Contacts of the helix formed by residues 228 - 238 (chain A) in PDB entry 2W9F
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 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A TYR 3.2 3.4 + - - -
227A TYR* 1.3 103.8 - - + +
229A LEU* 1.3 57.3 + - - +
230A THR* 3.2 4.3 - - - +
231A ARG* 3.1 58.4 + - + +
232A PHE* 2.9 29.2 + - + +
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Residues in contact with LEU 229 (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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168A MET* 3.6 36.3 - - + -
208A VAL* 4.2 7.4 - - + -
209A VAL* 4.2 15.7 - - + -
212A VAL* 4.0 29.4 - - + -
225A SER* 3.3 25.1 - - - +
226A TYR* 3.5 10.1 + - - +
227A TYR 3.1 2.3 - - - -
228A ARG* 1.3 76.8 - - - +
230A THR* 1.3 54.8 + - - +
232A PHE* 3.7 21.5 - - + -
233A LEU* 2.7 49.9 + - + +
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Residues in contact with THR 230 (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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209A VAL* 3.6 25.3 - - - +
213A GLN* 5.3 0.3 + - - -
228A ARG* 3.2 1.3 - - - +
229A LEU* 1.3 78.6 - - - +
231A ARG* 1.3 61.8 + - - +
234A SER* 2.9 27.0 + - - -
241A PRO* 3.5 30.7 - - + +
244A LEU* 3.5 23.6 - - + +
245A ARG* 3.7 25.7 + - - +
248A GLN* 4.0 6.9 + - - -
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG* 3.1 53.3 + - + +
230A THR* 1.3 79.3 - - - +
232A PHE* 1.3 66.3 + - - +
234A SER* 3.2 9.3 + - - -
235A ARG* 2.9 53.2 + - - +
241A PRO* 4.5 12.2 - - + +
245A ARG* 5.6 1.1 - - - +
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Residues in contact with PHE 232 (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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167A LYS* 3.6 41.3 - - + -
168A MET* 4.5 11.4 - - + -
169A PRO* 5.7 4.3 - - + -
227A TYR 5.5 1.1 - - - +
228A ARG* 2.9 18.1 + - + +
229A LEU* 3.5 24.7 - - + +
231A ARG* 1.3 78.4 - - - +
233A LEU* 1.3 71.3 + - + +
235A ARG* 3.1 34.2 - - + +
236A VAL* 3.2 20.2 + - + +
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Residues in contact with LEU 233 (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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164A PHE* 3.8 28.9 - - + -
168A MET* 3.4 28.3 - - + -
205A ALA* 4.2 19.5 - - + +
208A VAL* 4.2 6.3 - - + -
209A VAL* 3.7 28.3 - - + -
229A LEU* 2.7 31.5 + - + +
230A THR 4.1 2.2 - - - +
232A PHE* 1.3 84.0 - - + +
234A SER* 1.3 60.1 + - - +
236A VAL* 3.2 8.2 + - + +
237A ILE* 2.8 32.6 + - - +
244A LEU* 4.2 10.1 - - + -
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Residues in contact with SER 234 (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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230A THR 2.9 17.4 + - - -
231A ARG* 3.2 12.1 + - - -
233A LEU* 1.3 73.4 - - - +
235A ARG* 1.3 55.8 + - - +
237A ILE* 4.3 0.7 - - - +
238A LYS* 2.5 38.5 + - - -
239A CYS* 3.3 32.2 + - - -
241A PRO* 3.3 29.8 - - - +
244A LEU* 3.8 8.7 - - - +
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Residues in contact with ARG 235 (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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231A ARG* 2.9 47.2 + - - +
232A PHE* 3.1 22.4 - - + +
234A SER* 1.3 77.5 - - - +
236A VAL* 1.3 64.0 + - + +
238A LYS* 3.4 20.2 + - - +
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Residues in contact with VAL 236 (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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28A LEU* 3.3 34.8 - - + +
32A LEU* 4.8 0.2 - - - +
163A HIS* 4.0 8.3 - - + +
164A PHE* 3.4 27.4 - - + -
167A LYS* 4.0 31.2 - - + +
232A PHE* 3.2 26.8 + - + +
233A LEU* 3.4 15.7 - - + +
235A ARG* 1.3 78.4 - - + +
237A ILE* 1.3 61.6 + - - +
238A LYS* 3.3 13.7 + - - +
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Residues in contact with ILE 237 (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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28A LEU* 5.0 1.3 - - + -
32A LEU* 3.4 26.1 - - + +
160A PHE* 5.6 0.4 - - + -
164A PHE* 3.9 20.2 - - + -
201A SER* 3.5 47.3 - - - +
202A MET* 3.9 8.5 - - + +
205A ALA* 4.2 11.7 - - + -
233A LEU 2.8 19.4 + - - +
234A SER* 3.9 2.0 - - - +
236A VAL* 1.3 75.3 - - + +
238A LYS* 1.3 71.1 + - - +
239A CYS* 3.5 34.3 - - + -
244A LEU* 5.6 0.9 - - + -
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Residues in contact with LYS 238 (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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25A ASP* 5.1 15.8 + - - +
28A LEU* 4.9 8.3 - - - +
29A ARG* 5.5 8.5 - - - +
32A LEU* 4.9 7.7 - - + +
234A SER 2.5 15.5 + - - -
235A ARG* 3.4 13.3 + - - +
236A VAL* 3.3 18.5 + - - +
237A ILE* 1.3 79.9 - - - +
239A CYS* 1.3 59.8 + - - +
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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