Contacts of the helix formed by residues 137 - 148 (chain A) in PDB entry 2WMH
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 PRO 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASP* 3.3 6.3 - - - +
106A ARG* 3.3 31.6 - - - +
135A THR 3.5 2.7 - - - +
136A VAL* 1.3 89.1 - - + +
138A PRO* 1.3 72.6 - - + +
139A GLU* 3.4 30.7 - - + +
140A TRP* 3.0 21.2 + - + +
141A LEU* 3.2 11.8 + - - +
174A TYR* 4.3 0.2 - - - -
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Residues in contact with PRO 138 (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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136A VAL 3.5 3.8 - - - +
137A PRO* 1.3 81.9 - - + +
139A GLU* 1.3 66.5 + - - +
141A LEU* 3.3 4.1 + - + +
142A ASP* 3.0 28.1 + - - +
173A LYS* 4.4 19.5 - - + +
174A TYR* 4.1 25.4 - - + -
177A VAL* 3.9 22.4 - - + +
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Residues in contact with GLU 139 (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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137A PRO* 3.4 19.9 - - + +
138A PRO* 1.3 89.3 - - - +
140A TRP* 1.3 63.8 + - + +
142A ASP* 3.4 8.4 + - - +
143A GLU* 3.0 39.0 + - - +
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Residues in contact with TRP 140 (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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106A ARG* 3.6 45.4 - - + +
109A TYR* 3.4 43.7 - + + -
110A VAL* 4.3 13.1 - - + +
113A LEU* 5.1 0.7 - - + -
125A LEU* 4.3 12.3 - - + -
127A ILE* 5.2 1.1 - - + -
136A VAL* 3.7 29.8 - - + -
137A PRO* 3.0 23.9 + - + +
139A GLU* 1.3 81.4 - - + +
141A LEU* 1.3 85.7 + - + +
143A GLU* 3.2 15.6 + - - +
144A GLN* 3.0 65.0 + - + +
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Residues in contact with LEU 141 (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 LEU* 5.2 2.2 - - + -
127A ILE* 4.1 7.2 - - + -
136A VAL* 5.2 0.7 - - + -
137A PRO 3.2 8.5 + - - +
138A PRO* 3.6 8.3 - - + +
140A TRP* 1.3 99.2 - - + +
142A ASP* 1.3 63.9 + - - +
144A GLN* 2.9 13.7 + - + +
145A PHE* 2.9 37.8 + - + -
151A LEU* 4.2 14.6 - - + -
154A VAL* 3.6 36.1 - - + -
174A TYR* 3.9 29.8 - - + +
177A VAL* 4.1 10.8 - - + -
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Residues in contact with ASP 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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138A PRO 3.0 14.5 + - - +
139A GLU* 3.4 14.1 - - - +
141A LEU* 1.3 75.8 - - - +
143A GLU* 1.3 62.7 + - + +
145A PHE* 3.2 5.8 + - - +
146A GLN* 2.8 40.4 + - - +
177A VAL* 3.8 18.8 - - + +
180A LYS* 2.7 34.5 + - - +
181A TYR* 2.5 29.6 + - - -
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Residues in contact with GLU 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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139A GLU* 3.0 25.1 + - - +
140A TRP* 3.4 21.6 - - - +
141A LEU 3.2 0.2 - - - -
142A ASP* 1.3 75.6 + - + +
144A GLN* 1.3 71.5 + - - +
146A GLN* 3.3 20.2 + - - +
147A LYS* 3.1 22.9 + - - +
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Residues in contact with GLN 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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110A VAL* 4.1 15.7 - - - +
113A LEU* 4.2 10.2 - - + +
140A TRP* 3.0 68.4 + - + +
141A LEU* 2.9 7.8 + - - +
143A GLU* 1.3 83.7 - - - +
145A PHE* 1.3 60.8 + - - +
147A LYS* 3.2 4.5 + - - +
148A TYR* 2.9 58.5 + - - +
151A LEU* 3.8 18.6 - - + -
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Residues in contact with PHE 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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38A ARG* 3.0 33.7 + - - +
141A LEU* 2.9 45.4 + - + -
142A ASP 3.2 5.4 + - - +
144A GLN* 1.3 77.9 - - - +
146A GLN* 1.3 62.6 + - - +
147A LYS 3.3 0.5 + - - -
148A TYR 3.5 5.0 + - - +
151A LEU* 3.7 39.5 - - + -
153A GLY* 3.9 10.3 - - - -
154A VAL* 4.6 0.7 - - + -
177A VAL* 3.8 13.7 - - + -
178A CYS* 3.8 21.5 - - - -
181A TYR* 3.4 34.5 - + + -
183A ALA* 3.4 29.8 - - + -
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Residues in contact with GLN 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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38A ARG* 5.1 0.2 - - - +
142A ASP* 2.8 30.0 + - - +
143A GLU* 3.3 22.7 - - - +
144A GLN 3.2 0.2 - - - -
145A PHE* 1.3 76.6 - - - +
147A LYS* 1.3 62.0 + - + +
148A TYR 5.3 0.2 - - - -
180A LYS* 5.5 0.4 - - - +
181A TYR* 3.0 29.1 + - + +
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Residues in contact with LYS 147 (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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114A GLU* 4.1 9.8 + - - -
117A GLN* 4.6 3.5 - - - +
143A GLU 3.1 13.4 + - - +
144A GLN* 3.2 4.2 + - - +
146A GLN* 1.3 81.6 - - - +
148A TYR* 1.3 97.3 + - + +
149A SER 4.0 2.3 + - - -
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Residues in contact with TYR 148 (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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38A ARG* 2.9 20.1 + - - -
110A VAL* 3.8 12.5 - - + +
113A LEU* 3.8 54.3 - - + -
114A GLU* 2.6 38.7 + - - +
117A GLN* 3.3 22.4 - - + +
144A GLN* 2.9 41.9 + - - +
145A PHE 3.5 3.9 - - - +
146A GLN 3.6 0.2 - - - -
147A LYS* 1.3 103.9 + - + +
149A SER* 1.3 62.6 + - - +
150A VAL* 3.1 0.9 - - + -
151A LEU* 3.2 20.9 + - + +
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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