Contacts of the helix formed by residues 195 - 210 (chain A) in PDB entry 2CNW
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 ASP 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.3 35.2 + - + +
193A GLN 3.4 0.6 - - - -
194A ILE* 1.3 75.5 - - - +
196A GLU* 1.3 54.0 + - - +
197A PRO* 3.4 16.5 - - - +
198A LEU* 3.0 35.6 + - + +
199A MET* 2.8 33.9 + - - +
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Residues in contact with GLU 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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194A ILE 3.0 13.4 + - - +
195A ASP* 1.3 70.1 - - - +
197A PRO* 1.3 65.9 - - + +
199A MET* 3.5 15.9 - - - +
200A GLY* 2.7 28.9 + - - -
236A LYS* 3.1 37.8 + - - +
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Residues in contact with PRO 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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195A ASP* 3.4 11.9 - - - +
196A GLU* 1.3 92.7 - - + +
198A LEU* 1.3 54.0 + - + +
200A GLY* 3.3 2.1 + - - -
201A GLU* 2.7 33.1 + - - +
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Residues in contact with LEU 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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137A GLN* 6.4 2.2 - - + -
189A ALA* 6.4 1.1 - - + -
190A GLY 5.7 1.1 - - - +
191A ARG* 2.7 50.0 + - + +
195A ASP* 3.0 33.9 + - + +
197A PRO* 1.3 80.0 - - + +
199A MET* 1.3 60.7 + - - +
201A GLU* 3.3 26.0 + - + +
202A LEU 3.0 14.4 + - - -
284D GLU* 5.6 6.1 - - - +
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Residues in contact with MET 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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191A ARG* 3.9 18.8 - - - +
192A LEU 3.5 25.6 - - - +
193A GLN* 3.6 19.3 - - - +
195A ASP 2.8 14.4 + - - +
196A GLU* 3.5 17.5 - - - +
198A LEU* 1.3 72.5 - - - +
200A GLY* 1.3 57.6 + - - +
202A LEU* 3.4 4.3 + - - +
203A ALA* 3.0 27.0 + - - +
232A ALA 3.9 0.9 - - - +
233A PHE* 3.8 38.6 - - + +
236A LYS* 3.8 36.0 - - + +
237A VAL* 3.9 16.4 - - + +
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Residues in contact with GLY 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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196A GLU* 2.7 21.0 + - - -
197A PRO* 3.5 2.2 - - - -
199A MET* 1.3 69.8 - - - +
201A GLU* 1.3 58.5 + - - +
203A ALA* 3.2 7.7 + - - +
204A ARG* 2.8 31.3 + - - +
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Residues in contact with GLU 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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191A ARG* 2.7 31.2 + - - +
197A PRO 2.7 17.5 + - - +
198A LEU* 3.3 24.1 + - + +
200A GLY* 1.3 71.8 - - - +
202A LEU* 1.3 57.3 + - - +
204A ARG* 3.3 6.1 + - - +
205A LEU* 2.9 30.9 + - + +
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Residues in contact with LEU 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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102A PHE* 4.1 9.1 - - + -
104A VAL* 3.5 33.7 - - + -
105A GLY 5.5 0.2 - - - +
188A THR* 3.9 33.4 - - + +
191A ARG* 3.8 21.8 - - - +
198A LEU 3.0 16.7 + - - +
199A MET* 3.7 5.2 - - - +
200A GLY 3.2 0.2 - - - -
201A GLU* 1.3 78.0 - - - +
203A ALA* 1.3 58.1 + - - +
205A LEU* 3.3 8.2 + - + +
206A LYS* 2.9 28.4 + - - +
233A PHE* 4.1 15.3 - - + -
237A VAL* 3.8 24.9 - - + -
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Residues in contact with ALA 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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199A MET 3.0 16.3 + - - +
200A GLY* 3.6 8.1 - - - +
202A LEU* 1.3 74.9 - - - +
204A ARG* 1.3 59.8 + - - +
206A LYS* 3.3 8.2 + - - +
207A GLU* 2.8 28.9 + - - +
236A LYS 3.6 20.4 - - - +
237A VAL* 4.1 7.5 - - + +
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Residues in contact with ARG 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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164A SER* 5.2 1.2 - - - -
165A PRO* 3.3 26.5 - - + +
166A GLU* 2.8 41.2 + - - -
200A GLY 2.8 17.1 + - - +
201A GLU* 3.8 6.1 - - - +
203A ALA* 1.3 72.9 - - - +
205A LEU* 1.3 60.2 + - - +
207A GLU* 3.1 20.0 + - - +
208A VAL* 2.9 35.2 + - + +
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Residues in contact with LEU 205 (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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102A PHE* 3.6 26.9 - - + -
134A ALA* 5.2 6.3 - - + -
165A PRO* 4.1 26.8 - - + +
168A ILE* 4.1 20.6 - - + -
186A VAL* 4.3 8.3 - - + -
188A THR* 4.0 22.4 - - + -
201A GLU* 2.9 20.3 + - + +
202A LEU* 3.6 8.5 - - + +
203A ALA 3.3 0.2 - - - -
204A ARG* 1.3 76.9 - - - +
206A LYS* 1.3 55.9 + - - +
209A LEU* 2.9 52.5 + - + +
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Residues in contact with LYS 206 (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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102A PHE* 3.4 17.6 - - + -
202A LEU 2.9 13.7 + - - +
203A ALA* 3.5 10.5 - - - +
205A LEU* 1.3 77.0 - - - +
207A GLU* 1.3 57.4 + - - +
210A GLY* 2.8 29.0 + - - -
211A PRO* 3.4 19.3 - - + +
214A VAL* 4.0 12.1 - - + +
237A VAL* 3.1 32.8 + - + +
238A GLY* 2.8 31.1 + - - +
240A THR* 5.2 5.7 - - - +
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Residues in contact with GLU 207 (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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169A ARG* 5.4 0.3 + - - -
203A ALA 2.8 14.6 + - - +
204A ARG* 3.1 25.7 + - - +
206A LYS* 1.3 78.6 - - - +
208A VAL* 1.3 63.7 + - + +
210A GLY* 4.1 3.8 + - - -
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Residues in contact with VAL 208 (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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165A PRO* 3.7 38.4 - - + +
166A GLU* 3.7 22.2 - - + +
169A ARG* 3.1 60.4 + - + +
204A ARG* 2.9 27.8 + - + +
205A LEU 4.1 0.7 - - - +
207A GLU* 1.3 82.0 - - + +
209A LEU* 1.3 62.0 + - + +
210A GLY 3.7 0.3 + - - -
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Residues in contact with LEU 209 (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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98A ARG* 3.1 17.8 + - - -
100A LEU* 3.4 17.9 - - + +
102A PHE* 3.7 28.0 - - + -
165A PRO 4.4 3.1 - - - +
168A ILE* 4.4 12.1 - - + -
169A ARG* 3.4 47.1 - - + +
172A VAL* 5.5 6.1 - - + -
186A VAL* 4.2 17.7 - - + -
205A LEU* 2.9 42.6 + - + +
208A VAL* 1.3 74.4 - - + +
210A GLY* 1.3 65.1 + - - +
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Residues in contact with GLY 210 (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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98A ARG* 3.1 23.5 + - - -
206A LYS* 2.8 15.3 + - - -
207A GLU 4.1 4.2 + - - -
208A VAL 3.4 2.6 + - - -
209A LEU* 1.3 75.0 - - - +
211A PRO* 1.4 70.4 - - - +
212A ASP* 4.5 0.3 - - - +
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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