Contacts of the helix formed by residues 204 - 217 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A HIS* 1.3 81.4 - - + +
205A VAL* 1.3 70.8 + - - +
206A HIS 3.3 2.5 - - - -
207A PRO* 3.2 21.8 - - + +
208A VAL* 3.3 13.9 + - + +
285A ALA* 6.4 0.9 - - + -
288A LYS* 5.6 10.1 - - + +
289A GLU* 2.7 44.9 + - - +
290A THR* 5.6 1.0 + - - -
291A MET* 2.9 33.3 - - - +
305A GLY 4.1 1.2 + - - -
306A GLU* 5.9 0.7 - - - -
307A ALA* 3.8 34.6 + - + +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP* 4.0 25.6 - - + +
162A PRO* 4.2 12.1 - - + -
163A VAL* 6.1 0.9 - - + -
173A TYR* 6.0 0.2 - - + -
195A ALA 5.5 0.2 - - - -
196A GLY* 4.8 7.0 - - - -
197A MET* 4.9 8.7 + - + +
203A HIS* 3.9 21.4 - - + +
204A ARG* 1.3 73.6 - - - +
206A HIS* 1.3 69.1 + - - +
208A VAL* 4.1 0.5 - - - +
209A VAL* 3.1 27.9 + - + +
299A PHE* 3.8 28.9 - - + -
301A VAL* 3.6 28.8 - - + +
305A GLY 5.0 1.2 + - - -
307A ALA* 5.7 0.4 - - - +
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA* 3.2 38.3 + - + +
196A GLY 4.1 0.2 - - - +
197A MET 4.0 10.2 + - - +
198A ILE* 3.9 39.4 - - + +
203A HIS 5.0 0.2 + - - -
204A ARG 3.2 1.2 + - - -
205A VAL* 1.3 83.5 - - - +
207A PRO* 1.3 67.3 - - + +
209A VAL* 3.3 1.4 + - - +
210A HIS* 3.1 21.3 + - + -
222A SER* 2.7 32.6 + - - -
223A TYR 5.4 0.2 + - - -
235A GLY* 4.2 4.8 - - - -
236A PHE 4.0 13.4 + - - -
237A LEU* 4.7 3.8 - - + -
282A LEU* 4.3 8.0 - - + +
286A LEU* 3.6 18.9 - - + +
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Residues in contact with PRO 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 6.0 0.9 - - + -
200A LEU* 5.9 4.3 - - + -
203A HIS 4.7 4.5 - - - +
204A ARG* 3.2 26.5 - - + +
206A HIS* 1.3 88.0 - - + +
208A VAL* 1.3 57.9 + - - +
210A HIS* 3.4 3.6 + - - +
211A ARG* 2.9 27.9 + - - +
282A LEU* 5.1 4.7 - - + -
285A ALA* 4.0 28.0 - - + +
286A LEU* 4.1 31.5 - - + +
289A GLU* 3.5 18.0 - - + +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.3 17.4 + - - +
205A VAL 4.1 1.3 - - - +
207A PRO* 1.3 73.2 - - - +
209A VAL* 1.3 66.3 + - - +
210A HIS 3.1 0.2 - - - -
211A ARG* 3.0 2.3 + - - +
212A THR* 2.6 39.2 + - - +
289A GLU* 3.5 30.3 - - - +
291A MET* 3.7 29.6 - - + +
293A SER 4.9 0.7 - - - +
299A PHE* 4.1 27.1 - - + -
307A ALA* 4.2 21.8 - - + -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A TYR* 3.9 26.5 - - + -
178A TYR* 4.2 7.6 - - - +
193A MET* 3.7 20.2 - - + -
195A ALA* 3.4 30.1 - - + -
205A VAL* 3.1 26.6 + - + +
206A HIS 3.6 4.0 - - - +
208A VAL* 1.3 83.9 - - - +
210A HIS* 1.4 62.1 + - - +
212A THR* 3.5 3.6 - - - -
213A VAL* 3.0 27.2 + - + +
237A LEU* 4.6 2.7 - - + -
299A PHE* 4.4 13.0 - - + -
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Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A HIS* 3.1 15.0 + - + +
207A PRO 3.5 8.5 - - - +
