Contacts of the helix formed by residues 190 - 212 (chain A) in PDB entry 4GWR
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 CYS 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A ALA* 3.2 18.1 + - + +
188A PRO 3.4 1.1 - - - +
189A TRP* 1.3 85.9 - - + +
191A GLY* 1.3 66.4 + - - +
192A HIS* 3.9 13.2 - - - -
193A CYS* 3.0 53.1 + - - +
194A LYS* 3.0 12.5 + - - +
237A PHE* 4.0 22.7 - - + -
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Residues in contact with GLY 191 (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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189A TRP 3.2 7.6 + - - -
190A CYS* 1.3 72.4 - - - +
192A HIS* 1.3 54.1 + - - +
194A LYS* 3.2 9.4 + - - +
195A ASN* 2.8 35.2 + - - +
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Residues in contact with HIS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 3.3 8.9 - - - -
191A GLY* 1.3 76.1 - - - +
193A CYS* 1.3 58.8 + - - +
195A ASN* 3.6 7.6 + - - +
196A LEU* 3.1 27.9 + - - +
237A PHE 5.1 1.3 - - - +
238A PRO* 4.0 21.1 - - + +
256A ARG* 4.0 24.0 + - - +
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Residues in contact with CYS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 4.0 10.3 - - - +
186A TYR* 3.6 35.0 - - + -
187A ALA 3.8 6.1 - - - +
190A CYS* 3.0 41.0 + - + +
192A HIS* 1.3 75.5 - - - +
194A LYS* 1.3 58.7 + - - +
196A LEU* 3.3 4.3 + - - +
197A GLU* 3.0 27.7 + - - +
237A PHE* 3.7 10.3 - - - -
238A PRO* 3.7 20.0 - - - -
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Residues in contact with LYS 194 (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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188A PRO 6.0 1.8 - - - +
190A CYS 3.0 12.0 + - - +
191A GLY* 3.5 12.3 - - - +
193A CYS* 1.3 76.7 - - - +
195A ASN* 1.3 61.9 + - - +
197A GLU* 3.3 28.1 + - - +
198A PRO* 3.4 6.6 - - - +
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Residues in contact with ASN 195 (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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191A GLY 2.8 19.1 + - - +
192A HIS* 3.7 9.0 - - - +
194A LYS* 1.3 73.2 - - - +
196A LEU* 1.3 59.5 + - - +
198A PRO* 3.5 10.8 - - - +
199A GLU* 4.6 6.2 + - - +
256A ARG* 6.1 1.3 - - - +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A GLU* 3.7 29.4 - - + +
192A HIS 3.1 17.3 + - - +
193A CYS 3.7 2.9 - - - +
194A LYS 3.2 0.6 - - - -
195A ASN* 1.3 76.2 - - - +
197A GLU* 1.3 67.0 + - - +
198A PRO 3.4 0.4 - - - -
199A GLU* 3.0 8.3 + - + +
200A TRP* 2.8 52.5 + - + +
238A PRO* 4.0 22.4 - - + -
240A ILE* 4.4 11.0 - - + -
256A ARG* 3.7 44.6 - - + +
261A ILE* 4.9 1.6 - - + -
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Residues in contact with GLU 197 (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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184A GLU* 5.4 3.8 - - - -
193A CYS 3.0 11.5 + - - +
194A LYS* 3.3 16.9 - - - +
196A LEU* 1.3 77.0 - - - +
198A PRO* 1.4 65.4 - - + +
200A TRP* 3.4 6.9 + - - +
201A ALA* 3.0 29.7 + - + +
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Residues in contact with PRO 198 (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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194A LYS 3.4 11.4 - - - +
195A ASN* 3.5 13.7 - - - +
197A GLU* 1.4 96.7 - - + +
199A GLU* 1.3 55.8 + - + +
201A ALA* 3.5 7.4 + - + +
202A ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 199 (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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195A ASN 4.6 4.2 + - - +
196A LEU* 3.0 16.7 + - + +
198A PRO* 1.3 78.0 - - + +
200A TRP* 1.3 59.9 + - - +
202A ALA* 3.3 17.0 + - - +
203A ALA* 2.9 31.0 + - - +
256A ARG* 3.3 30.4 - - + +
257A THR* 3.7 4.9 - - - -
258A ARG* 3.5 20.6 + - - +
261A ILE* 4.4 2.8 - - - +
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Residues in contact with TRP 200 (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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162A VAL* 3.9 27.1 - - + +
182A MET* 3.5 30.3 - - + -
184A GLU* 3.6 32.5 - - + +
196A LEU* 2.8 36.5 + - + +
197A GLU* 3.6 6.3 - - - +
199A GLU* 1.3 68.5 - - - +
201A ALA* 1.3 62.0 + - - +
203A ALA* 3.5 2.3 + - - +
204A ALA* 2.9 29.6 + - - +
217A LEU* 3.7 28.0 - - + +
218A ALA 3.0 24.5 + - - +
219A ALA* 5.0 0.7 - - + -
240A ILE* 3.7 37.5 - - + -
252A TYR* 5.7 0.4 - + - -
261A ILE* 3.9 30.1 - - + -
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Residues in contact with ALA 201 (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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161A ASP* 5.8 3.8 - - + +
