Contacts of the helix formed by residues 202 - 214 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200E GLY 4.3 0.2 + - - -
201E TRP* 1.3 77.0 - - - +
203E VAL* 1.3 65.7 + - - +
204E HIS* 3.5 11.9 + - - -
205E ASP* 3.4 29.6 + - - +
206E ALA* 2.9 20.4 + - - +
225E THR* 4.5 0.9 - - - -
292H GLY 5.7 1.1 - - - -
294H LYS* 4.0 39.3 + - - +
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Residues in contact with VAL 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E SER* 1.3 74.8 - - - +
204E HIS* 1.3 61.7 + - - +
206E ALA* 3.3 2.8 + - - +
207E ILE* 3.1 26.6 + - + +
225E THR* 4.4 5.0 - - + +
232E ALA* 4.4 15.7 - - + +
235E HIS* 3.7 20.9 - - + +
236E VAL* 4.0 19.8 - - + +
263H ARG* 4.5 2.7 - - - +
266H ASP* 3.7 36.3 + - + +
292H GLY 3.5 24.7 + - - +
293H LEU* 3.8 11.0 - - + +
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Residues in contact with HIS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E SER* 3.4 11.4 + - - -
203E VAL* 1.3 78.8 - - - +
205E ASP* 1.3 86.3 + - - +
207E ILE* 3.4 7.4 + - - +
208E ASN* 3.0 28.4 + - - -
2500E GOL 3.6 9.6 - - - -
192H ARG* 5.8 0.2 - - - -
194H ARG* 4.7 0.4 - - - -
219H GLU* 2.9 46.9 + - + +
220H PHE* 4.0 12.0 - + + -
243H PRO* 3.8 18.3 - - + +
245H VAL* 5.7 0.7 - - + -
266H ASP* 3.9 16.6 + - + +
267H MSE 4.4 26.4 - - + +
294H LYS* 6.1 1.8 - - + +
321H ASP* 4.6 7.0 - - - -
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Residues in contact with ASP 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E TRP* 4.3 12.5 - - + -
202E SER* 3.3 28.1 + - - +
204E HIS* 1.3 92.1 + - - +
206E ALA* 1.3 60.7 + - - +
208E ASN* 3.4 0.3 + - - +
209E MSE 2.8 38.4 + - + +
2500E GOL 2.8 32.2 + - - -
192H ARG* 5.9 0.2 + - - -
219H GLU* 4.3 1.4 - - - +
294H LYS* 5.3 4.2 + - - -
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E TRP* 3.8 29.1 - - + +
202E SER 2.9 18.6 + - - +
203E VAL 3.5 5.8 - - - +
205E ASP* 1.3 77.5 - - - +
207E ILE* 1.3 61.9 + - - +
209E MSE 4.0 0.7 - - - +
210E CYS* 3.0 32.0 + - - -
224E PRO* 4.2 8.7 - - + -
225E THR* 4.4 2.7 - - + -
236E VAL* 3.9 23.6 - - + -
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Residues in contact with ILE 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E VAL* 3.1 21.6 + - + +
204E HIS* 3.6 7.4 - - - +
205E ASP 3.2 0.2 - - - -
206E ALA* 1.3 77.5 - - - +
208E ASN* 1.3 63.1 + - - +
210E CYS* 3.8 2.9 - - - +
211E ARG* 3.3 20.9 + - - +
235E HIS* 4.8 1.8 - - + +
236E VAL* 4.5 7.9 - - + -
239E LYS* 4.1 36.6 - - + +
240E VAL* 3.7 16.9 - - + +
241H GLY 4.2 14.6 - - - +
243H PRO* 3.7 18.8 - - + -
266H ASP* 3.5 33.4 - - - +
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Residues in contact with ASN 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E HIS* 3.0 17.3 + - - +
205E ASP 3.9 0.2 - - - +
207E ILE* 1.3 75.0 - - - +
209E MSE 1.3 64.6 + - - +
211E ARG* 3.2 29.5 + - - +
212E LYS* 3.1 29.6 + - - +
2500E GOL 2.7 41.3 + - - +
218H ILE 4.1 3.5 - - - +
219H GLU* 2.9 29.7 + - - +
241H GLY 5.0 0.2 - - - +
