Contacts of the helix formed by residues 208 - 225 (chain B) in PDB entry 6QVC
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 THR 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B LYS 4.4 0.8 + - - -
205B GLU* 2.5 31.3 + - - -
206B TYR 3.3 4.0 + - - -
207B LEU* 1.3 77.7 - - - +
209B MET* 1.3 65.2 + - + +
210B LYS* 3.4 26.0 - - + +
211B ALA* 3.4 21.1 + - - +
212B PHE* 3.6 7.6 + - - +
241B ILE* 4.4 8.2 - - - +
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU 3.6 3.6 + - - -
208B THR* 1.3 75.5 - - + +
210B LYS* 1.3 70.3 + - - +
212B PHE* 2.8 39.8 + - + +
213B VAL* 3.7 25.7 + - + +
241B ILE* 4.7 6.1 - - + -
245B VAL* 4.5 24.3 - - + +
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 4.6 15.4 - - + +
208B THR* 3.2 15.9 - - + +
209B MET* 1.3 91.8 - - - +
211B ALA* 1.3 61.3 + - - +
212B PHE 3.4 0.3 + - - -
213B VAL* 4.0 4.5 + - + +
214B ALA* 3.4 18.4 + - - +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 5.7 1.3 - - - -
183B SER* 5.2 10.3 - - - +
184B PRO* 5.4 5.8 - - + -
186B ALA* 4.6 20.8 - - + +
206B TYR 5.7 3.1 - - - +
208B THR* 3.4 21.0 + - - +
209B MET 3.2 0.4 - - - -
210B LYS* 1.3 76.7 - - - +
212B PHE* 1.3 53.7 + - - +
214B ALA* 3.0 10.3 + - - +
215B LYS* 2.6 38.5 + - - +
237B HIS* 6.3 0.7 - - - +
241B ILE* 5.6 3.8 - - + -
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Residues in contact with PHE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 5.9 1.3 - - + -
131B VAL* 5.3 13.5 - - + -
208B THR 3.6 1.4 + - - +
209B MET* 2.8 31.1 + - + +
211B ALA* 1.3 76.4 - - - +
213B VAL* 1.3 82.5 + - + -
215B LYS* 3.0 20.4 + - - +
216B VAL* 3.1 27.1 + - + +
238B ILE* 3.6 40.6 - - + +
241B ILE* 4.0 30.7 - - + +
242B CYS* 3.6 27.8 - - - -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B MET* 3.7 22.5 + - + +
210B LYS* 4.0 4.2 + - + +
212B PHE* 1.3 96.0 - - + +
214B ALA* 1.3 61.7 + - - +
215B LYS 3.3 0.5 + - - -
216B VAL* 3.7 15.0 + - + +
217B VAL* 3.4 23.3 - - + +
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Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 4.0 28.6 - - - +
182B ILE* 3.7 32.8 - - + -
183B SER* 4.8 9.9 - - - +
210B LYS 3.4 14.7 + - - +
211B ALA* 3.0 16.3 + - + +
213B VAL* 1.3 79.9 - - - +
215B LYS* 1.3 58.3 + - - +
217B VAL* 4.9 1.3 - - - -
218B ALA* 4.1 2.6 + - - +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B SER* 5.8 1.2 - - - -
186B ALA* 2.7 45.6 + - + +
189B SER* 3.3 20.7 - - - +
211B ALA* 2.6 17.5 + - - +
212B PHE* 3.0 5.3 + - - +
214B ALA* 1.3 76.0 - - - +
216B VAL* 1.3 58.1 + - - +
217B VAL 3.3 1.3 - - - -
218B ALA* 3.0 10.5 + - - +
219B LEU* 2.8 32.2 + - + -
234B PRO* 4.0 24.7 - - + -
237B HIS* 4.0 9.6 - - + -
238B ILE* 4.0 18.8 - - + -
241B ILE* 5.9 0.7 - - - -
480B PRO* 4.1 20.3 - - + +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 4.8 8.3 - - + -
135B MET* 3.7 31.9 - - + -
212B PHE* 3.1 26.9 + - + +
213B VAL* 3.7 18.3 + - + +
215B LYS* 1.3 79.5 - - - +
217B VAL* 1.3 55.6 + - + +
219B LEU* 3.0 13.3 + - + +
220B THR* 2.6 38.1 + - - +
238B ILE* 4.9 15.3 - - + -
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 5.3 6.5 - - + -
178B PHE* 4.0 26.9 - - + -
213B VAL* 3.4 22.9 - - + +
214B ALA* 4.8 1.6 - - - +
216B VAL* 1.3 82.5 - - + +
218B ALA* 1.3 54.4 + - - +
220B THR* 3.0 14.9 + - + -
221B ALA* 2.7 32.6 + - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B PHE* 5.9 0.2 - - - -
175B SER* 3.3 24.4 + - - +
178B PHE* 3.7 34.5 - - + -