208A VAL 3.1 0.4 - - - -
209A VAL* 1.4 76.9 - - - +
211A ARG* 1.3 66.6 + - + +
214A ARG* 3.1 26.7 + - + +
220A VAL* 3.3 43.2 + - + +
222A SER* 3.2 34.2 - - - -
237A LEU* 3.6 14.4 - - + +
286A LEU* 3.8 30.5 - - + +
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PRO 2.9 17.8 + - - +
208A VAL 3.0 4.2 + - - +
210A HIS* 1.3 83.0 - - + +
212A THR* 1.3 57.2 + - - +
214A ARG* 3.2 21.7 - - - +
215A GLU* 3.0 33.8 + - - +
286A LEU 5.6 2.0 - - - +
289A GLU* 3.5 30.8 + - + +
290A THR* 4.2 9.4 + - - +
291A MET 3.4 20.9 - - - +
292A VAL* 3.2 21.5 - - + +
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A TYR 3.6 20.4 + - - +
175A VAL* 3.8 17.4 - - + +
178A TYR* 3.8 7.1 - - + -
208A VAL* 2.6 28.2 + - - +
209A VAL* 3.5 4.7 - - - -
211A ARG* 1.3 73.4 - - - +
213A VAL* 1.3 69.6 + - - +
214A ARG 2.9 1.1 - - - -
215A GLU* 2.9 21.2 + - - +
216A ALA 3.6 2.6 + - - -
292A VAL* 3.7 11.0 - - - -
293A SER* 3.3 41.3 + - - +
299A PHE* 5.5 0.5 - - - -
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Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.4 40.8 - - + +
191A MET* 4.1 4.0 - - + -
193A MET* 4.1 15.9 - - - -
209A VAL* 3.0 15.0 + - + +
210A HIS 4.0 2.9 - - - +
212A THR* 1.3 80.6 - - - +
214A ARG* 1.3 59.9 + - - +
216A ALA* 3.0 12.7 + - - +
217A PHE* 3.1 28.3 + - + +
220A VAL* 3.5 22.9 - - + -
237A LEU* 4.2 8.7 - - + -
239A ALA* 4.0 9.6 - - + -
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A HIS* 3.1 23.4 + - + +
211A ARG* 3.2 26.2 - - - +
212A THR 2.9 1.4 + - - -
213A VAL* 1.3 73.9 - - - +
215A GLU* 1.3 59.0 + - - +
217A PHE 2.8 32.8 + - - +
218A ARG* 3.0 49.2 + - - +
220A VAL* 3.3 28.8 - - + +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 4.0 12.1 - - + -
179A ARG* 3.1 32.7 + - - +
211A ARG* 3.0 36.2 + - - +
212A THR 2.9 13.2 + - - +
214A ARG* 1.3 78.2 - - - +
216A ALA* 1.3 55.3 + - - -
292A VAL* 4.5 16.3 - - + +
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A VAL* 3.9 5.4 - - + -
178A TYR* 3.6 18.4 - - + -
179A ARG* 3.5 44.1 + - + +
182A LYS* 3.3 31.4 + - - -
212A THR 3.6 1.2 + - - +
213A VAL 3.0 6.5 + - - +
215A GLU* 1.3 76.5 - - - +
217A PHE* 1.3 65.7 + - + +
241A ASP* 4.0 0.3 - - - +
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Residues in contact with PHE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.8 18.6 - - + -
181A VAL* 4.3 2.7 - - + -
182A LYS* 3.1 42.4 - - + -
185A LEU* 4.2 16.8 - - + -
191A MET* 3.4 33.4 - - + -
213A VAL* 3.1 20.3 + - + +
214A ARG* 2.8 32.1 + - - +
216A ALA* 1.3 85.5 - - + +
218A ARG* 1.3 64.3 + - - +
219A TYR 4.4 0.4 - - - +
220A VAL* 3.9 5.3 - - + +
239A ALA* 3.5 24.5 - - + -
240A SER* 3.7 28.3 - - - +
241A ASP* 3.5 6.7 - - - -
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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