Contacts of the helix formed by residues 208 - 219 (chain B) in PDB entry 3UGV
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 ASP 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B GLY 4.3 0.2 + - - -
207B LEU* 1.3 76.8 - - - +
209B MET* 1.3 59.0 + - - +
210B ALA* 3.1 7.3 + - - +
211B GLU* 2.8 41.2 + - - +
212B ALA* 2.9 23.4 + - - +
231B VAL* 3.9 2.2 - - - -
300C PRO* 5.0 6.5 - - + +
319C THR 5.7 0.5 - - - +
320C ALA 4.9 6.4 - - - +
321C HIS* 4.4 16.5 - - - -
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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
----------------------------------------------------------
208B ASP* 1.3 74.8 - - - +
210B ALA* 1.3 58.1 + - - +
212B ALA* 3.6 1.0 - - - +
213B MET* 2.8 57.9 + - + +
231B VAL* 3.9 19.6 - - + +
235B ASN* 3.5 22.7 - - - +
238B GLY* 3.7 37.2 - - - +
241B GLN* 4.4 10.8 - - + -
242B LEU* 4.1 12.3 - - + -
272C ASP 5.9 0.4 - - - +
298C GLY 3.6 18.3 + - - +
299C ILE* 5.7 2.9 - - + -
300C PRO* 3.9 13.5 - - + +
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Residues in contact with ALA 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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208B ASP* 3.1 6.1 + - - +
209B MET* 1.3 76.0 - - - +
211B GLU* 1.3 66.6 + - + +
213B MET* 3.4 7.8 + - - +
214B HIS* 3.0 38.5 + - + +
225C GLU* 5.2 0.4 - - - +
249C PRO* 5.7 1.3 - - + -
273C LEU* 4.2 9.9 - - + -
300C PRO* 3.7 11.3 - - + +
321C HIS* 3.3 39.5 - - + +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY 4.3 3.3 - - - +
207B LEU* 3.7 24.7 - - + +
208B ASP* 2.8 44.6 + - - +
210B ALA* 1.3 73.5 - - + +
212B ALA* 1.3 58.3 + - - +
214B HIS* 3.3 6.0 + - - +
215B ARG* 2.8 44.5 + - - +
321C HIS* 6.1 1.1 - - + +
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Residues in contact with ALA 212 (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 18.8 - - + +
208B ASP 2.9 17.1 + - - +
209B MET 3.6 4.7 - - - +
211B GLU* 1.3 78.2 - - - +
213B MET* 1.3 53.4 + - - +
216B THR* 2.6 41.8 + - - -
230B PRO* 4.1 5.4 - - + -
231B VAL* 3.5 24.0 - - + -
242B LEU* 4.0 16.4 - - + -
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Residues in contact with MET 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B MET* 2.8 36.6 + - + +
210B ALA* 3.7 7.6 - - - +
211B GLU 3.3 0.2 - - - -
212B ALA* 1.3 75.1 - - - +
214B HIS* 1.3 62.7 + - - +
216B THR* 3.8 1.3 + - - -
217B ARG* 3.2 25.8 + - - +
241B GLN* 6.2 2.7 - - + -
242B LEU* 4.1 18.6 - - + -
245B ASP* 4.5 14.8 - - - +
247C LYS 4.1 15.3 - - - +
248C THR 4.8 0.2 - - - -
249C PRO* 3.8 31.6 - - + -
272C ASP* 3.7 42.2 - - - +
273C LEU* 5.3 1.6 - - - -
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Residues in contact with HIS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ALA* 3.0 27.7 + - + +
211B GLU* 3.9 5.0 - - - +
213B MET* 1.3 79.5 - - - +
215B ARG* 1.3 63.3 + - + +
217B ARG* 3.5 11.6 - - - +
218B GLN* 3.1 35.9 + - - +
223C GLY* 6.1 0.9 - - - -
224C LEU 3.5 16.6 + - - -
225C GLU* 3.3 51.2 + - - -
248C THR* 6.1 0.2 - - - -
249C PRO* 3.9 20.6 - - + +
273C LEU* 6.3 0.4 - - + -
321C HIS* 6.1 0.2 - + - -
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Residues in contact with ARG 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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175B GLY* 3.8 11.5 - - - -
176B ARG 2.7 29.4 + - - -
177B ASP* 3.4 17.6 + - - +
179B PRO* 3.7 34.8 - - + +
182B ASP* 3.2 20.8 + - - -
203B PHE* 4.4 10.3 - - + -
207B LEU* 3.8 36.5 - - + +
211B GLU* 2.8 29.0 + - - +
214B HIS* 1.3 74.4 - - + +
216B THR* 1.3 64.5 + - - +
218B GLN* 3.2 19.9 + - - +
219B ILE* 3.4 19.7 + - - +
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 4.5 7.9 - - + -
207B LEU* 5.1 1.1 - - + -
212B ALA* 2.6 30.2 + - + +
213B MET 3.8 2.1 + - - -
215B ARG* 1.3 72.4 - - - +
217B ARG* 1.3 67.4 + - - +
219B ILE* 3.3 11.5 + - - +
220B ASP 3.2 16.8 + - - -
227B ILE* 4.2 19.3 - - + -
230B PRO* 4.1 26.9 - - + -
242B LEU* 3.8 13.6 - - + +
246B LEU* 3.4 33.6 - - + +
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Residues in contact with ARG 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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213B MET 3.2 21.4 + - - +
214B HIS* 3.5 12.2 - - - +
215B ARG 3.2 0.4 - - - -
216B THR* 1.3 79.2 + - - +
218B GLN* 1.3 62.0 + - + +
219B ILE 3.3 0.7 + - - -
220B ASP* 3.3 18.7 + - + +
221B ASP* 4.9 3.5 + - - +
246B LEU* 4.3 3.3 - - - +
220C ASP* 3.0 22.1 + - - -
221C ASP* 3.1 21.8 + - - +
223C GLY* 6.1 1.4 - - - +
247C LYS* 3.5 43.2 - - - +
248C THR* 3.3 37.6 + - - +
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Residues in contact with GLN 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PRO* 3.5 36.4 - - - +
180B ALA* 4.6 1.6 + - - -
183B ILE* 3.8 29.1 - - + +
214B HIS* 3.1 26.5 + - - +
215B ARG* 3.5 16.0 - - - +
216B THR 3.2 0.6 - - - -
217B ARG* 1.3 79.3 - - + +
219B ILE* 1.3 60.8 + - + +
220B ASP 3.4 0.7 + - - -
221B ASP* 4.8 2.6 + - - +
222B LEU* 4.8 3.8 - - - +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B MET* 4.3 17.3 - - - -
182B ASP* 5.7 1.6 - - + -
183B ILE* 4.0 16.2 - - + -
201B VAL* 4.4 0.9 - - + -
203B PHE* 3.8 31.0 - - + -
215B ARG 3.5 10.1 - - - +
216B THR* 3.4 13.2 - - - +
217B ARG 3.2 0.2 - - - -
218B GLN* 1.3 80.1 - - + +
220B ASP* 1.3 63.3 + - - +
221B ASP 3.1 4.6 + - - -
222B LEU* 3.3 41.8 + - + +
223B GLY 4.8 0.2 + - - -
224B LEU* 3.7 19.4 - - + +
227B ILE* 3.4 26.8 - - + +
248B THR* 4.6 1.4 + - - -
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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