162A VAL* 3.9 17.7 - - + +
197A GLU* 3.0 17.6 + - + +
198A PRO* 3.7 8.3 - - + +
200A TRP* 1.3 76.3 - - - +
202A ALA* 1.3 62.8 + - - +
204A ALA* 3.2 3.1 + - - +
205A SER* 3.1 25.3 + - - -
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Residues in contact with ALA 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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198A PRO 3.0 17.5 + - - +
199A GLU* 3.7 19.3 - - - +
200A TRP 3.3 0.2 - - - -
201A ALA* 1.3 73.5 - - - +
203A ALA* 1.3 66.1 + - - +
205A SER* 3.2 5.1 + - - -
206A GLU 3.1 8.7 + - - -
258A ARG* 3.0 41.7 + - - +
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Residues in contact with ALA 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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199A GLU 2.9 17.4 + - - +
200A TRP 3.7 4.0 - - - +
202A ALA* 1.3 75.5 - - - +
204A ALA* 1.3 57.9 + - - +
206A GLU* 3.1 2.8 + - - +
207A VAL* 2.9 33.1 + - - +
217A LEU* 3.9 4.3 - - + -
258A ARG* 4.0 18.5 - - + +
261A ILE* 3.6 42.4 - - + -
262A VAL* 4.6 2.7 - - + -
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Residues in contact with ALA 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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161A ASP* 3.9 18.4 - - - +
162A VAL* 3.8 21.1 - - + -
200A TRP 2.9 18.7 + - - +
201A ALA 3.4 6.1 - - - +
202A ALA 3.2 0.2 - - - -
203A ALA* 1.3 77.4 - - - +
205A SER* 1.3 56.6 + - - +
207A VAL* 4.0 3.1 - - - +
208A LYS* 3.0 29.8 + - - +
217A LEU* 3.7 24.7 - - + +
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Residues in contact with SER 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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161A ASP* 5.4 8.0 - - - +
201A ALA 3.1 13.5 + - - -
202A ALA* 3.2 9.4 + - - -
204A ALA* 1.3 73.6 - - - +
206A GLU* 1.3 65.2 + - - +
208A LYS* 3.5 20.3 + - - +
209A GLU* 3.0 23.2 + - - +
258A ARG* 4.2 8.5 - - - -
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Residues in contact with GLU 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 ALA 3.1 1.8 + - - -
203A ALA 3.1 6.7 + - - +
205A SER* 1.3 79.3 - - - +
207A VAL* 1.3 57.6 + - - +
209A GLU* 3.2 7.0 + - + +
210A GLN* 2.9 54.8 + - + +
258A ARG* 2.9 52.2 - - - +
259A SER* 5.7 0.5 - - - -
262A VAL* 3.4 23.4 - - + +
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Residues in contact with VAL 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 ALA 2.9 21.0 + - - +
204A ALA 4.0 4.0 - - - +
206A GLU* 1.3 73.2 - - - +
208A LYS* 1.3 59.0 + - - +
210A GLN* 4.5 4.9 - - - -
211A THR* 2.8 43.3 + - + +
215A VAL* 3.4 39.0 - - + +
216A LYS* 5.2 0.2 - - - -
217A LEU* 4.0 17.3 - - + -
261A ILE* 4.9 3.6 - - + -
262A VAL* 4.0 17.0 - - + -
265A ALA* 3.5 27.4 - - + -
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Residues in contact with LYS 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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161A ASP* 4.3 24.7 - - - +
204A ALA 3.0 19.2 + - - +
205A SER* 3.7 20.1 + - - +
206A GLU 3.3 0.2 - - - -
207A VAL* 1.3 75.5 - - - +
209A GLU* 1.3 62.9 + - - +
211A THR* 4.5 0.2 - - - -
212A LYS* 2.9 33.1 + - - +
213A GLY* 4.4 14.4 - - - +
215A VAL 5.1 2.5 - - - -
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Residues in contact with GLU 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 SER 3.0 14.5 + - - +
206A GLU* 3.2 10.9 + - + +
208A LYS* 1.3 84.6 - - - +
210A GLN* 1.3 64.4 + - + +
212A LYS* 4.2 10.4 + - - +
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Residues in contact with GLN 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 GLU* 2.9 48.5 + - + +
207A VAL* 3.9 4.0 - - - +
209A GLU* 1.3 76.0 - - + +
211A THR* 1.3 60.6 + - + +
212A LYS* 3.6 1.4 - - - +
262A VAL* 4.6 6.7 - - + -
266A LEU* 3.8 39.0 - - + +
269A PHE* 5.0 7.3 - - - -
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Residues in contact with THR 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 VAL* 2.8 35.5 + - + +
210A GLN* 1.3 81.6 - - + +
212A LYS* 1.3 69.6 + - - +
213A GLY 3.4 3.3 + - - -
214A LYS* 3.1 15.4 + - - +
215A VAL* 3.2 39.6 + - + -
265A ALA* 4.9 3.1 - - + +
266A LEU* 4.4 7.9 - - + -
269A PHE* 3.8 37.3 - - + -
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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 LYS* 2.9 17.2 + - - +
209A GLU* 4.4 11.2 - - - +
210A GLN 5.4 1.1 - - - +
211A THR* 1.3 79.2 - - - +
213A GLY* 1.3 58.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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