Contacts of the helix formed by residues 191 - 206 (chain A) in PDB entry 6CNB
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 ALA 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A LEU* 5.7 5.8 - - + -
182A THR* 5.9 2.5 - - + -
185A TRP* 4.9 9.0 - - + +
189A LYS* 3.3 20.3 + - - +
190A SER* 1.3 76.4 - - - +
192A PRO* 1.3 63.1 - - + +
193A GLU* 4.5 3.4 - - + +
194A LYS* 3.7 26.1 - - + +
195A ASP* 2.8 37.2 + - - +
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Residues in contact with PRO 192 (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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160A LEU* 6.1 1.6 - - + -
190A SER* 3.3 15.0 - - - +
191A ALA* 1.3 83.8 - - + +
193A GLU* 1.3 71.0 + - + +
195A ASP* 3.3 13.5 + - + +
196A ILE* 2.9 29.0 + - + +
339O LEU* 5.2 27.6 - - + +
343O LYS* 5.6 5.2 - - + +
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Residues in contact with GLU 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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159A ALA* 5.4 11.1 - - - +
160A LEU* 4.0 37.5 - - + +
182A THR* 5.5 7.0 - - + +
191A ALA* 3.2 2.0 - - + -
192A PRO* 1.3 84.2 - - + +
194A LYS* 1.3 58.4 + - - +
196A ILE* 2.8 31.1 + - - +
197A TRP* 2.8 13.2 + - - +
339O LEU* 6.0 2.2 - - + -
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Residues in contact with LYS 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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182A THR* 5.0 13.7 - - + +
185A TRP* 3.2 50.1 - - + +
187A GLY* 5.0 4.9 - - - -
191A ALA* 3.2 21.1 + - + +
193A GLU* 1.3 77.6 - - - +
195A ASP* 1.3 65.1 - - - +
197A TRP* 2.9 19.9 + - + -
198A VAL* 2.9 31.0 + - + +
217A ARG* 5.5 4.1 - - - +
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Residues in contact with ASP 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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190A SER* 5.3 5.2 - - - -
191A ALA 2.8 27.0 + - - +
192A PRO* 3.3 16.1 - - + +
194A LYS* 1.3 73.4 - - - +
196A ILE* 1.3 65.0 + - + +
198A VAL* 3.3 11.3 - - - +
199A GLY* 3.2 18.9 + - - -
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Residues in contact with ILE 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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192A PRO* 2.9 20.4 + - + +
193A GLU* 2.8 20.3 + - - +
195A ASP* 1.3 73.0 - - + +
197A TRP* 1.3 57.3 + - - +
199A GLY* 3.3 3.1 + - - -
200A GLU* 2.9 51.3 + - + +
515O LYS* 5.1 10.9 + - - +
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Residues in contact with TRP 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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182A THR* 5.8 7.0 - - - +
193A GLU 2.8 12.2 + - - +
194A LYS* 2.9 24.8 + - + +
196A ILE* 1.3 77.4 - - - +
198A VAL* 1.3 66.6 + - + +
200A GLU* 3.0 41.1 - - - +
201A TRP* 3.0 55.5 - + - +
216A LYS* 4.4 6.2 - - - +
217A ARG* 6.2 0.2 - - - +
219A MET* 3.4 56.8 - - + +
220A ASP* 4.5 4.0 - - + -
516O LEU* 6.1 0.2 - - + -
549O GLN* 3.4 21.3 - - - -
567O ARG* 3.4 24.9 - - - -
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Residues in contact with VAL 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 LYS* 2.9 19.8 + - + +
195A ASP* 3.3 19.7 - - - +
197A TRP* 1.3 80.8 - - + +
199A GLY* 1.3 64.9 + - - +
200A GLU 3.2 0.7 + - - -
201A TRP* 3.2 16.6 + - - +
202A LYS* 3.2 11.1 + - - +
213A ARG* 4.0 28.9 + - - +