179B CYS* 5.0 5.6 - - - +
214B ALA 4.1 3.1 - - - +
215B LYS* 3.0 10.4 + - - +
217B VAL* 1.3 81.7 - - - +
219B LEU* 1.3 49.8 + - - +
221B ALA* 3.0 12.2 + - - +
222B GLY* 2.5 31.7 + - - -
480B PRO* 5.3 4.3 - - + -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 4.2 24.0 - - + -
215B LYS* 2.8 16.0 + - + +
216B VAL* 3.2 14.1 - - + +
218B ALA* 1.3 71.4 - - - +
220B THR* 1.3 54.8 + - - +
222B GLY* 3.0 6.3 + - - +
223B LEU* 2.4 47.6 + - + +
229B VAL* 5.6 1.1 - - + -
230B GLY 4.5 14.8 - - - +
231B LYS* 4.6 19.5 - - + +
234B PRO* 4.5 20.4 - - + -
235B PHE* 5.5 5.4 - - + +
480B PRO* 3.9 32.2 - - + +
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 3.8 40.1 - - - +
138B VAL* 4.6 18.8 - - + -
139B SER* 4.7 6.1 - - - +
216B VAL* 2.6 22.7 + - - +
217B VAL* 3.0 21.5 - - + -
219B LEU* 1.3 71.3 - - - +
221B ALA* 1.3 52.8 + - - +
223B LEU* 3.4 5.3 - - - +
224B GLY* 2.5 35.9 + - - -
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Residues in contact with ALA 221 (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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171B LEU* 3.2 40.0 - - + +
172B ILE* 4.6 1.6 - - - +
174B PHE* 4.6 12.8 - - + -
175B SER* 3.8 21.3 - - - +
217B VAL 2.7 15.5 + - - +
218B ALA* 3.1 13.7 - - - +
220B THR* 1.3 72.6 - - - +
222B GLY* 1.3 58.7 + - - +
224B GLY* 5.0 0.2 - - - -
225B SER* 3.3 9.0 + - - -
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Residues in contact with GLY 222 (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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172B ILE* 5.0 6.3 - - - -
175B SER* 4.3 5.3 + - - -
218B ALA 2.5 18.3 + - - -
219B LEU* 3.0 10.2 + - - -
221B ALA* 1.3 75.2 - - - +
223B LEU* 1.3 59.3 + - - +
225B SER* 3.5 15.7 + - - +
229B VAL* 3.3 30.3 - - - +
479B ILE* 5.7 5.8 - - - -
480B PRO 6.1 0.4 - - - -
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Residues in contact with LEU 223 (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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135B MET* 4.5 10.8 - - + +
136B ASP* 4.2 22.9 - - + +
139B SER* 3.3 26.0 + - - +
219B LEU* 2.4 25.7 + - + +
220B THR* 3.0 6.0 + - - +
222B GLY* 1.3 72.9 - - - +
224B GLY* 1.3 61.9 + - - +
225B SER 3.2 9.5 + - - +
229B VAL* 4.2 14.8 - - + +
230B GLY 5.1 1.1 - - - +
231B LYS* 4.6 35.2 - - + +
421B ARG* 5.9 11.9 - - - +
485B MET* 6.4 1.3 - - + -
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Residues in contact with GLY 224 (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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139B SER* 3.3 15.3 + - - -
142B SER* 4.1 21.1 + - - -
143B LEU* 4.3 16.6 - - - +
167B PHE* 5.2 4.2 - - - -
171B LEU* 3.9 13.8 - - - +
220B THR 2.5 21.2 + - - -
221B ALA 4.1 1.1 - - - -
222B GLY 3.4 0.2 - - - -
223B LEU* 1.3 69.9 - - - +
225B SER* 1.3 62.9 + - - +
226B GLY 3.8 0.7 + - - -
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 5.3 2.6 - - - +
168B PRO* 4.6 2.9 - - - +
171B LEU* 3.8 16.2 - - - +
172B ILE* 3.8 19.8 - - - +
221B ALA 3.3 16.7 + - - -
222B GLY 3.6 9.0 - - - -
223B LEU 3.1 10.8 - - - +
224B GLY* 1.3 80.3 - - - +
226B GLY* 1.3 59.7 + - - +
227B ILE* 2.9 39.2 + - - +
229B VAL* 5.7 0.2 - - - -
420B PRO* 5.5 3.3 - - - +
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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
------------------------------------------------------------
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