Contacts of the helix formed by residues 201 - 210 (chain A) in PDB entry 6BFN
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 PRO 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A PHE* 6.2 0.2 - - + -
199A CYS 4.3 2.9 - - - +
200A TRP* 1.3 90.2 - - + +
202A LEU* 1.3 65.3 + - - +
203A CYS* 4.1 17.3 - - - -
204A GLU* 3.2 41.3 + - + +
205A ILE* 3.4 13.3 + - - +
232A ARG* 5.0 3.4 - - - +
278A CYS* 4.2 0.7 - - - -
280A GLN* 3.7 10.3 - - - +
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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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201A PRO* 1.3 72.3 - - - +
203A CYS* 1.3 59.1 + - - +
205A ILE* 3.2 6.3 + - + -
206A SER* 2.9 30.0 + - - -
212A PHE* 4.8 13.2 - - + -
278A CYS* 3.7 16.9 - - - -
280A GLN* 3.4 38.9 + - + +
281A ASN* 4.0 16.8 - - + +
283A PHE* 3.8 49.6 - - + -
285A CYS* 5.4 1.3 - - - -
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Residues in contact with CYS 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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201A PRO* 4.1 16.4 - - - -
202A LEU* 1.3 79.1 - - - +
204A GLU* 1.3 61.4 + - - +
206A SER* 3.6 6.8 - - - -
207A ARG* 2.9 31.5 + - - +
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Residues in contact with GLU 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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200A TRP* 3.5 16.4 - - + -
201A PRO* 3.2 33.2 + - + +
202A LEU 3.2 0.2 - - - -
203A CYS* 1.3 82.0 - - - +
205A ILE* 1.3 59.6 + - - +
207A ARG* 3.5 6.3 + - + +
208A GLY* 2.9 24.6 + - - -
231A MET* 3.6 12.0 - - + +
232A ARG* 2.9 55.6 + - - +
331B GLN* 5.2 0.5 - - - +
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Residues in contact with ILE 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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200A TRP* 4.0 10.1 - - + -
201A PRO 3.4 8.2 + - - +
202A LEU* 3.2 10.2 + - + +
204A GLU* 1.3 74.2 - - - +
206A SER* 1.3 55.1 + - - +
208A GLY* 3.7 0.3 - - - -
209A THR* 2.7 40.0 + - + +
212A PHE* 4.1 19.3 - - + -
231A MET* 3.7 21.8 - - + -
238A VAL* 4.1 21.8 - - + -
278A CYS* 3.6 30.3 - - + -
285A CYS* 4.1 11.9 - - + -
287A VAL* 3.8 24.7 - - + -
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Residues in contact with SER 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 LEU* 2.9 21.4 + - - -
203A CYS* 3.6 9.2 - - - -
205A ILE* 1.3 75.8 - - - +
207A ARG* 1.3 60.7 + - - +
209A THR* 3.3 5.9 + - - -
210A HIS 2.9 9.5 + - - -
211A ASN* 2.7 62.1 + - - +
212A PHE* 4.7 11.4 - - - -
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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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203A CYS 2.9 19.5 + - - +
204A GLU* 3.8 5.8 - - - +
206A SER* 1.3 75.2 + - - +
208A GLY* 1.3 61.5 + - - +
210A HIS* 3.4 23.2 + - - +
211A ASN* 5.8 0.4 - - - +
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Residues in contact with GLY 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 GLU 2.9 17.3 + - - -
205A ILE 3.7 2.5 - - - -
206A SER 3.2 0.2 - - - -
207A ARG* 1.3 79.2 - - - +
209A THR* 1.3 60.1 + - - +
210A HIS* 4.4 3.5 + - - -
216A LEU* 3.8 8.8 - - - +
229A ALA* 3.6 18.4 - - - -
230A VAL* 3.6 25.6 + - - +
231A MET* 4.1 7.2 - - - -
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Residues in contact with THR 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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205A ILE* 2.7 23.7 + - + +
206A SER* 3.3 5.9 + - - -
208A GLY* 1.3 78.6 - - - +
210A HIS* 1.3 61.5 + - - +
212A PHE* 3.2 38.3 + - + -
213A SER 2.9 22.7 + - - -
216A LEU* 3.5 16.5 - - - +
227A TYR* 4.0 23.1 - - + -
229A ALA* 3.9 17.5 - - + -
238A VAL* 4.4 11.9 - - + -
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Residues in contact with HIS 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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206A SER 2.9 6.4 + - - -
207A ARG* 3.4 16.2 + - - +
208A GLY 4.4 2.9 + - - -
209A THR* 1.3 80.0 - - - +
211A ASN* 1.3 73.9 + - - +
212A PHE 3.3 0.5 + - - -
213A SER* 3.3 21.4 + - - -
216A LEU* 3.9 26.1 - - + +
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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