Contacts of the helix formed by residues 210 - 222 (chain A) in PDB entry 4WFH
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 VAL 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A CYS* 2.7 36.7 + - + +
209A PHE* 1.3 78.4 - - + +
211A LEU* 1.3 76.7 + - + +
212A THR 3.5 0.2 - - - -
213A PRO* 3.3 3.3 - - - +
214A THR* 3.0 32.6 + - + +
229A ILE* 5.1 7.4 - - + -
232A VAL* 4.2 16.8 - - + +
233A ILE* 5.1 11.4 - - + -
236A LEU* 4.7 0.2 - - + -
271A TYR* 5.2 3.1 - - + -
272A PHE* 4.3 25.1 - - + -
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Residues in contact with LEU 211 (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 CYS* 2.9 33.1 + - - +
207A LEU* 3.6 30.7 - - + +
210A VAL* 1.3 78.9 - - + +
212A THR* 1.3 64.5 + - - +
214A THR* 2.5 23.0 + - - +
215A PHE* 3.2 27.7 + - + -
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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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207A LEU* 2.4 40.8 + - - +
208A LEU* 3.6 17.0 - - + +
211A LEU* 1.3 75.5 - - - +
213A PRO* 1.3 66.0 - - + +
215A PHE* 3.3 6.4 + - - +
216A VAL* 2.9 39.7 + - + +
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Residues in contact with PRO 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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208A LEU 3.4 10.3 - - - +
209A PHE 3.2 20.2 - - - +
210A VAL 3.3 13.5 - - - +
212A THR* 1.3 95.0 - - + +
214A THR* 1.3 55.4 + - - +
216A VAL* 3.0 10.4 + - + +
217A PHE* 2.7 58.7 + - + -
232A VAL* 4.0 4.0 - - + -
264A TRP* 3.2 27.1 - - + +
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Residues in contact with THR 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 VAL* 3.0 17.7 + - + +
211A LEU* 2.5 28.1 + - - +
213A PRO* 1.3 74.2 - - - +
215A PHE* 1.3 65.2 + - - +
217A PHE* 4.4 0.2 - - - -
218A CYS* 3.0 28.9 + - - +
225A LYS* 5.0 2.4 - - - -
228A ALA* 3.4 15.7 - - - +
229A ILE* 3.4 41.1 - - + +
232A VAL* 3.5 22.9 - - + -
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Residues in contact with PHE 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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211A LEU* 3.2 30.4 + - + +
212A THR* 3.6 9.4 - - - +
214A THR* 1.3 84.3 + - - +
216A VAL* 1.3 67.6 + - + +
218A CYS* 3.3 20.6 - - + +
219A TYR* 3.5 9.0 + - - +
225A LYS* 6.6 0.2 - - + -
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Residues in contact with VAL 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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212A THR* 2.9 35.9 + - + +
213A PRO* 3.2 11.4 - - + +
215A PHE* 1.3 76.9 - - + +
217A PHE* 1.3 65.1 + - + +
219A TYR* 3.2 6.4 + - - +
220A MET* 3.0 42.2 + - + +
257A TYR* 4.8 10.5 - - + -
260A LEU* 6.1 5.8 - - + -
261A VAL* 6.5 0.2 - - + -
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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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213A PRO* 2.7 47.3 + - + +
214A THR* 4.1 3.4 - - - +
216A VAL* 1.3 74.9 - - + +
218A CYS* 1.3 67.7 - - - +
220A MET* 4.2 3.8 - - - +
221A GLU* 2.7 31.0 + - + +
223A TRP* 3.9 21.2 + + + -
228A ALA* 4.3 3.6 - - + -
231A PHE* 3.8 22.7 - + - -
232A VAL* 4.1 6.5 - - + -
246A ALA* 3.5 24.9 - - + -
257A TYR* 3.7 22.7 - + - -
261A VAL* 4.1 15.5 - - + -
264A TRP* 3.8 31.2 - + + -
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Residues in contact with CYS 218 (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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214A THR 3.0 19.4 + - - +
215A PHE* 3.3 16.2 - - + +
217A PHE* 1.3 77.1 - - - +
219A TYR* 1.3 60.9 + - - +
222A ASP* 3.3 17.3 + - - +
223A TRP 3.4 29.4 + - - +
224A SER* 4.7 0.7 - - - -
225A LYS* 3.9 24.7 - - - -
228A ALA* 4.1 5.6 - - + +
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Residues in contact with TYR 219 (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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215A PHE 3.5 7.2 + - - +
216A VAL* 3.2 9.0 + - - +
217A PHE 3.2 0.2 - - - -
218A CYS* 1.3 80.9 - - + +
220A MET* 1.3 79.9 + - + +
222A ASP* 4.1 5.4 + - - +
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Residues in contact with MET 220 (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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216A VAL* 3.0 28.0 + - + +
217A PHE* 3.2 3.3 + - - +
219A TYR* 1.3 96.6 - - + +
221A GLU* 1.3 58.6 + - - +
222A ASP 3.4 0.8 + - - -
251A ARG* 2.3 51.7 + - - +
254A SER* 4.4 20.0 - - - +
257A TYR* 3.5 40.4 - - + +
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Residues in contact with GLU 221 (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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217A PHE* 2.7 22.8 + - + +
220A MET* 1.3 74.4 - - - +
222A ASP* 1.3 70.8 + - - +
223A TRP* 3.4 53.4 + - + -
245A VAL 4.3 3.3 - - - +
246A ALA* 3.7 17.6 - - + +
251A ARG* 4.2 5.6 + - - -
257A TYR* 2.5 34.4 + - - +
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Residues in contact with ASP 222 (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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218A CYS 3.3 11.7 + - - +
219A TYR 4.1 4.9 + - - +
220A MET 3.4 2.8 - - - -
221A GLU* 1.3 81.1 - - - +
223A TRP* 1.3 64.7 + - - +
227A GLU* 4.7 1.0 - - - +
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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