Contacts of the helix formed by residues 208 - 227 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D ARG* 5.2 5.6 - - - -
550D ARG* 3.6 11.7 + - - -
206F GLY 4.2 0.8 + - - -
207F LEU* 1.3 75.5 - - - +
209F PHE* 1.3 65.4 + - - +
210F LEU* 3.4 13.2 + - - +
211F ASP* 3.0 35.6 + - - +
212F LEU* 3.0 12.3 + - - +
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Residues in contact with PHE 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F VAL* 3.9 33.7 - - + -
85F LEU* 5.6 0.9 - - + -
196F VAL* 4.0 12.1 - - + -
199F ALA* 4.0 4.9 - - + -
200F LYS* 3.6 35.4 - - + -
203F THR* 4.2 18.6 - - + +
207F LEU 3.8 1.2 + - - -
208F SER* 1.3 71.6 + - - +
210F LEU* 1.3 57.3 + - - +
212F LEU* 3.2 10.6 + - + +
213F ILE* 2.9 48.8 + - + +
8H G 3.2 43.1 - - - -
9H G 6.5 0.2 - - - -
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Residues in contact with LEU 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D ARG* 5.1 2.2 - - - +
569D ASN* 4.0 24.0 - - - +
572D ARG* 6.4 0.2 - - + -
573D MET* 3.6 28.7 - - + -
80F PRO* 3.6 32.3 - - + +
81F VAL* 3.9 29.6 - - + -
84F TYR* 4.5 6.7 - - + -
208F SER* 3.3 7.4 + - - +
209F PHE* 1.3 78.6 - - - +
211F ASP* 1.3 62.9 + - - +
213F ILE* 3.2 22.7 + - + +
214F GLN* 2.9 26.9 + - - +
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Residues in contact with ASP 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D ARG* 4.7 5.0 + - - +
550D ARG* 3.0 42.0 + - - +
553D ARG* 3.2 21.1 + - - +
573D MET* 3.1 10.1 - - - +
207F LEU* 4.4 15.1 - - + +
208F SER* 3.0 28.7 + - - +
210F LEU* 1.3 78.4 - - - +
212F LEU* 1.3 56.9 + - - +
214F GLN* 3.2 3.1 + - - +
215F GLU* 3.0 35.2 + - - +
254F GLN* 5.7 0.7 - - - -
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Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F ALA* 3.8 22.0 - - + +
202F TYR 3.4 28.7 - - - +
203F THR* 3.7 15.3 - - + +
207F LEU* 3.7 26.7 - - + +
208F SER 3.0 13.5 + - - +
209F PHE* 3.4 7.0 - - - +
211F ASP* 1.3 72.5 - - - +
213F ILE* 1.3 60.5 + - - +
215F GLU* 3.4 4.8 + - - -
216F GLY* 2.9 27.5 + - - -
247F ILE* 3.7 34.5 - - + +
250F ALA* 5.7 0.2 - - + -
251F ILE* 3.7 25.4 - - + -
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Residues in contact with ILE 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D ASN* 4.3 5.6 - - - +
81F VAL* 5.5 1.6 - - + -
84F TYR* 3.5 39.9 - - + +
85F LEU* 5.7 1.6 - - + -
195F VAL* 3.3 9.8 - - + +
196F VAL* 4.5 13.5 - - + -
199F ALA* 4.0 12.3 - - + +
209F PHE* 2.9 52.2 + - + +
210F LEU* 3.4 28.3 - - + +
212F LEU* 1.3 77.0 - - - +
214F GLN* 1.3 55.7 + - - +
217F ASN* 2.9 34.3 + - - +
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Residues in contact with GLN 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ARG* 3.6 21.9 - - - +
557D LEU* 3.4 23.8 - - - +
566D ILE* 3.5 19.9 + - - +
569D ASN* 2.7 32.4 + - - +
570D GLU* 2.9 25.7 + - - +
573D MET* 3.7 13.0 - - - -
210F LEU 2.9 17.9 + - - +
