Contacts of the helix formed by residues 208 - 227 (chain P) in PDB entry 4G7H
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 208 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546N ARG* 5.4 5.2 - - - -
550N ARG* 3.6 11.6 + - - -
206P GLY 4.3 0.4 + - - -
207P LEU* 1.3 75.3 - - - +
209P PHE* 1.3 66.3 + - - +
210P LEU* 3.7 4.9 + - - +
211P ASP* 3.0 39.2 + - - -
212P LEU* 3.0 12.2 + - - +
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Residues in contact with PHE 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81P VAL* 3.9 35.4 - - + -
85P LEU* 5.4 1.3 - - + -
196P VAL* 4.0 13.5 - - + -
199P ALA* 4.0 9.6 - - + -
200P LYS* 3.7 28.5 - - + -
203P THR* 4.5 15.0 - - + +
207P LEU 3.9 0.4 + - - -
208P SER* 1.3 73.1 - - - +
210P LEU* 1.3 57.1 + - - +
212P LEU* 3.1 9.1 + - + +
213P ILE* 2.9 51.6 + - + +
8R G 3.2 42.0 - - - -
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Residues in contact with LEU 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550N ARG* 5.1 2.9 - - - +
569N ASN* 3.9 26.2 - - - +
572N ARG* 6.2 0.2 - - + -
573N MET* 3.6 30.3 - - + -
80P PRO* 3.6 31.4 - - + -
81P VAL* 3.7 25.8 - - + -
84P TYR* 4.3 13.0 - - + -
208P SER* 3.3 6.7 + - - +
209P PHE* 1.3 78.0 - - - +
211P ASP* 1.3 58.2 + - - +
213P ILE* 3.4 16.8 + - + +
214P GLN* 2.9 33.3 + - - +
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Residues in contact with ASP 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546N ARG* 4.7 5.7 + - - +
550N ARG* 3.1 41.1 + - - +
553N ARG* 3.0 25.7 + - - +
573N MET* 3.1 7.8 - - - +
207P LEU* 4.3 17.2 - - + +
208P SER* 3.0 24.5 + - - +
210P LEU* 1.3 73.7 - - - +
212P LEU* 1.3 67.1 + - - +
214P GLN* 3.2 2.8 + - - +
215P GLU* 3.0 30.5 + - - +
254P GLN* 5.7 0.2 - - - -
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Residues in contact with LEU 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199P ALA* 3.7 22.4 - - + +
202P TYR* 3.3 32.8 - - + +
203P THR* 3.7 16.2 - - + +
207P LEU* 3.6 37.5 - - + +
208P SER 3.0 14.6 + - - +
209P PHE* 3.4 7.9 - - - +
211P ASP* 1.3 76.9 - - - +
213P ILE* 1.3 56.4 + - - +
215P GLU* 3.3 5.5 + - - +
216P GLY* 2.9 27.4 + - - -
247P ILE* 3.9 23.0 - - + +
251P ILE* 3.9 19.1 - - + -
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Residues in contact with ILE 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569N ASN* 4.5 4.5 - - - +
81P VAL* 5.6 0.7 - - + -
84P TYR* 3.5 47.1 - - + +
85P LEU* 5.2 1.8 - - + -
195P VAL* 3.2 12.2 - - + +
196P VAL* 4.2 14.4 - - + -
199P ALA* 3.9 11.4 - - + -
209P PHE* 2.9 56.9 + - + +
210P LEU* 3.5 18.8 - - + +
212P LEU* 1.3 76.0 - - - +
214P GLN* 1.3 57.8 + - - +
216P GLY 3.2 1.4 + - - -
217P ASN* 2.9 28.6 + - - +
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Residues in contact with GLN 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553N ARG* 3.6 20.8 - - - +
557N LEU* 3.4 24.6 - - - +
566N ILE* 3.5 11.8 + - - +
569N ASN* 2.8 30.9 + - - +
570N GLU* 2.7 33.5 + - - +
573N MET* 3.6 13.2 - - + -