243H PRO* 3.2 22.7 - - - +
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Residues in contact with MSE 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E GLU* 3.6 30.7 - - + +
177E ASP* 3.6 36.8 - - + +
178E LEU* 4.4 7.0 - - + -
201E TRP* 3.7 35.2 - - + +
205E ASP* 2.8 26.5 + - + +
206E ALA 4.0 1.6 - - - +
208E ASN* 1.3 72.0 - - - +
210E CYS* 1.3 63.6 + - - +
212E LYS* 3.2 5.8 + - - +
213E LEU* 2.9 48.7 + - + +
2500E GOL 3.3 25.8 - - - +
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Residues in contact with CYS 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E TRP* 4.7 5.6 - - - -
206E ALA* 3.0 26.5 + - - +
208E ASN 3.3 0.2 - - - -
209E MSE 1.3 75.8 - - - +
211E ARG* 1.3 63.9 + - - +
213E LEU 3.2 0.7 + - - +
214E GLU* 3.0 28.8 + - - +
221E ILE* 3.6 26.7 - - - -
224E PRO* 5.6 0.9 - - - -
236E VAL* 5.2 1.8 - - - -
240E VAL* 3.5 39.0 - - + -
241E GLY 5.3 0.4 - - - +
242E ILE* 3.3 16.4 - - + +
244E ILE* 4.5 10.5 - - - -
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Residues in contact with ARG 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E ILE* 3.3 10.2 + - - +
208E ASN* 3.2 30.1 + - - +
209E MSE 3.2 0.6 - - - -
210E CYS* 1.3 81.8 - - - +
212E LYS* 1.3 82.2 + - - +
213E LEU 3.3 0.5 + - - -
214E GLU* 3.5 29.9 + - - +
215E LYS* 4.7 1.6 + - - +
240E VAL* 5.5 0.2 - - - +
2500E GOL 5.8 0.2 + - - -
214H GLU* 4.8 24.4 + - - +
217H ASP* 3.4 27.6 + - - +
218H ILE 4.4 8.9 + - - +
241H GLY 4.9 12.2 + - - -
242H ILE* 6.2 0.6 - - - +
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Residues in contact with LYS 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E GLU* 2.8 48.2 + - + +
178E LEU* 3.6 26.8 - - + +
208E ASN* 3.1 18.1 + - - +
209E MSE 3.2 8.3 + - - +
211E ARG* 1.3 96.8 - - - +
213E LEU* 1.3 57.8 + - - +
214E GLU 3.5 0.2 - - - -
215E LYS* 3.4 25.9 - - - +
216E TYR* 4.1 0.2 - - - -
2500E GOL 3.5 15.0 + - - +
217H ASP* 3.1 36.7 + - - -
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Residues in contact with LEU 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E VAL* 5.2 2.7 - - + -
177E ASP* 4.5 4.0 - - + +
178E LEU* 3.8 17.7 - - + -
181E THR* 3.5 33.9 - - + +
195E LEU* 4.0 22.9 - - + -
201E TRP* 3.9 28.0 - - + -
209E MSE 2.9 34.5 + - + +
210E CYS 3.9 3.1 - - - +
211E ARG 3.2 0.2 - - - -
212E LYS* 1.3 76.8 - - - +
214E GLU* 1.3 63.5 + - - +
215E LYS 3.1 3.1 - - - -
216E TYR* 3.0 24.0 + - + +
218E ILE* 3.7 5.9 - - + +
221E ILE* 4.1 5.6 - - + -
242E ILE* 4.4 10.1 - - + -
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Residues in contact with GLU 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ARG* 5.1 14.4 + - - -
210E CYS 3.0 24.4 + - - +
211E ARG* 3.5 25.7 + - - +
213E LEU* 1.3 76.9 - - - +
215E LYS* 1.3 62.4 + - - +
216E TYR 3.0 1.6 + - - -
217E ASP* 3.1 14.6 + - - +
218E ILE* 4.6 2.1 + - - +
241E GLY* 3.9 26.6 + - - -
242E ILE* 3.9 20.6 - - + -
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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