Contacts of the helix formed by residues 204 - 215 (chain B) in PDB entry 3ANX
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 ARG 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B LEU* 5.7 2.5 - - + +
203B HIS* 1.3 79.5 - - - +
205B VAL* 1.3 55.4 - - - +
206B HIS 3.2 2.5 - - - -
207B PRO* 2.9 16.4 - - + +
208B VAL* 2.7 40.9 + - - +
289B GLU* 2.8 45.5 + - - +
290B THR* 4.6 8.3 - - - +
291B MET* 3.9 25.8 - - - +
306B GLU* 5.6 7.1 + - - -
307B ALA* 3.6 33.7 + - - +
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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
----------------------------------------------------------
161B ASP* 4.2 13.7 - - + +
162B PRO* 5.7 0.9 - - + -
195B ALA 4.0 2.0 - - - +
196B GLY* 3.8 24.2 - - - -
197B MET 4.7 0.2 - - - +
203B HIS* 3.0 33.0 + - + +
204B ARG* 1.3 75.0 - - - +
206B HIS* 1.3 55.3 + - - +
208B VAL* 3.5 4.2 - - - +
209B VAL* 2.6 50.1 + - + +
299B PHE* 4.7 11.4 - - + -
301B VAL* 4.3 26.2 - - + -
305B GLY 5.4 0.2 - - - +
306B GLU* 5.2 0.4 - - - -
307B ALA* 4.6 12.4 - - - +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA* 3.0 41.8 + - + +
196B GLY 4.7 0.2 - - - +
197B MET 3.8 18.0 + - - +
198B ILE* 3.9 23.2 - - + +
203B HIS* 4.6 0.4 - - - -
205B VAL* 1.3 77.5 - - - +
207B PRO* 1.3 76.9 - - + +
209B VAL* 3.0 2.8 + - - +
210B HIS* 2.8 25.3 + - + +
222B SER* 3.3 25.9 + - - -
223B TYR 4.6 1.1 + - - -
235B GLY* 3.6 7.1 - - - -
236B PHE 3.1 31.4 - - - -
237B LEU* 4.8 2.7 - - + -
282B LEU* 4.6 8.0 - - + +
286B LEU* 4.1 13.9 - - + -
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Residues in contact with PRO 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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198B ILE* 6.6 0.2 - - + -
200B LEU* 4.5 9.6 - - + -
203B HIS* 5.0 1.3 - - + +
204B ARG* 2.9 26.5 - - + +
206B HIS* 1.3 95.2 - - + +
208B VAL* 1.3 49.9 + - - +
210B HIS* 2.8 6.6 + - - +
211B ARG* 2.6 35.0 + - - +
282B LEU* 5.4 2.5 - - + -
285B ALA* 3.6 41.7 - - + +
286B LEU* 3.8 17.7 - - + +
289B GLU* 3.7 17.4 - - + +
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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
----------------------------------------------------------
204B ARG* 2.7 28.5 + - + +
205B VAL* 3.7 3.1 - - - +
207B PRO* 1.3 69.8 - - - +
209B VAL* 1.3 61.9 + - - +
211B ARG* 3.8 1.5 - - - +
212B THR* 2.8 32.0 + - - +
289B GLU* 3.8 28.3 - - + +
291B MET* 3.5 38.1 - - + +
293B SER 5.3 0.4 - - - +
299B PHE* 4.3 17.3 - - + -
307B ALA* 3.8 21.3 - - + -
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Residues in contact with VAL 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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173B TYR* 4.4 15.0 - - + -
178B TYR* 3.8 17.9 - - - +
193B MET* 4.0 16.6 - - + -
195B ALA* 3.8 35.2 - - + +
205B VAL* 2.6 35.8 + - + +
206B HIS 3.7 3.6 - - - +
208B VAL* 1.3 72.6 - - - +
210B HIS* 1.3 60.7 + - - +
212B THR* 3.7 6.4 + - - -
213B VAL* 3.2 22.2 + - + +
237B LEU* 4.5 1.1 - - + -
299B PHE* 4.3 19.1 - - + -
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Residues in contact with HIS 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 HIS* 2.8 14.2 + - - +
207B PRO 2.8 12.2 + - - +
209B VAL* 1.3 75.1 - - - +
211B ARG* 1.3 56.0 + - - -
213B VAL* 3.0 5.9 + - - +
214B ARG* 2.7 51.7 + - + +
220B VAL* 3.2 48.0 + - + +
222B SER* 2.8 29.1 + - - +
237B LEU* 3.7 15.4 - - + +
286B LEU* 3.8 32.7 - - + +
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Residues in contact with ARG 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 PRO 2.6 16.4 + - - +
208B VAL 3.8 1.8 - - - +
210B HIS* 1.3 70.9 - - - +
212B THR* 1.3 67.0 + - - +
214B ARG* 3.2 29.8 + - - +
215B GLU* 2.6 32.6 + - - +
286B LEU 5.0 4.7 - - - -
289B GLU* 2.9 38.4 + - + +
290B THR* 3.4 24.3 + - - +
291B MET 3.5 12.6 - - - +
292B VAL* 3.3 13.3 - - + +
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Residues in contact with THR 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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173B TYR 3.7 9.9 + - - +
175B VAL* 2.9 32.2 - - + +
178B TYR* 3.4 24.5 - - + -
208B VAL* 2.8 32.2 + - - +
209B VAL* 3.7 7.6 - - - -
211B ARG* 1.3 75.3 - - - +
213B VAL* 1.3 61.7 + - - +
215B GLU* 3.2 2.3 - - - +
291B MET 4.3 0.8 + - - -
292B VAL* 3.8 8.1 - - - -
293B SER* 3.3 41.9 + - - +
299B PHE* 4.8 2.5 - - - -
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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
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178B TYR* 3.5 36.1 - - + -
191B MET* 4.3 9.0 - - + -
193B MET* 4.5 2.5 - - - -
209B VAL 3.2 14.5 + - - +
210B HIS 3.0 7.8 + - - +
212B THR* 1.3 71.6 - - - +
214B ARG* 1.3 66.2 + - - +
215B GLU 3.0 2.0 - - - -
216B ALA 3.1 11.3 + - - +
217B PHE* 3.2 32.7 + - + -
220B VAL* 3.9 9.0 - - + +
237B LEU* 4.2 14.1 - - + -
239B ALA* 3.8 18.6 - - + -
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B HIS* 2.7 38.5 + - + +
211B ARG* 3.2 30.7 + - - +
213B VAL* 1.3 70.7 - - - +
215B GLU* 1.3 60.6 + - - +
217B PHE 2.8 27.3 + - - +
218B ARG* 2.5 43.6 + - - +
220B VAL* 3.4 27.3 - - + +
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Residues in contact with GLU 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 VAL* 3.1 25.4 - - + -
179B ARG* 3.3 24.7 + - - +
211B ARG* 2.6 41.9 + - - -
212B THR 3.2 4.3 - - - +
214B ARG* 1.3 80.8 + - - +
216B ALA* 1.3 55.9 + - - +
217B PHE 3.7 0.2 - - - -
292B VAL* 3.5 24.0 - - + -
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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