0.4 - - - +
135B GLN* 3.3 24.8 - - - +
136B MET 2.8 11.5 + - - +
137B PRO* 3.6 9.0 - - + +
139B GLN* 1.3 80.7 - - - +
141B GLU* 1.3 56.1 - - + +
143B LEU* 2.9 35.4 + - - +
144B ASP* 3.0 25.6 + - - +
147B TYR* 3.6 29.0 + - - -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PRO* 2.9 28.8 + - - +
138B GLU* 4.0 11.8 - - - +
139B GLN 3.3 0.4 - - - -
140B ARG* 1.3 76.4 - - + +
142B LYS* 1.3 63.4 + - + +
143B LEU 2.9 2.0 + - - -
144B ASP* 2.9 37.4 + - + +
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Residues in contact with LYS 142 (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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138B GLU* 3.8 29.6 + - - +
139B GLN* 3.5 24.3 - - - +
140B ARG 3.1 1.2 - - - -
141B GLU* 1.3 75.4 - - + +
143B LEU* 1.3 58.0 + - + +
144B ASP 3.4 2.8 - - - +
146B LEU* 3.4 20.3 - - - +
179B TYR* 5.3 1.9 - - - +
183B ILE* 3.4 40.5 - - + +
185B SER* 6.4 1.3 - - - -
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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