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Residues in contact with GLY 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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195A ASP 3.2 9.5 + - - -
196A ILE* 3.6 4.0 - - - -
198A VAL* 1.3 84.2 - - - +
200A GLU* 1.3 63.8 + - - +
202A LYS* 3.3 19.7 - - - +
203A GLU* 4.2 6.1 + - - +
515O LYS* 4.9 3.2 - - - +
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Residues in contact with GLU 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 ILE* 2.9 41.6 + - + +
197A TRP* 3.0 41.2 - - - +
198A VAL 3.1 0.4 - - - -
199A GLY* 1.3 76.7 - - - +
201A TRP* 1.3 58.9 + - + +
202A LYS 2.9 6.6 + - - -
203A GLU* 3.0 17.5 + - - +
515O LYS* 3.6 24.2 - - + +
516O LEU* 2.4 50.6 - - + +
567O ARG* 4.4 15.3 + - - -
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Residues in contact with TRP 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 TRP* 3.0 69.5 - + - -
198A VAL* 3.2 10.9 + - - +
200A GLU* 1.3 79.9 + - + +
202A LYS* 1.3 54.0 + - - +
203A GLU 3.0 0.2 - - - -
204A VAL* 2.7 25.8 + - + -
205A LEU* 2.9 38.0 + - + +
211A LEU* 4.2 16.6 - - + -
212A GLU 6.1 0.2 - - - -
213A ARG* 5.1 6.5 - - - +
216A LYS* 3.0 36.7 - - + +
218A CYS* 6.2 1.1 - - + -
219A MET 5.0 3.1 - - - -
516O LEU* 3.6 17.5 - - + -
549O GLN* 4.9 9.6 - - + -
550O GLU 5.5 0.4 - - - -
551O VAL* 4.0 22.9 - - + -
565O LEU* 3.6 33.0 - - + -
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Residues in contact with LYS 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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198A VAL 3.2 10.9 + - - +
199A GLY* 3.3 17.9 - - - +
200A GLU 2.9 1.0 + - - -
201A TRP* 1.3 76.6 - - - +
203A GLU* 1.3 68.6 + - - +
204A VAL 3.5 0.3 + - - -
205A LEU* 5.0 2.0 - - + +
206A ALA* 3.2 40.7 + - + +
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Residues in contact with GLU 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 GLY 4.6 5.6 - - - +
200A GLU 3.0 14.1 + - - +
202A LYS* 1.3 88.6 - - - +
204A VAL* 1.3 62.1 + - - +
207A HIS* 3.2 22.4 - - - +
514O ASN* 4.9 17.3 - - + +
515O LYS* 4.5 22.0 - - + +
517O VAL* 6.0 1.4 - - + +
521O ILE* 4.7 5.4 - - - +
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Residues in contact with VAL 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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201A TRP* 2.7 14.2 + - + +
203A GLU* 1.3 79.7 - - - +
205A LEU* 1.3 67.4 + - + +
206A ALA 3.4 0.2 - - - -
207A HIS* 2.8 2.0 + - - -
208A ASN* 2.3 53.7 + - + +
211A LEU* 4.6 19.3 - - + -
516O LEU* 3.0 43.3 - - + +
517O VAL* 4.7 4.9 - - - -
518O SER* 5.2 5.2 - - - +
521O ILE* 5.8 4.7 - - + -
565O LEU* 4.3 11.4 - - + -
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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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201A TRP* 2.9 47.5 + - + +
202A LYS* 5.2 1.6 - - + +
204A VAL* 1.3 80.4 - - + +
206A ALA* 1.3 64.8 + - - +
208A ASN 3.8 6.5 - - - -
209A PRO* 3.0 28.1 - - + +
211A LEU* 5.6 1.3 - - + -
212A GLU* 3.6 45.8 - - + +
213A ARG* 3.6 36.1 - - + +
216A LYS* 5.2 2.5 - - - +
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Residues in contact with ALA 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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202A LYS* 3.2 37.8 + - + +
204A VAL 3.4 0.6 - - - -
205A LEU* 1.3 76.6 - - - +
207A HIS* 1.3 58.4 + - - +
209A PRO* 4.6 5.7 - - - +
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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