Contacts of the helix formed by residues 139 - 148 (chain A) in PDB entry 1WMA
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 SER 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A SER* 1.3 82.6 + - - +
140A ILE* 1.4 60.6 + - - +
141A MET* 2.9 23.7 + - - +
142A SER* 2.8 30.1 + - - -
193A TYR* 3.9 5.4 - - - -
197A LYS* 4.0 12.1 - - - -
225A CYS 3.7 1.0 + - - -
226A CYS* 3.9 9.6 - - - -
267A PHE* 3.3 8.0 - - - -
307A AB3 2.5 31.9 + - - -
309A NDP 3.7 3.1 - - - -
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Residues in contact with ILE 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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139A SER* 1.4 73.9 + - - +
141A MET* 1.3 69.0 + - + +
143A VAL* 3.0 29.6 + - + +
144A ARG* 3.1 13.7 + - + +
226A CYS* 3.2 26.2 - - + +
267A PHE* 3.9 22.0 - - + -
269A SER* 5.2 7.2 - - - +
274A GLU* 4.6 16.6 - - + +
307A AB3 3.9 28.5 - - + +
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Residues in contact with MET 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 2.9 20.7 + - - +
140A ILE* 1.3 83.7 - - + +
142A SER* 1.3 55.7 + - - +
144A ARG* 3.7 10.3 - - - +
145A ALA* 2.8 31.4 + - - +
191A SER* 5.9 0.2 - - - +
193A TYR* 4.1 14.8 - - + -
194A GLY* 4.0 9.3 - - - -
197A LYS* 5.4 0.2 - - + -
307A AB3 3.6 50.9 - - + +
310A PE5 3.4 64.8 - - - +
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Residues in contact with SER 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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139A SER 2.8 21.0 + - - -
141A MET* 1.3 75.8 - - - +
143A VAL* 1.3 61.3 + - - +
146A LEU* 3.0 28.8 + - - +
194A GLY 4.0 10.5 - - - -
197A LYS* 3.4 36.1 - - - +
198A ILE* 3.5 10.4 - - - +
201A THR* 3.0 16.9 + - - -
267A PHE* 3.5 6.8 - - - -
276A TRP* 3.6 8.4 - - - -
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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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140A ILE* 3.0 21.0 + - + +
142A SER* 1.3 76.9 + - - +
144A ARG* 1.3 62.1 + - - +
146A LEU* 3.4 14.1 + - + +
147A LYS* 3.5 11.8 + - - +
267A PHE* 4.1 30.3 - - + -
274A GLU* 5.1 7.9 - - + +
275A GLN 4.6 15.0 - - - +
276A TRP* 3.8 26.7 - - + +
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Residues in contact with ARG 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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140A ILE* 3.1 13.2 + - + +
141A MET* 3.7 17.7 - - - +
143A VAL* 1.3 77.8 - - - +
145A ALA* 1.3 61.6 + - - +
147A LYS* 3.4 20.4 + - - +
148A SER* 3.8 8.2 + - - -
310A PE5 3.9 53.9 + - - -
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Residues in contact with ALA 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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141A MET 2.8 22.5 + - - +
142A SER 4.0 0.4 - - - +
144A ARG* 1.3 74.2 - - - +
146A LEU* 1.3 65.4 + - - +
148A SER* 3.0 13.6 + - - +
149A CYS* 3.3 7.6 + - - -
189A PRO* 3.5 25.1 - - + +
191A SER* 5.2 4.0 - - - +
194A GLY* 3.8 27.6 - - - +
195A VAL 4.3 0.2 - - - +
198A ILE* 3.8 12.6 - - + -
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Residues in contact with LEU 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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142A SER 3.0 18.1 + - - +
143A VAL* 3.5 9.6 - - + +
144A ARG 3.3 0.2 - - - -
145A ALA* 1.3 75.1 - - - +
147A LYS* 1.3 64.2 + - - +
149A CYS* 3.1 13.3 + - - +
154A GLN* 3.2 38.3 - - + +
157A PHE* 3.8 35.2 - - + -
158A ARG* 3.5 32.5 - - + +
198A ILE* 3.7 6.9 - - + +
276A TRP* 3.6 43.7 - - + +
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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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143A VAL 3.5 6.5 + - - +
144A ARG* 3.4 14.7 + - - +
145A ALA 3.2 0.8 - - - -
146A LEU* 1.3 79.2 - - - +
148A SER* 1.3 59.9 - - - +
149A CYS 3.8 1.2 - - - +
154A GLN* 3.4 20.8 + - - +
158A ARG* 5.8 2.0 - - - +
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Residues in contact with SER 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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144A ARG* 3.8 8.1 + - - -
145A ALA* 3.0 10.9 + - - -
147A LYS* 1.3 77.8 - - - +
149A CYS* 1.3 62.6 + - - +
150A SER 4.0 0.3 + - - -
187A GLY 4.2 1.9 - - - +
188A TRP 4.3 2.1 - - - +
189A PRO* 3.8 29.2 - - - +
190A SER 5.4 0.7 - - - -
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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