Contacts of the helix formed by residues 197 - 212 (chain B) in PDB entry 4UQJ
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 GLU 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ASP* 4.7 4.1 + - - +
140B ASP* 5.6 4.9 - - + +
141B ARG* 3.5 16.1 - - - +
196B CYS* 1.3 75.5 - - - +
198B ARG* 1.3 65.9 + - - +
199B ASP* 3.0 12.4 + - + +
200B LYS* 3.4 8.6 + - + +
201B VAL* 3.0 25.0 + - - +
224B ASN* 4.7 1.6 - - - +
280B TYR* 6.1 1.3 - - - -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLU* 1.3 74.0 - - - +
199B ASP* 1.3 66.9 + - - +
201B VAL* 4.1 3.7 - - - +
202B ASN* 3.7 27.4 + - - +
224B ASN* 4.5 14.5 - - - +
226B GLY 5.8 0.2 - - - +
229B ASP* 5.1 20.2 - - + +
230B GLY* 5.3 5.3 - - - +
280B TYR* 6.0 6.8 - - + -
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Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLU* 3.0 6.4 - - + -
198B ARG* 1.3 85.2 - - - +
200B LYS* 1.3 64.1 + - - +
201B VAL 3.0 5.9 + - - -
202B ASN* 3.1 16.0 + - - +
203B ASP* 3.2 19.6 + - - +
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Residues in contact with LYS 200 (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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138B ASP* 4.1 15.5 - - - +
165B VAL* 5.9 3.6 - - + +
177B TYR* 5.0 0.3 + - - -
196B CYS* 3.6 24.7 - - + -
197B GLU* 3.4 7.7 + - + +
199B ASP* 1.3 77.9 - - - +
201B VAL* 1.3 60.6 + - - +
203B ASP* 3.7 12.9 + - - +
204B ILE* 3.2 29.4 + - + +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.6 10.1 - - + -
196B CYS* 3.8 25.1 - - + +
197B GLU 3.0 23.3 + - - +
198B ARG* 4.1 6.3 - - - +
199B ASP 3.0 0.2 - - - -
200B LYS* 1.3 76.8 - - - +
202B ASN* 1.3 66.7 + - - +
204B ILE* 3.2 7.1 + - - +
205B VAL* 2.8 43.0 + - + +
222B ILE* 4.0 36.8 - - + -
224B ASN* 4.6 2.7 - - - +
230B GLY* 6.4 1.1 - - - -
232B LEU* 6.5 0.9 - - + -
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Residues in contact with ASN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG 3.7 15.2 + - - +
199B ASP* 3.1 9.8 + - - +
201B VAL* 1.3 86.2 - - - +
203B ASP* 1.3 61.0 + - - +
205B VAL* 3.8 3.8 - - - +
206B ASP* 2.9 39.5 + - - +
230B GLY* 4.2 7.2 - - - -
231B ASP* 3.8 26.7 + - - +
234B LYS* 3.7 24.6 + - - +
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Residues in contact with ASP 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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170B ASN* 4.8 13.2 + - - +
177B TYR* 4.3 12.3 - - + +
199B ASP* 3.2 15.3 + - - +
200B LYS* 3.7 13.4 - - - +
201B VAL 3.2 0.4 - - - -
202B ASN* 1.3 81.1 - - - +
204B ILE* 1.3 63.0 + - - +
206B ASP* 3.6 8.0 - - - +
207B GLN* 3.1 28.6 + - + +
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.5 5.8 - - + -
165B VAL* 4.1 19.7 - - + -
177B TYR* 3.9 24.0 - - + +
181B PHE* 4.8 10.5 - - + -
194B LEU* 3.6 43.7 - - + -
196B CYS* 4.0 18.6 - - - -
200B LYS* 3.2 16.1 + - + +
201B VAL* 3.2 6.8 + - - +
203B ASP* 1.3 74.5 - - - +
205B VAL* 1.3 55.1 + - - +
207B GLN* 3.1 8.3 + - - +
208B VAL* 2.8 50.0 + - + +
220B TYR* 5.8 0.2 - - + -
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 4.6 9.6 - - + -
201B VAL* 2.8 39.1 + - + +
202B ASN* 3.8 8.3 - - - +
204B ILE* 1.3 71.4 - - - +
206B ASP* 1.3 62.7 + - - +
208B VAL* 3.3 9.1 + - - +
