Contacts of the helix formed by residues 202 - 217 (chain B) in PDB entry 4QOZ
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 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 3.9 1.3 - - - -
175B ARG* 3.7 35.9 - - - +
177B GLU* 3.6 27.6 - - + +
201B ASP* 1.3 79.1 - - - +
203B PHE* 1.3 66.5 + - - +
204B PRO* 3.6 13.9 - - - +
205B GLN* 3.0 26.8 + - - +
206B VAL* 3.1 20.8 + - - +
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Residues in contact with PHE 203 (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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151B ILE* 3.9 21.1 - - + -
154B PHE* 3.8 32.1 - + - -
174B VAL* 3.6 26.2 - - + +
175B ARG 4.7 1.8 + - - -
202B THR* 1.3 74.4 - - - +
204B PRO* 1.3 71.4 - - + +
206B VAL* 3.3 1.7 + - - -
207B LEU* 2.9 42.2 + - + +
239B LEU* 3.5 29.6 - - + -
242B GLN* 3.4 38.6 - - + +
243B CYS* 4.3 9.9 - - - -
246B SER* 3.9 7.6 - - - +
248B LEU* 4.2 9.0 - - + -
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Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLU* 6.3 1.3 - - - -
202B THR* 3.6 14.4 - - - +
203B PHE* 1.3 93.2 - - + +
205B GLN* 1.3 62.3 + - + +
207B LEU* 3.4 1.1 + - + -
208B LYS* 3.0 20.8 + - - +
246B SER* 4.0 15.3 - - - +
248B LEU* 3.8 24.9 - - + -
344B MET* 3.4 21.4 - - + +
347B PHE* 4.1 25.4 - - + -
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Residues in contact with GLN 205 (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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175B ARG* 5.0 1.9 + - - -
201B ASP* 3.5 28.9 + - + +
202B THR* 3.0 42.6 + - - +
203B PHE 3.2 0.6 - - - -
204B PRO* 1.3 77.7 - - + +
206B VAL* 1.3 62.5 + - - +
208B LYS* 3.2 9.5 + - - +
209B LYS* 3.0 27.5 + - - +
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Residues in contact with VAL 206 (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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154B PHE* 4.0 28.0 - - + -
172B GLN* 3.7 32.3 - - + +
173B TYR 3.7 19.7 - - - +
174B VAL* 4.0 11.7 - - + -
201B ASP* 3.8 16.8 - - + +
202B THR 3.1 16.6 + - - +
203B PHE* 3.8 3.4 - - - +
205B GLN* 1.3 72.7 - - - +
207B LEU* 1.3 61.3 + - - +
209B LYS* 3.0 10.9 + - - +
210B VAL* 2.9 28.8 + - + +
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Residues in contact with LEU 207 (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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154B PHE* 4.1 22.8 - - + -
203B PHE* 2.9 40.7 + - + +
204B PRO* 3.7 4.7 - - + +
206B VAL* 1.3 76.7 - - - +
208B LYS* 1.3 63.0 + - - +
210B VAL* 3.2 8.7 + - + +
211B ILE* 2.9 46.5 + - + +
239B LEU* 5.6 2.9 - - + -
243B CYS* 5.4 1.1 - - - -
248B LEU* 4.3 5.8 - - + -
251B PRO* 4.3 11.2 - - + -
253B PHE* 4.6 12.8 - - + -
344B MET* 4.1 8.1 - - + -
345B PRO* 3.8 32.1 - - + -
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Residues in contact with LYS 208 (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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204B PRO 3.0 13.8 + - - +
205B GLN* 3.3 12.1 - - - +
207B LEU* 1.3 76.7 - - - +
209B LYS* 1.3 64.2 + - + +
211B ILE* 3.3 4.3 + - + +
212B ASP* 2.6 63.3 + - - +
344B MET* 3.7 32.2 - - + -
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Residues in contact with LYS 209 (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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170B PHE* 3.9 16.2 - - + -
172B GLN* 3.9 25.8 - - - +
201B ASP* 2.8 29.1 + - - +
205B GLN* 3.0 17.0 + - - +
206B VAL* 3.0 11.9 + - - +
208B LYS* 1.3 79.1 - - + +
210B VAL* 1.3 62.6 + - - +
212B ASP* 3.4 8.8 + - - +
213B TRP* 3.0 24.8 + - - +
