Contacts of the helix formed by residues 202 - 217 (chain M) in PDB entry 6O81
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 GLU 202 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198M CYS* 5.1 0.4 - - - +
201M TYR* 1.3 89.2 - - + +
203M GLY* 1.3 59.7 + - - +
204M ILE 3.6 1.8 - - - -
205M ASP* 3.7 22.4 - - + -
206M ALA* 3.0 28.6 + - + +
342T LYS* 4.6 6.5 - - + -
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Residues in contact with GLY 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198M CYS* 3.3 34.7 + - - +
200M GLY 4.3 6.1 + - - -
201M TYR 3.3 7.7 + - - -
202M GLU* 1.3 76.5 - - - +
204M ILE* 1.3 56.7 + - - +
206M ALA* 3.8 1.9 - - - +
207M VAL* 2.9 28.8 + - - +
342T LYS 4.0 4.2 + - - -
343T ILE* 5.5 0.4 - - - +
344T ASP* 4.8 10.3 - - - -
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Residues in contact with ILE 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203M GLY* 1.3 72.4 - - - +
205M ASP* 1.3 60.1 + - - +
207M VAL* 3.7 7.1 - - - +
208M LYS* 2.9 30.1 + - - +
274T LEU 5.3 7.4 - - - +
276T GLY* 5.2 8.1 - - - +
342T LYS* 4.1 16.1 + - + -
343T ILE 3.5 26.9 - - - +
344T ASP* 4.4 3.8 - - - +
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Residues in contact with ASP 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202M GLU* 3.6 23.9 + - + -
203M GLY 3.2 0.4 - - - -
204M ILE* 1.3 79.2 - - - +
206M ALA* 1.3 56.6 + - - +
208M LYS* 3.4 6.0 + - - +
209M GLU* 2.9 28.1 + - - +
342T LYS* 5.3 7.8 + - + +
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Residues in contact with ALA 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198M CYS* 4.4 13.2 - - + -
202M GLU* 3.0 20.3 + - + +
203M GLY 3.9 2.5 - - - +
205M ASP* 1.3 73.4 - - - +
207M VAL* 1.3 60.0 + - - +
209M GLU* 3.7 7.1 - - - +
210M ALA* 2.9 30.1 + - - +
260M LYS 5.3 1.9 - - - +
261M ILE* 5.8 1.4 - - - -
264M LYS* 3.8 30.3 - - + +
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Residues in contact with VAL 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196M VAL* 5.2 11.4 - - - +
197M ALA* 5.4 7.6 - - - +
198M CYS* 5.3 1.9 - - - +
203M GLY 2.9 17.7 + - - +
204M ILE* 3.7 9.4 - - - +
205M ASP 3.3 0.2 - - - -
206M ALA* 1.3 77.6 - - - +
208M LYS* 1.3 56.7 + - - +
210M ALA* 3.4 5.8 + - - +
211M LEU* 2.9 28.6 + - - +
234M TYR* 5.5 10.3 - - + -
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Residues in contact with LYS 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204M ILE 2.9 18.3 + - - +
205M ASP* 3.8 4.9 - - - +
207M VAL* 1.3 76.1 - - - +
209M GLU* 1.3 57.2 + - - +
211M LEU* 3.4 7.3 + - - +
212M ARG* 2.9 29.5 + - - +
271T VAL 4.5 15.0 - - - +
272T ASP* 5.2 7.2 - - - +
274T LEU* 6.0 4.0 - - + -
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Residues in contact with GLU 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205M ASP 2.9 18.5 + - - +
206M ALA* 3.7 8.5 - - - +
207M VAL 3.3 0.2 - - - -
208M LYS* 1.3 75.4 - - - +
210M ALA* 1.3 57.8 + - - +
212M ARG* 3.4 6.1 + - - +
213M ALA* 2.9 29.5 + - - +
260M LYS* 5.4 1.3 - - - -
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Residues in contact with ALA 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196M VAL* 5.7 6.5 - - + -
206M ALA 2.9 18.1 + - - +
207M VAL* 3.8 6.3 - - - +
209M GLU* 1.3 73.6 - - - +
211M LEU* 1.3 60.1 + - - +
213M ALA* 3.4 1.8 + - - +
214M GLY* 2.9 25.3 + - - -
257M ILE* 4.2 23.3 - - + +
260M LYS* 4.1 26.0 - - + +
261M ILE* 4.5 11.0 - - + +
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Residues in contact with LEU 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207M VAL 2.9 17.6 + - - +
208M LYS* 3.7 8.7 - - - +
209M GLU 3.3 0.2 - - - -
210M ALA* 1.3 77.3 - - - +
212M ARG* 1.3 57.2 + - - +
214M GLY* 3.4 2.1 + - - -
215M LEU* 2.9 29.0 + - - +
226M ILE* 5.4 8.7 - - + +
271T VAL* 3.9 31.2 - - + +
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Residues in contact with ARG 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208M LYS 2.9 17.4 + - - +
209M GLU* 3.8 7.0 - - - +
211M LEU* 1.3 75.7 - - - +
213M ALA* 1.3 58.3 + - - +
215M LEU* 3.8 6.4 - - - +
216M ASN* 2.9 30.5 + - - +
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Residues in contact with ALA 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209M GLU 2.9 17.8 + - - +
210M ALA* 3.8 7.4 - - - +
212M ARG* 1.3 75.9 - - - +
214M GLY* 1.3 61.1 + - - +
216M ASN* 3.6 7.0 + - - +
217M CYS* 3.4 20.8 + - - +
256M VAL* 5.1 9.4 - - + +
260M LYS* 4.4 14.8 - - + -
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Residues in contact with GLY 214 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210M ALA 2.9 16.9 + - - -
211M LEU* 3.8 2.2 - - - -
213M ALA* 1.3 77.5 - - - +
215M LEU* 1.3 60.3 + - - +
217M CYS* 3.5 15.9 + - - +
218M SER 3.9 4.2 + - - -
224M ILE* 4.6 6.8 - - - +
253M ALA* 4.3 25.7 - - - +
256M VAL* 5.5 0.9 - - - -
257M ILE* 4.9 8.2 - - - +
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Residues in contact with LEU 215 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M LEU 2.9 17.9 + - - +
212M ARG* 4.0 6.3 - - - +
214M GLY* 1.3 75.8 - - - +
216M ASN* 1.3 60.3 + - - +
217M CYS 3.3 0.2 - - - -
218M SER* 3.5 18.8 + - - +
224M ILE 4.5 16.4 - - - +
226M ILE* 6.1 3.8 - - + -
271T VAL* 5.9 4.9 - - + -
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Residues in contact with ASN 216 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M ARG 2.9 18.8 + - - +
213M ALA* 3.9 8.1 - - - +
214M GLY 3.3 0.4 - - - -
215M LEU* 1.3 77.7 - - - +
217M CYS* 1.3 58.9 + - - +
218M SER 3.2 6.6 + - - +
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Residues in contact with CYS 217 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M ALA 3.4 13.0 + - - +
214M GLY* 3.9 8.7 - - - +
215M LEU 3.3 1.0 - - - -
216M ASN* 1.3 77.3 - - - +
218M SER* 1.3 62.6 + - - +
219M THR* 3.4 3.8 + - - -
249M VAL 5.7 0.9 - - - +
252M GLN 5.9 0.7 - - - -
253M ALA* 4.9 18.2 - - - +
256M VAL* 4.9 9.9 - - + -
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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