Contacts of the helix formed by residues 202 - 213 (chain A) in PDB entry 3BNF
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 THR 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A LYS* 4.2 8.5 - - - +
201A SER* 1.3 77.1 - - - +
203A HIS* 1.3 58.8 + - - +
204A GLN* 3.5 8.5 + - - +
205A GLU* 2.8 42.5 + - - +
206A LYS* 2.9 29.0 + - - +
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Residues in contact with HIS 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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179A LEU* 4.3 21.3 - - + -
202A THR* 1.3 74.5 - - - +
204A GLN* 1.3 61.6 + - - +
206A LYS* 3.2 17.4 + - - +
207A ARG* 3.0 34.3 + - - +
302A TYR* 5.6 0.7 - - - -
509A HEM 2.0 33.1 + - + -
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Residues in contact with GLN 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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202A THR* 3.3 7.6 + - - +
203A HIS* 1.3 78.2 - - - +
205A GLU* 1.3 65.2 + - - +
207A ARG* 3.1 42.4 + - - +
208A SER* 3.8 1.2 + - - -
292A GLY* 2.9 27.3 - - - +
293A VAL* 4.1 0.2 - - - -
294A SER* 3.2 15.5 + - - -
297A ASP* 2.7 26.3 + - - +
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Residues in contact with GLU 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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196A LYS* 2.6 38.3 + - - -
201A SER* 3.3 16.1 - - - +
202A THR* 2.8 33.0 + - - +
204A GLN* 1.3 77.3 - - - +
206A LYS* 1.3 63.1 + - - +
208A SER* 3.0 9.4 + - - -
209A LEU* 3.0 29.3 + - + +
284A LYS* 5.3 13.9 + - - +
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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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178A GLU* 5.3 6.7 + - - -
179A LEU* 4.0 16.9 + - + +
198A PHE* 3.2 65.5 - - + +
199A ALA* 4.5 10.3 + - - +
201A SER* 3.9 14.1 + - - -
202A THR 2.9 17.5 + - - +
203A HIS* 3.2 22.6 + - - +
205A GLU* 1.3 75.5 - - - +
207A ARG* 1.3 57.3 + - - +
208A SER 3.0 0.4 + - - -
209A LEU* 4.2 2.2 - - - -
210A VAL* 3.1 35.2 + - - +
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Residues in contact with ARG 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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179A LEU* 4.0 14.4 - - + -
203A HIS* 3.0 34.7 + - - +
204A GLN* 3.1 31.7 - - - +
205A GLU 3.2 1.0 - - - -
206A LYS* 1.3 74.8 - - - +
208A SER* 1.3 57.4 + - - +
210A VAL* 4.1 9.1 - - - +
211A CYS* 4.1 1.6 - - - -
294A SER* 3.7 6.0 + - - +
295A CYS* 4.0 2.3 - - - +
296A ALA* 3.4 35.2 + - + +
297A ASP* 2.9 42.0 + - - +
300A MET 4.9 2.2 + - - -
301A PRO* 6.1 0.2 - - - +
302A TYR* 2.8 25.4 + - - -
311A SER* 4.7 0.4 + - - -
509A HEM 2.4 58.7 + - + +
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Residues in contact with SER 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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204A GLN 3.8 2.4 + - - -
205A GLU* 3.0 9.4 + - - -
206A LYS 3.0 0.2 - - - -
207A ARG* 1.3 75.4 - - - +
209A LEU* 1.3 63.8 + - - +
210A VAL 3.2 2.2 - - - -
211A CYS* 3.1 21.9 + - - +
212A ALA* 3.2 7.1 + - - +
280A TRP* 4.1 17.6 - - - -
283A TYR* 3.1 19.5 + - - -
284A LYS* 6.3 0.2 - - - -
294A SER* 3.2 6.5 - - - -
295A CYS* 3.1 38.1 + - - -
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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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186A LEU* 3.5 11.3 - - + +
190A LEU* 4.0 24.7 - - + -
196A LYS 5.0 0.7 - - - +
198A PHE* 3.5 38.1 - - + -
201A SER* 3.5 30.7 - - - +
205A GLU* 3.0 22.2 + - + +
206A LYS 3.2 0.4 + - - -
208A SER* 1.3 77.9 - - - +
210A VAL* 1.3 61.8 + - - +
212A ALA* 2.9 19.5 + - + +
213A GLN* 3.2 9.7 + - - +
280A TRP* 3.8 34.1 - - + +
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Residues in contact with VAL 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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171A CYS* 4.4 13.7 - - + +
179A LEU* 3.9 18.6 - - + -
180A LYS 4.1 11.2 - - - +
198A PHE* 3.6 24.0 - - + -
206A LYS 3.1 18.5 + - - +
207A ARG 4.1 7.9 - - - +
209A LEU* 1.3 76.1 - - - +
211A CYS* 1.3 68.4 + - - +
213A GLN* 2.9 28.0 + - - +
509A HEM 3.8 30.5 - - + -
510A HEM 3.4 15.3 - - + +
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Residues in contact with CYS 211 (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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207A ARG 4.1 7.0 - - - -
208A SER 3.2 10.3 - - - +
210A VAL* 1.3 77.3 - - - +
212A ALA* 1.4 51.0 + - - +
213A GLN 3.2 1.3 - - - -
214A CYS* 3.1 6.8 + - - +
215A HIS* 2.9 37.0 + - - +
295A CYS* 3.5 20.4 - - - -
510A HEM 1.8 78.8 - - + -
511A HEM 3.9 16.8 - - + -
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Residues in contact with ALA 212 (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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186A LEU* 3.9 21.4 - - + +
208A SER 3.2 2.4 + - - +
209A LEU* 2.9 16.5 + - + +
211A CYS* 1.4 74.3 - - - +
213A GLN* 1.3 64.8 - - - +
214A CYS 3.0 2.3 + - - -
215A HIS 4.2 1.1 - - - +
216A VAL* 3.2 32.1 - - + +
240A LEU* 5.0 0.2 - - - +
280A TRP* 3.7 39.5 - - + +
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Residues in contact with GLN 213 (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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133A CYS* 3.9 0.2 - - - -
170A ASN* 2.8 28.4 + - - +
171A CYS* 4.2 2.2 - - - -
180A LYS 4.0 3.4 + - - -
181A SER* 3.6 21.5 - - - +
182A LYS* 2.6 34.8 + - - +
183A VAL* 3.7 18.8 + - + +
185A TYR* 2.6 36.2 + - - -
186A LEU* 3.8 7.1 - - + +
209A LEU 3.2 8.8 + - - +
210A VAL* 2.9 29.3 + - - +
212A ALA* 1.3 77.9 - - - +
214A CYS* 1.3 64.3 + - - +
216A VAL* 4.7 0.4 - - - -
508A HEM 4.0 1.2 - - - +
510A HEM 4.0 7.6 - - - +
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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