Contacts of the helix formed by residues 202 - 217 (chain A) in PDB entry 5F85
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 ARG 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A PHE 4.0 2.2 - - - -
187A TRP* 2.8 66.2 + - - +
201A GLY* 1.3 75.0 - - - +
203A TRP* 1.3 61.0 + - - +
204A ASP* 2.6 37.8 + - - +
205A GLN* 3.1 44.8 + - + +
206A MET* 3.0 23.7 + - - +
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Residues in contact with TRP 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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185A THR 4.8 1.1 - - - +
186A PHE* 3.0 44.2 + + + +
201A GLY 3.3 2.7 + - - -
202A ARG* 1.3 72.0 - - - +
204A ASP* 1.3 58.7 + - - +
206A MET* 4.0 16.8 - - + -
207A ARG* 2.9 59.0 + - + +
300A LYS* 3.5 55.0 - - + -
301A HIS* 3.7 24.2 - + - -
304A LEU* 3.6 15.7 - - + -
367A ILE* 3.7 22.2 - - + -
371A LEU* 2.9 35.0 + - + +
373A MET* 4.3 13.0 - - - -
376A ILE* 4.8 3.1 - - + -
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Residues in contact with ASP 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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187A TRP* 4.0 11.3 - - - -
202A ARG* 2.6 52.3 + - - -
203A TRP* 1.3 75.0 + - - +
205A GLN* 1.3 72.4 + - - +
207A ARG* 3.5 12.6 + - - +
208A GLU* 3.6 18.3 + - - +
373A MET* 3.5 31.2 - - + -
505A SO4 5.2 3.6 - - - +
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Residues in contact with GLN 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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202A ARG* 3.1 56.1 + - + +
204A ASP* 1.3 82.2 + - - +
206A MET* 1.3 66.0 + - - +
208A GLU* 3.2 10.2 + - - +
209A LYS* 3.0 24.0 + - - +
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Residues in contact with MET 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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196A HIS* 4.3 8.5 - - + -
200A ILE* 5.6 2.2 - - + -
201A GLY 4.8 8.5 - - - +
202A ARG 3.0 15.2 + - - +
203A TRP* 3.4 15.5 + - + +
205A GLN* 1.3 76.7 - - - +
207A ARG* 1.3 63.0 + - - +
209A LYS* 3.3 18.0 + - - +
210A LEU* 2.9 42.1 + - + +
278A PHE* 3.8 21.1 - - + -
301A HIS* 3.4 31.6 - - + +
503A SO4 3.3 26.9 - - - +
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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 TRP* 2.9 58.7 + - + +
204A ASP* 3.7 7.4 - - - +
206A MET* 1.3 76.6 - - - +
208A GLU* 1.3 55.3 + - - +
210A LEU* 3.3 1.6 + - - +
211A GLU* 2.8 36.0 + - - +
304A LEU* 3.8 15.6 - - + +
367A ILE* 3.1 21.6 + - - +
368A TRP* 2.8 61.8 + - + +
371A LEU* 2.9 22.5 + - - +
372A ARG* 3.8 16.1 - - - +
373A MET 4.6 0.7 - - - +
505A SO4 3.8 20.9 + - - -
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Residues in contact with GLU 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 ASP 3.6 14.2 + - - +
205A GLN* 3.2 8.8 + - - +
207A ARG* 1.3 80.6 + - - +
209A LYS* 1.3 62.7 + - - +
211A GLU* 3.7 8.4 - - - +
212A LYS* 3.1 33.5 + - + +
368A TRP* 3.9 23.1 - - - -
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Residues in contact with LYS 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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196A HIS* 4.7 3.2 - - - -
205A GLN 3.0 17.2 + - - +
206A MET* 3.3 19.8 + - - +
208A GLU* 1.3 78.2 - - - +
210A LEU* 1.3 57.0 + - + +
212A LYS* 3.5 9.6 + - - +
213A ARG* 3.2 24.9 + - - +
279A GLU* 3.3 32.1 + - + +
503A SO4 2.6 43.3 + - - +
