Contacts of the helix formed by residues 192 - 204 (chain A) in PDB entry 2IWR
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 GLY 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ARG* 3.8 5.6 - - - -
190A VAL 3.9 3.8 + - - -
191A VAL* 1.3 78.9 - - - +
193A ASP* 1.3 66.2 + - - -
194A ALA* 3.1 4.8 + - - -
195A ARG* 3.3 11.0 + - - +
196A ALA* 3.1 19.2 + - - +
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Residues in contact with ASP 193 (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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189A ARG* 3.5 8.7 + - - +
192A GLY* 1.3 71.9 - - - -
194A ALA* 1.3 60.3 + - - +
196A ALA* 3.7 6.9 - - - +
197A ARG* 2.8 47.4 + - + +
208A TYR* 4.3 9.6 - - + -
210A GLU* 3.8 20.5 - - - +
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Residues in contact with ALA 194 (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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192A GLY* 3.1 1.9 - - - -
193A ASP* 1.3 82.8 + - - +
195A ARG* 1.3 64.4 + - + +
197A ARG* 3.4 31.2 + - - +
198A ALA* 3.0 24.1 + - - +
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Residues in contact with ARG 195 (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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148A GLU* 2.8 42.6 + - - -
151A PHE* 3.6 30.9 - - + -
152A GLN* 3.4 14.3 - - - +
190A VAL 4.2 12.9 + - - -
191A VAL* 4.7 6.2 - - + +
192A GLY* 3.3 12.9 + - - +
194A ALA* 1.3 80.2 - - + +
196A ALA* 1.3 63.0 + - - +
198A ALA* 3.3 7.6 + - - +
199A LEU* 3.1 17.3 + - - +
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Residues in contact with ALA 196 (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 PHE* 4.2 13.0 - - + -
151A PHE* 3.9 12.7 - - + -
176A LEU* 3.4 10.2 - - + +
191A VAL* 4.5 2.4 - - + +
192A GLY 3.1 15.7 + - - +
193A ASP* 3.9 2.7 - - - +
194A ALA 3.2 0.4 - - - -
195A ARG* 1.3 76.2 - - - +
197A ARG* 1.3 60.0 + - - +
199A LEU 3.2 2.6 + - - -
200A CAF 2.9 24.0 + - - +
208A TYR* 3.4 39.7 - - + +
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Residues in contact with ARG 197 (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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193A ASP* 2.8 34.5 + - + +
194A ALA* 3.4 38.1 - - - +
196A ALA* 1.3 78.8 - - - +
198A ALA* 1.3 57.4 + - - +
200A CAF 3.4 35.2 - - + +
201A ALA* 2.9 25.8 + - - +
208A TYR* 5.1 8.9 - - + -
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Residues in contact with ALA 198 (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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194A ALA 3.0 17.4 + - - +
195A ARG* 3.6 8.3 - - - +
196A ALA 3.2 0.2 - - - -
197A ARG* 1.3 76.4 - - - +
199A LEU* 1.3 64.5 + - - +
201A ALA* 3.3 7.4 + - - +
202A ASP* 3.1 31.0 + - - +
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Residues in contact with LEU 199 (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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151A PHE* 3.5 33.9 - - + +
154A VAL* 3.9 26.9 - - + -
155A SER* 3.5 25.1 - - - +
176A LEU* 4.1 9.0 - - + -
195A ARG 3.1 12.4 + - - +
196A ALA 3.2 7.6 + - - +
198A ALA* 1.3 75.0 - - - +
200A CAF 1.6 58.8 + - - +
202A ASP* 3.0 17.6 + - + +
203A MET* 3.0 37.2 + - + +
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Residues in contact with CAF 200 (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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176A LEU* 3.8 9.1 - - + +
196A ALA 2.9 17.2 + - - +
197A ARG* 3.4 39.4 - - + +
199A LEU* 1.6 58.4 + - - +
201A ALA* 1.7 92.3 + - + +
203A MET* 3.4 6.9 + - - -
204A LYS* 3.7 2.1 + - - -
206A CYS* 3.2 76.2 + - - +
207A SER* 3.8 21.1 - - - +
208A TYR* 3.8 18.1 + - + +
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Residues in contact with ALA 201 (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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197A ARG 2.9 14.1 + - - +
198A ALA* 3.6 11.0 - - - +
199A LEU 3.2 0.4 - - - -
200A CAF 1.7 79.2 + - + +
202A ASP* 1.3 64.7 + - - +
203A MET 3.3 0.5 + - - -
204A LYS* 3.7 12.5 + - - +
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Residues in contact with ASP 202 (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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158A HIS* 5.0 3.1 - - - -
198A ALA* 3.1 20.2 + - - +
199A LEU* 3.0 23.7 + - + +
201A ALA* 1.3 80.2 - - - +
203A MET* 1.3 63.2 + - + +
204A LYS* 3.6 12.8 + - - +
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Residues in contact with MET 203 (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 PHE* 3.7 27.4 - - + -
154A VAL* 3.9 20.0 - - + -
158A HIS* 3.3 57.7 + - + +
174A LEU* 3.5 12.6 - - + +
176A LEU* 4.1 16.6 - - + -
199A LEU* 3.0 29.1 + - + +
200A CAF 3.4 4.9 + - - +
201A ALA 3.2 0.8 - - - -
202A ASP* 1.3 78.0 - - + +
204A LYS* 1.3 73.6 + - - +
206A CYS* 3.9 22.0 - - + -
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Residues in contact with LYS 204 (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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172A LEU 4.1 1.0 - - - +
174A LEU* 3.4 14.2 - - - +
200A CAF 3.7 6.6 + - - -
201A ALA 3.7 9.2 + - - +
202A ASP 3.4 11.8 + - - +
203A MET* 1.3 87.3 - - - +
205A ARG* 1.3 76.4 + - + +
206A CYS* 3.0 3.9 + - - +
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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