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Residues in contact with VAL 210 (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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133B ILE* 5.9 1.3 - - + -
154B PHE* 3.6 44.4 - - + -
156B VAL* 4.3 11.0 - - + -
170B PHE* 3.4 34.1 - - + -
206B VAL 2.9 16.1 + - - +
207B LEU* 3.4 11.7 - - + +
209B LYS* 1.3 75.4 - - - +
211B ILE* 1.3 61.6 + - + +
213B TRP* 3.2 5.8 + - + +
214B MET* 2.9 51.0 + - + +
253B PHE* 5.2 2.5 - - + -
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Residues in contact with ILE 211 (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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207B LEU* 2.9 40.1 + - + +
208B LYS* 3.8 5.4 - - + +
210B VAL* 1.3 74.9 - - + +
212B ASP* 1.3 69.9 + - - +
214B MET* 3.0 9.2 + - - +
215B LYS* 2.9 33.6 + - - +
253B PHE* 4.1 23.6 - - + -
342B PRO* 3.8 28.5 - - + +
343B GLN 3.6 20.9 - - - +
344B MET* 3.6 23.8 - - + +
345B PRO* 4.2 1.6 - - + -
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Residues in contact with ASP 212 (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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208B LYS* 2.6 58.5 + - - +
209B LYS* 3.8 8.1 - - - +
211B ILE* 1.3 77.0 - - - +
213B TRP* 1.3 58.1 + - - +
215B LYS* 3.2 18.2 + - - +
216B LEU* 2.9 33.3 + - + +
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Residues in contact with TRP 213 (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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131B CYS* 5.4 1.1 - - - -
156B VAL* 3.6 32.5 - - + -
158B LEU* 3.9 32.1 - - + -
168B ASP* 3.2 36.1 + - + -
169B THR 3.8 19.0 + - - -
170B PHE* 3.7 33.4 - + + -
209B LYS 3.0 17.8 + - - +
210B VAL* 3.4 5.6 - - - +
212B ASP* 1.3 78.1 - - - +
214B MET* 1.3 78.2 + - + +
216B LEU* 3.4 14.1 + - + +
217B LYS* 3.3 39.1 + - + +
219B LEU* 5.4 0.4 - - + -
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Residues in contact with MET 214 (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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131B CYS* 4.4 8.3 - - - -
156B VAL* 5.7 3.1 - - + -
210B VAL* 2.9 34.8 + - + +
211B ILE* 3.0 7.2 + - - +
213B TRP* 1.3 90.5 - - + +
215B LYS* 1.3 62.0 + - - +
217B LYS* 3.1 13.0 + - - +
218B GLU 3.2 8.1 + - - -
219B LEU* 3.2 31.1 + - + +
225B TYR* 3.5 39.0 - - + +
227B LEU* 4.4 4.0 - - + -
253B PHE* 3.9 26.2 - - + -
342B PRO* 3.7 19.7 - - + -
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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
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211B ILE* 2.9 26.9 + - + +
212B ASP* 3.5 20.2 - - - +
214B MET* 1.3 74.9 - - - +
216B LEU* 1.3 60.4 + - - +
218B GLU* 2.8 26.0 + - - +
219B LEU 4.9 1.1 - - - +
341B PRO* 6.1 2.0 - - + +
342B PRO* 3.6 31.6 + - + +
343B GLN* 4.9 10.5 - - - +
344B MET 5.7 0.4 - - - +
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Residues in contact with LEU 216 (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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212B ASP* 2.9 16.6 + - + +
213B TRP* 3.6 16.2 - - + +
214B MET 3.3 0.2 - - - -
215B LYS* 1.3 76.0 - - - +
217B LYS* 1.3 64.3 + - + +
218B GLU* 3.2 7.3 + - - +
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Residues in contact with LYS 217 (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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129B TYR* 5.3 1.8 - - + -
158B LEU* 3.7 22.8 - - + +
167B GLU* 5.1 3.9 + - - +
168B ASP* 2.7 43.9 + - - +
213B TRP* 3.3 34.5 + - + +
214B MET* 3.1 9.1 + - - +
215B LYS 3.1 0.8 - - - -
216B LEU* 1.3 79.7 - - + +
218B GLU* 1.3 70.4 + - - +
219B LEU* 3.4 14.6 + - + +
223B TYR* 3.3 19.9 - - - -
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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