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Residues in contact with LEU 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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203A TRP* 4.6 0.4 - - + -
206A MET* 2.9 41.7 + - + +
207A ARG 4.0 0.9 - - - +
209A LYS* 1.3 73.5 - - + +
211A GLU* 1.3 56.3 + - - +
213A ARG* 3.8 2.8 - - - +
214A ALA* 2.8 30.3 + - - +
278A PHE* 3.9 36.3 - - + +
279A GLU* 4.0 11.7 - - + +
282A CYS* 4.2 10.1 - - - -
301A HIS* 3.6 35.0 - - + +
304A LEU* 3.2 39.4 - - + +
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Residues in contact with GLU 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 2.8 17.9 + - - +
208A GLU* 3.7 10.1 - - - +
210A LEU* 1.3 76.6 - - - +
212A LYS* 1.3 72.5 + - - +
214A ALA* 3.5 3.0 + - - +
215A ALA* 3.1 27.5 + - - +
304A LEU* 4.3 1.9 + - - +
364A TYR* 3.2 26.3 + - - +
368A TRP* 3.4 31.8 - - + -
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Residues in contact with LYS 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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208A GLU* 3.1 23.4 + - + +
209A LYS* 3.7 9.0 - - - +
211A GLU* 1.3 84.7 + - - +
213A ARG* 1.3 61.6 + - - +
215A ALA* 3.5 7.2 + - - +
216A ALA* 3.1 22.6 + - - +
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Residues in contact with ARG 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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209A LYS 3.2 15.3 + - - +
210A LEU* 3.2 5.8 + - - +
212A LYS* 1.3 79.0 - - - +
214A ALA* 1.3 63.7 + - - +
216A ALA* 3.2 8.6 + - - +
217A ILE* 3.0 44.4 + - - +
279A GLU* 3.0 73.4 + - + +
280A ASP* 3.3 20.4 + - - +
282A CYS* 3.8 10.5 - - + -
283A LYS* 5.3 2.2 - - - +
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Residues in contact with ALA 214 (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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210A LEU 2.8 20.8 + - - +
211A GLU 3.9 4.0 - - - +
213A ARG* 1.3 68.9 - - - +
215A ALA* 1.3 66.1 + - - +
217A ILE 3.2 22.1 + - - +
218A PRO* 3.9 3.6 - - - +
222A LYS* 5.1 1.1 - - - +
282A CYS* 4.9 1.3 - - - -
304A LEU 3.4 15.9 - - - +
305A CYS* 3.7 23.1 - - - +
306A LYS* 4.2 15.4 - - + +
364A TYR* 4.1 13.9 - - + -
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Residues in contact with ALA 215 (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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211A GLU* 3.1 27.0 + - - +
212A LYS* 3.6 7.2 - - - +
214A ALA* 1.3 76.0 - - - +
216A ALA* 1.3 61.8 + - - +
217A ILE 3.6 0.2 + - - -
218A PRO* 3.7 14.4 - - - +
306A LYS* 5.7 4.6 - - - +
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Residues in contact with ALA 216 (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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212A LYS 3.1 14.2 + - - +
213A ARG* 3.5 17.7 - - - +
214A ALA 3.2 0.6 - - - -
215A ALA* 1.3 78.3 - - - +
217A ILE* 1.3 63.0 + - + +
218A PRO* 3.3 9.4 - - - +
221A GLN* 4.2 5.4 - - - +
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Residues in contact with ILE 217 (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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213A ARG* 3.0 43.9 + - + +
214A ALA 3.2 10.1 + - - +
216A ALA* 1.3 82.5 - - + +
218A PRO* 1.3 61.4 - - - +
221A GLN* 4.0 18.4 - - + +
222A LYS* 3.3 39.7 + - + +
282A CYS 4.0 7.9 - - - +
283A LYS* 4.0 33.2 - - + +
306A LYS* 5.7 0.2 - - - +
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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