211F ASP 3.2 3.8 + - - +
213F ILE* 1.3 73.4 - - - +
215F GLU* 1.3 67.2 + - - +
217F ASN* 3.1 22.3 + - - +
218F GLN* 3.0 22.0 + - - +
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Residues in contact with GLU 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ARG* 2.9 29.6 + - - +
207F LEU* 4.8 2.0 - - + -
211F ASP 3.0 18.7 + - - +
212F LEU* 3.9 5.4 - - - +
214F GLN* 1.3 75.4 - - - +
216F GLY* 1.3 63.3 + - - +
218F GLN* 3.0 37.2 + - - +
219F GLY 3.0 10.0 + - - -
246F ALA* 3.3 18.8 - - - +
247F ILE* 4.5 2.2 - - - -
249F ARG* 3.4 15.6 + - - -
250F ALA* 3.4 30.1 - - + +
254F GLN* 3.1 22.7 + - - -
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Residues in contact with GLY 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F VAL* 3.5 27.3 - - - +
212F LEU 2.9 13.9 + - - -
215F GLU* 1.3 78.3 - - - +
217F ASN* 1.3 55.4 + - - +
219F GLY* 3.1 3.9 + - - -
220F LEU 2.9 23.6 + - - -
243F ILE* 3.7 12.4 - - - +
247F ILE* 3.9 15.8 - - - +
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Residues in contact with ASN 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D ILE* 3.8 27.1 - - + +
84F TYR* 3.2 18.9 + - - -
192F LEU* 3.3 24.4 - - - +
195F VAL* 3.5 16.5 - - - +
213F ILE* 2.9 18.0 + - - +
214F GLN* 3.1 34.0 + - - +
216F GLY* 1.3 74.6 - - - +
218F GLN* 1.3 63.4 + - - +
220F LEU* 3.1 8.7 + - - +
221F ILE* 2.9 28.7 + - - +
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Residues in contact with GLN 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ARG* 4.0 20.0 - - - +
556D LYS* 3.0 50.9 + - - +
557D LEU* 4.3 16.2 - - + +
560D GLN* 4.4 7.0 - - - +
214F GLN 3.0 8.0 + - - +
215F GLU* 3.0 41.4 + - - +
217F ASN* 1.3 76.3 - - - +
219F GLY* 1.3 60.7 - - - +
221F ILE* 3.3 11.8 + - + +
222F ARG* 3.1 27.4 + - + +
246F ALA* 4.7 2.5 - - + -
249F ARG* 5.2 2.4 - - - +
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Residues in contact with GLY 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F GLU 3.0 10.9 + - - -
216F GLY 3.1 4.2 + - - -
218F GLN* 1.3 74.5 - - - +
220F LEU* 1.3 58.8 + - - +
222F ARG* 3.2 8.9 + - - +
223F ALA 2.9 23.4 + - - -
242F TRP* 3.4 26.2 - - - +
243F ILE* 4.2 2.0 - - - -
246F ALA* 3.6 19.6 - - - +
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Residues in contact with LEU 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F ILE* 3.7 23.3 - - + +
191F ASN* 3.6 30.7 - - + +
192F LEU* 3.6 29.8 - - + -
195F VAL* 3.7 18.2 - - + -
216F GLY 2.9 13.3 + - - +
217F ASN* 3.3 9.0 - - - +
219F GLY* 1.3 74.1 - - - +
221F ILE* 1.3 58.1 + - - +
223F ALA* 3.1 6.5 + - - +
224F VAL* 2.9 29.6 + - + +
235F PHE* 3.6 20.2 - - + -
239F ALA* 4.4 7.4 - - + -
243F ILE* 3.7 10.4 - - + +
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Residues in contact with ILE 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D LEU* 4.3 15.0 - - + -
560D GLN* 4.7 13.7 - - + +
562D ALA* 3.8 34.1 - - + +
566D ILE* 4.3 7.2 - - + -