210P LEU 2.9 20.7 + - - +
211P ASP 3.7 3.4 - - - +
213P ILE* 1.3 72.5 - - - +
215P GLU* 1.3 66.4 + - - +
217P ASN* 3.1 24.6 + - - +
218P GLN* 3.0 20.4 + - - +
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Residues in contact with GLU 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553N ARG* 3.1 29.2 + - - +
207P LEU* 4.8 2.0 - - + -
211P ASP 3.0 21.7 + - - +
212P LEU* 3.8 4.5 - - - +
214P GLN* 1.3 74.8 - - - +
216P GLY* 1.3 63.1 + - - +
218P GLN* 2.9 31.8 + - - +
219P GLY 3.0 16.8 + - - -
246P ALA* 3.3 20.3 - - - +
247P ILE* 4.6 2.0 - - - -
249P ARG* 3.5 13.8 + - - -
250P ALA* 3.5 31.4 - - + +
254P GLN* 3.1 23.3 + - - -
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Residues in contact with GLY 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195P VAL* 3.6 20.5 - - - +
212P LEU 2.9 13.4 + - - -
213P ILE 3.5 4.5 - - - -
215P GLU* 1.3 77.5 - - - +
217P ASN* 1.3 56.1 + - - +
219P GLY* 2.8 17.2 + - - -
220P LEU 2.9 11.8 + - - -
243P ILE* 3.9 11.6 - - - +
247P ILE* 3.9 16.7 - - - +
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Residues in contact with ASN 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557N LEU* 5.5 0.2 - - + -
566N ILE* 3.6 29.6 - - + +
84P TYR* 3.1 23.0 + - - -
192P LEU* 3.3 22.9 - - - +
195P VAL* 3.4 18.1 - - - +
213P ILE* 2.9 15.9 + - - +
214P GLN* 3.1 29.9 + - - +
216P GLY* 1.3 73.8 - - - +
218P GLN* 1.3 62.2 + - - +
220P LEU* 3.1 7.5 + - - +
221P ILE* 3.0 30.6 + - - +
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Residues in contact with GLN 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553N ARG* 4.2 20.5 + - - +
556N LYS* 3.1 56.2 - - - +
557N LEU* 4.1 17.2 - - + +
560N GLN* 4.6 6.5 - - - +
214P GLN 3.0 9.8 + - - +
215P GLU* 2.9 38.0 + - - +
217P ASN* 1.3 76.6 - - - +
219P GLY* 1.3 59.2 + - - +
221P ILE* 3.8 8.8 + - - +
222P ARG* 3.6 22.9 + - - +
246P ALA* 4.6 3.6 - - + -
249P ARG* 5.0 2.4 + - - -
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Residues in contact with GLY 219 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215P GLU 3.0 6.7 + - - -
216P GLY 2.8 8.4 + - - -
218P GLN* 1.3 75.6 - - - +
220P LEU* 1.3 64.9 + - - +
222P ARG* 3.0 11.8 + - - +
223P ALA 2.9 17.5 + - - -
242P TRP* 3.7 22.0 - - - +
243P ILE* 4.4 1.6 - - - -
246P ALA* 3.6 19.7 - - - +
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Residues in contact with LEU 220 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188P ILE* 3.6 40.8 - - + +
191P ASN* 3.7 24.7 - - + +
192P LEU* 4.2 8.5 - - + -
194P LEU* 5.0 0.2 - - + -
195P VAL* 3.8 22.2 - - + -
216P GLY 2.9 5.3 + - - -
217P ASN* 3.5 8.1 - - - +
219P GLY* 1.3 74.5 - - - +
221P ILE* 1.3 58.6 + - - +
223P ALA* 3.0 6.9 + - - +
224P VAL* 2.9 27.4 + - + +
235P PHE* 3.5 31.9 - - + -
239P ALA* 4.1 10.5 - - + -
243P ILE* 3.9 11.9 - - + +
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Residues in contact with ILE 221 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557N LEU* 4.1 15.7 - - + -