209B ILE* 3.0 28.4 + - - +
222B ILE* 5.1 5.4 - - + -
231B ASP 4.9 2.5 - - - +
232B LEU* 6.6 0.4 - - + -
234B LYS* 3.7 24.5 - - + -
235B ILE* 3.5 39.9 - - + -
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ASN* 2.9 25.5 + - - +
203B ASP* 3.6 8.5 - - - +
205B VAL* 1.3 77.0 - - - +
207B GLN* 1.3 64.1 + - + +
209B ILE* 3.3 9.1 + - - +
210B THR* 3.0 25.5 + - - -
234B LYS* 3.1 34.0 + - - +
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Residues in contact with GLN 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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173B LYS 4.1 10.3 + - - -
174B ASP* 3.3 26.8 + - - +
177B TYR* 3.9 43.0 - - + +
181B PHE* 5.0 5.2 - - + -
203B ASP* 3.1 15.5 + - + +
204B ILE 3.1 8.4 + - - +
206B ASP* 1.3 74.8 - - - +
208B VAL* 1.3 62.9 + - - +
210B THR* 3.1 14.3 + - - +
211B ILE* 3.0 35.5 + - + +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PHE* 4.0 19.7 - - + -
194B LEU* 5.8 0.4 - - + -
204B ILE* 2.8 32.5 + - + +
205B VAL* 3.5 12.1 - - - +
206B ASP 3.2 0.2 - - - -
207B GLN* 1.3 73.4 - - - +
209B ILE* 1.3 57.4 + - - +
211B ILE* 3.3 8.4 - - - +
212B GLY 3.0 6.6 + - - -
213B LYS* 2.9 58.1 + - + +
214B HIS* 3.7 11.2 - - + -
220B TYR* 3.2 27.6 - - + +
235B ILE* 4.8 3.8 - - + -
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B VAL* 3.0 18.1 + - + +
206B ASP* 3.7 9.4 - - - +
207B GLN 3.2 0.2 - - - -
208B VAL* 1.3 73.7 - - - +
210B THR* 1.3 67.3 + - - +
212B GLY* 3.1 12.5 + - - -
214B HIS* 3.3 29.6 + - + +
234B LYS* 3.4 44.0 - - + +
235B ILE* 3.4 24.5 - - + -
209D ILE* 4.4 16.5 - - + +
210D THR* 5.2 4.0 - - - -
214D HIS* 3.9 7.4 + - - -
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Residues in contact with THR 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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206B ASP 3.0 16.2 + - - -
207B GLN* 3.1 18.8 + - - +
209B ILE* 1.3 78.7 - - - +
211B ILE* 1.3 66.3 + - + +
212B GLY 3.3 0.7 + - - -
209D ILE* 5.2 4.9 - - - -
214D HIS* 3.5 17.1 - - - -
233D LEU 5.7 1.8 - - - +
234D LYS* 4.9 13.4 - - - +
237D PHE* 4.9 15.1 - - + +
238D GLY* 4.5 6.1 + - - -
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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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177B TYR* 6.1 1.3 - - + +
178B ARG* 5.9 7.6 - - + -
181B PHE* 3.6 47.3 - - + -
207B GLN* 3.0 21.9 + - - +
208B VAL* 3.3 10.8 - - - +
210B THR* 1.3 79.6 - - + +
212B GLY* 1.3 60.7 + - - +
213B LYS* 3.6 27.6 + - + +
214D HIS* 5.0 2.0 - - - -
215D VAL* 5.3 0.9 - - - +
237D PHE* 4.9 14.6 - - + +
238D GLY 4.7 8.7 - - - +
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Residues in contact with GLY 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 VAL 3.0 4.2 + - - -
209B ILE 3.1 11.6 + - - -
210B THR 3.1 4.8 - - - -
211B ILE* 1.3 80.1 - - - +
213B LYS* 1.3 57.4 + - - +
214B HIS* 3.1 18.2 + - - -
215B VAL* 3.7 22.8 - - - +
218B TYR* 4.7 0.7 - - - -
212D GLY* 6.3 0.2 - - - -
214D HIS* 4.4 10.5 - - - -
215D VAL* 4.6 12.1 - - - +
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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
------------------------------------------------------------
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