184F ARG* 3.7 25.4 - - - +
188F ILE* 3.6 29.8 - - + -
217F ASN 2.9 17.2 + - - +
218F GLN* 3.5 7.9 - - - +
219F GLY 3.2 0.2 - - - -
220F LEU* 1.3 72.0 - - - +
222F ARG* 1.3 82.5 + - - +
224F VAL* 3.1 3.9 + - - +
225F GLU* 3.0 28.7 + - + +
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Residues in contact with ARG 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556D LYS* 5.3 4.4 - - - +
560D GLN* 3.5 35.9 + - - +
218F GLN* 3.1 16.5 + - + +
219F GLY* 3.2 10.3 + - - +
221F ILE* 1.3 83.5 - - - +
223F ALA* 1.3 57.6 + - - +
225F GLU* 3.1 42.6 + - - +
226F LYS* 3.0 49.7 + - - +
242F TRP* 3.9 31.0 - - + -
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Residues in contact with ALA 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLY 2.9 13.2 + - - +
220F LEU* 3.3 10.3 - - - +
221F ILE 3.1 0.4 - - - -
222F ARG* 1.3 77.0 - - - +
224F VAL* 1.3 57.5 + - - +
226F LYS 3.8 0.5 - - - -
227F PHE* 2.9 33.4 + - - +
235F PHE* 3.9 9.0 - - + -
238F TYR* 3.8 4.7 - - + -
239F ALA* 3.7 32.3 - - + +
242F TRP* 4.0 19.2 - - + -
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Residues in contact with VAL 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F VAL* 4.2 15.8 - - + +
184F ARG* 4.1 31.6 - - + +
187F LEU* 3.8 28.6 - - + +
188F ILE* 3.6 28.3 - - + +
220F LEU* 2.9 19.3 + - + +
221F ILE 3.1 6.3 + - - +
223F ALA* 1.3 75.8 - - - +
225F GLU* 1.3 63.0 + - - +
226F LYS 3.6 0.2 + - - -
227F PHE* 3.8 10.1 + - - +
235F PHE* 3.5 25.1 - - + -
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Residues in contact with GLU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D GLN* 4.7 1.7 - - - +
106F VAL* 5.5 1.6 - - - -
110F MET* 4.0 35.1 - - + +
128F ARG* 6.0 1.9 - - - -
132F ARG* 4.2 6.9 + - - -
184F ARG* 2.8 43.0 + - - +
221F ILE* 3.0 18.6 + - + +
222F ARG* 3.1 33.5 + - - +
224F VAL* 1.3 79.2 - - + +
226F LYS* 1.3 63.7 - - + +
227F PHE 3.5 2.0 + - - +
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Residues in contact with LYS 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F ARG* 3.0 34.4 + - - +
225F GLU* 1.3 80.4 - - + +
227F PHE* 1.3 66.2 + - - +
228F GLU* 3.4 8.8 + - - +
238F TYR* 3.2 26.5 - - + +
242F TRP* 4.1 25.9 - - + +
1H T 3.6 20.9 - - + +
2H A 3.5 13.9 + - - -
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Residues in contact with PHE 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F GLU* 4.5 6.3 - - + -
100F VAL* 6.3 0.4 - - - -
103F ALA* 3.7 34.0 - - + +
107F GLU* 3.6 12.5 - - - +
187F LEU* 5.2 2.5 - - + -
223F ALA 2.9 17.5 + - - +
224F VAL* 3.8 8.8 + - - +
225F GLU 3.5 3.3 - - - +
226F LYS* 1.3 77.6 - - - +
228F GLU* 1.3 60.2 + - - +
229F TYR* 4.0 17.9 + - + -
233F PHE 3.5 24.0 - - - -
234F LYS 4.0 3.6 - - - -
235F PHE* 3.6 51.1 - + + -
238F TYR* 3.8 14.6 - + + -
2H A 3.5 27.1 - + - -
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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