560N GLN* 4.7 13.2 - - + +
562N ALA* 3.8 33.7 - - + +
566N ILE* 4.3 6.3 - - + -
184P ARG* 3.6 26.5 - - - +
188P ILE* 3.8 29.6 - - + -
217P ASN 3.0 19.3 + - - +
218P GLN* 3.9 7.4 - - - +
219P GLY 3.2 0.4 - - - -
220P LEU* 1.3 73.0 - - - +
222P ARG* 1.3 75.6 + - - +
224P VAL* 3.2 3.8 + - - +
225P GLU* 3.0 28.1 + - - +
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Residues in contact with ARG 222 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556N LYS* 5.2 5.3 - - - +
560N GLN* 3.5 37.6 + - - +
218P GLN 3.6 13.5 + - - +
219P GLY* 3.0 12.0 + - - +
221P ILE* 1.3 85.0 - - - +
223P ALA* 1.3 56.9 + - - +
225P GLU* 3.2 41.2 + - - +
226P LYS* 3.0 53.2 + - - +
242P TRP* 4.0 31.9 - - + -
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Residues in contact with ALA 223 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219P GLY 2.9 11.0 + - - +
220P LEU* 3.0 11.9 + - - +
222P ARG* 1.3 73.1 - - - +
224P VAL* 1.3 61.5 + - - +
226P LYS 3.1 1.0 + - - -
227P PHE* 2.9 33.3 + - - +
235P PHE* 4.0 6.5 - - + -
238P TYR* 3.6 4.1 - - + -
239P ALA* 3.7 36.1 - - + +
242P TRP* 4.1 18.8 - - + -
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Residues in contact with VAL 224 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106P VAL* 4.3 14.4 - - + +
184P ARG* 3.9 34.5 - - + -
187P LEU* 3.8 29.1 - - + +
188P ILE* 3.7 28.5 - - + +
220P LEU* 2.9 12.8 + - + +
221P ILE 3.2 7.2 + - - +
223P ALA* 1.3 76.2 - - - +
225P GLU* 1.3 65.1 + - - +
227P PHE* 3.7 10.2 + - - +
235P PHE* 3.4 27.6 - - + -
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Residues in contact with GLU 225 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560N GLN* 4.7 1.4 - - - +
106P VAL* 5.4 1.8 - - - -
110P MET* 3.8 33.5 - - + +
132P ARG* 4.3 6.6 + - - -
184P ARG* 2.9 43.4 + - - +
221P ILE 3.0 14.4 + - - +
222P ARG* 3.2 42.2 + - - +
223P ALA 3.2 0.2 - - - -
224P VAL* 1.3 79.6 - - - +
226P LYS* 1.3 64.4 + - + +
227P PHE 3.6 1.8 + - - +
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Residues in contact with LYS 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222P ARG* 3.0 41.6 + - + +
223P ALA 3.1 0.2 + - - -
225P GLU* 1.3 81.7 - - + +
227P PHE* 1.3 64.2 + - - +
228P GLU* 3.5 5.5 + - - +
238P TYR* 3.2 18.8 - - + +
242P TRP* 4.0 27.4 - - + -
1R T 3.8 21.9 - - + +
2R A 3.3 18.5 + - - -
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Residues in contact with PHE 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLU* 4.8 6.1 - - + -
100P VAL* 6.2 0.4 - - - -
103P ALA* 3.8 28.1 - - + +
107P GLU* 3.6 16.3 - - - +
187P LEU* 5.3 2.5 - - + -
223P ALA 2.9 16.4 + - - +
224P VAL 3.7 8.2 + - - +
225P GLU 3.6 3.5 - - - +
226P LYS* 1.3 77.1 - - - +
228P GLU* 1.3 62.1 + - - +
229P TYR* 3.7 25.0 + - + -
233P PHE 3.2 27.1 - - - -
234P LYS 4.2 1.1 - - - -
235P PHE* 3.6 44.2 - + + -
238P TYR* 3.6 19.7 - + + -
2R A 3.4 27.8 - + - -
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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