Contacts of the helix formed by residues 202 - 214 (chain B) in PDB entry 2PGW
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 SER 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B GLY 4.3 0.6 + - - -
201B TRP* 1.3 78.6 - - - +
203B VAL* 1.3 65.1 + - - +
204B HIS* 3.3 15.6 + - - -
205B ASP* 3.2 30.9 + - - +
206B ALA* 3.0 18.1 + - - +
225B THR* 4.5 0.4 - - - -
292C GLY 5.8 0.9 - - - -
294C LYS* 3.4 36.6 - - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B SER* 1.3 74.5 - - - +
204B HIS* 1.3 63.6 + - - +
206B ALA* 3.4 2.6 + - - +
207B ILE* 3.2 24.1 + - + +
225B THR* 4.4 5.4 - - + +
232B ALA* 4.3 17.5 - - + +
235B HIS* 3.6 36.1 - - + +
236B VAL* 3.8 20.9 - - + +
263C ARG* 4.4 2.5 - - - +
266C ASP* 3.6 22.2 + - - +
292C GLY 3.5 24.4 + - - +
293C LEU* 3.9 9.8 - - + +
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Residues in contact with HIS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER* 3.3 20.7 + - - -
203B VAL* 1.3 75.8 - - - +
205B ASP* 1.3 81.5 + - - +
207B ILE* 3.3 4.3 + - - +
208B ASN* 3.0 31.6 + - - -
2200B GOL 3.6 10.8 - - - -
194C ARG* 4.5 0.7 - - - -
219C GLU* 2.8 40.0 + - + -
220C PHE* 4.1 11.6 - + + -
243C PRO* 3.7 23.1 - - + +
245C VAL* 5.9 0.4 - - + -
266C ASP* 4.0 18.3 + - + +
267C MSE 4.4 28.0 - - + +
294C LYS* 6.0 3.4 - - + -
321C ASP* 4.5 7.6 - - - -
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Residues in contact with ASP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TRP* 4.2 14.3 - - + -
202B SER* 3.2 30.6 + - - +
204B HIS* 1.3 88.6 + - - +
206B ALA* 1.3 57.0 + - - +
208B ASN* 3.3 0.5 + - - +
209B MSE 2.7 41.7 + - + +
2200B GOL 2.7 39.3 + - - -
219C GLU* 4.3 1.4 - - - +
294C LYS* 5.3 4.0 + - - -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B TRP* 3.7 28.1 - - + +
202B SER 3.0 17.9 + - - +
203B VAL 3.6 5.2 - - - +
205B ASP* 1.3 77.3 - - - +
207B ILE* 1.3 57.4 + - - +
209B MSE 4.0 0.5 - - - +
210B CYS* 3.0 37.4 + - - -
224B PRO* 4.1 9.2 - - + -
225B THR* 4.4 2.0 - - + -
236B VAL* 3.9 23.8 - - + -
240B VAL* 4.6 0.7 - - - -
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Residues in contact with ILE 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 3.2 19.2 + - + +
204B HIS* 3.6 7.9 - - - +
205B ASP 3.2 0.2 - - - -
206B ALA* 1.3 77.8 - - - +
208B ASN* 1.3 63.4 + - - +
210B CYS* 3.9 2.6 - - - +
211B ARG* 3.3 21.2 + - - +
235B HIS* 4.8 1.8 - - + +
236B VAL* 4.6 8.1 - - + -
239B LYS* 3.8 38.6 - - + +
240B VAL* 3.7 17.4 - - + +
241C GLY 4.2 14.8 - - - +
242C ILE 5.6 0.2 - - - -
243C PRO* 3.8 18.6 - - + -
266C ASP* 3.7 30.7 - - - +
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Residues in contact with ASN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B HIS* 3.0 17.2 + - - +
205B ASP 3.9 0.2 - - - +
207B ILE* 1.3 76.6 - - - +
209B MSE 1.3 63.5 + - - +
211B ARG* 3.2 28.8 + - - +
212B LYS* 3.1 27.9 + - - +
2200B GOL 2.8 44.3 + - - +
218C ILE 4.0 2.5 - - - +
219C GLU* 2.9 29.1 + - - +
241C GLY 5.0 0.2 - - - +
243C PRO* 3.2 23.7 - - - +
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Residues in contact with MSE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 3.6 28.3 - - - +
177B ASP* 3.7 35.4 - - + +
178B LEU* 4.3 8.7 - - + -
201B TRP* 3.7 35.2 - - + +
205B ASP* 2.7 26.1 + - + +
206B ALA 4.0 1.1 - - - +
208B ASN* 1.3 73.2 - - - +
210B CYS* 1.3 64.0 + - - +
212B LYS* 3.2 5.3 + - - +
213B LEU* 2.9 50.1 + - + +
2200B GOL 3.3 26.9 - - - +
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Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TRP* 4.7 4.9 - - - -
206B ALA* 3.0 26.7 + - - +
207B ILE 3.9 0.4 - - - +
209B MSE 1.3 76.1 - - - +
211B ARG* 1.3 63.1 + - - +
213B LEU 3.3 0.2 + - - -
214B GLU* 3.1 23.0 + - - +
221B ILE* 3.5 26.9 - - - -
224B PRO* 5.7 0.4 - - - -
236B VAL* 5.2 2.0 - - - -
240B VAL* 3.6 39.7 - - + -
241B GLY 5.3 0.4 - - - +
242B ILE* 3.3 23.3 - - + +
244B ILE* 4.4 9.6 - - - -
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ILE* 3.3 10.2 + - - +
208B ASN* 3.2 30.5 + - - +
209B MSE 3.2 0.4 - - - -
210B CYS* 1.3 81.7 - - - +
212B LYS* 1.3 81.7 + - - +
214B GLU* 3.4 26.7 - - - +
215B LYS* 4.7 0.7 + - - +
2200B GOL 4.9 0.4 + - - -
214C GLU* 4.6 24.1 + - - +
217C ASP* 3.1 34.9 + - - +
218C ILE 4.3 9.8 + - - +
241C GLY 5.1 9.6 + - - -
242C ILE* 6.2 0.8 - - - +
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Residues in contact with LYS 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLU* 2.7 47.3 + - + +
178B LEU* 3.8 27.3 - - + +
208B ASN 3.1 16.6 + - - +
209B MSE 3.2 7.2 + - - +
211B ARG* 1.3 96.1 - - - +
213B LEU* 1.3 60.6 + - - +
214B GLU 3.4 0.4 - - - -
215B LYS* 3.7 19.8 - - - +
216B TYR* 3.9 1.7 - - - -
2200B GOL 3.0 16.8 + - - -
190C ASP 5.7 0.4 + - - -
217C ASP* 3.0 38.9 + - - -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 5.2 3.1 - - + -
177B ASP* 4.5 4.9 - - + +
178B LEU* 3.7 19.1 - - + -
181B THR* 3.7 29.8 - - + +
195B LEU* 3.8 26.9 - - + -
201B TRP* 3.8 27.1 - - + -
209B MSE 2.9 34.9 + - + +
210B CYS 4.0 2.9 - - - +
212B LYS* 1.3 76.2 - - - +
214B GLU* 1.3 66.1 + - - +
215B LYS 3.2 2.7 - - - -
216B TYR* 2.9 23.8 + - + +
218B ILE* 3.5 8.5 - - + +
221B ILE* 4.0 6.1 - - + -
242B ILE* 4.4 5.8 - - + -
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B CYS 3.1 8.7 + - - +
211B ARG* 3.4 27.3 - - - +
212B LYS 3.4 0.4 - - - -
213B LEU* 1.3 76.8 - - - +
215B LYS* 1.3 61.2 + - - +
216B TYR 3.0 1.9 + - - -
217B ASP* 3.1 14.2 + - - -
218B ILE* 4.6 2.1 + - - +
241B GLY* 4.6 20.9 + - - -
242B ILE* 4.2 18.6 - - + +
211G ARG* 4.1 32.3 + - - +
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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