Contacts of the helix formed by residues 233 - 247 (chain A) in PDB entry 5WN0
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 THR 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A LEU* 3.7 33.7 - - + -
182A LEU* 3.7 6.4 - - + +
227A LYS 3.8 7.6 - - - +
228A LYS* 4.4 2.0 - - - +
229A ASN 3.4 18.2 - - - +
231A GLY 3.7 0.2 - - - -
232A PHE* 1.4 81.1 - - - +
234A PRO* 1.3 67.0 - - - +
235A GLN* 3.3 15.6 + - - -
236A GLU* 3.0 34.8 + - - +
237A ARG* 2.8 27.9 + - - +
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Residues in contact with PRO 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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227A LYS* 3.5 44.4 - - + +
228A LYS* 4.7 8.1 - - - +
232A PHE 3.8 1.1 - - - +
233A THR* 1.3 87.1 - - - +
235A GLN* 1.3 74.4 + - - +
237A ARG* 3.7 6.9 - - + +
238A GLN* 2.9 35.1 + - - +
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Residues in contact with GLN 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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182A LEU* 3.9 16.4 - - + +
186A GLN* 3.1 41.5 + - - +
189A ASP* 4.9 1.9 - - - +
228A LYS* 3.9 11.8 + - - +
233A THR* 3.3 21.1 + - - +
234A PRO* 1.3 93.3 - - - +
236A GLU* 1.3 62.6 + - - +
238A GLN* 3.9 14.4 + - - +
239A GLY* 3.2 18.4 + - - -
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Residues in contact with GLU 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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175A ALA* 3.3 22.6 + - - +
182A LEU* 4.0 10.7 - - + +
185A ARG* 3.1 39.0 + - + +
186A GLN* 6.2 0.2 - - - -
189A ASP* 4.4 7.5 - - - +
212A ASN 3.8 2.0 - - - +
213A VAL* 4.0 17.9 - - + +
231A GLY* 2.6 36.7 + - - -
233A THR* 3.0 34.8 + - - +
235A GLN* 1.3 76.2 - - - +
237A ARG* 1.3 64.2 + - - +
239A GLY* 2.9 12.6 + - - -
240A PHE 3.1 10.4 + - - -
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Residues in contact with ARG 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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213A VAL* 3.9 10.5 - - + -
214A ALA 3.7 11.0 - - - +
215A HIS* 3.2 27.8 + - + +
216A GLU* 3.2 25.9 + - - +
217A GLU* 4.0 18.6 + - - +
227A LYS* 3.6 23.2 - - - +
232A PHE* 3.1 51.5 - - + -
233A THR 2.8 24.6 + - - +
234A PRO* 3.7 7.4 - - + +
236A GLU* 1.3 71.5 - - - +
238A GLN* 1.3 62.7 + - - +
240A PHE* 3.0 16.0 + - - +
241A GLY* 3.1 9.2 + - - -
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Residues in contact with GLN 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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186A GLN* 5.6 1.2 + - - -
193A ARG* 5.2 3.2 - - - +
234A PRO 2.9 16.5 + - - +
235A GLN* 3.9 18.0 + - - +
237A ARG* 1.3 73.5 - - - +
239A GLY* 1.3 62.6 + - - +
241A GLY* 3.3 3.6 + - - +
242A GLU* 2.7 46.8 + - + +
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Residues in contact with GLY 239 (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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189A ASP* 3.9 17.6 - - - +
193A ARG* 4.5 8.2 + - - -
235A GLN 3.2 11.6 + - - -
236A GLU 2.9 9.7 + - - -
238A GLN* 1.3 80.4 - - - +
240A PHE* 1.3 59.5 + - - +
242A GLU* 3.1 10.6 + - - +
243A LEU* 2.8 27.6 + - - +
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Residues in contact with PHE 240 (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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189A ASP* 4.8 0.8 + - - -
211A LEU* 3.7 27.8 - - + -
213A VAL* 3.5 27.8 - - + +
215A HIS* 3.3 37.7 - + + +
236A GLU 3.1 9.2 + - - +
237A ARG 3.0 11.3 + - - +
239A GLY* 1.3 74.1 - - - +
241A GLY* 1.3 57.2 + - - +
243A LEU* 2.9 16.3 + - + +
244A LEU* 2.9 49.1 + - + +
251A ASP* 4.3 4.9 - - - -
284A TYR* 3.8 33.4 - + - -
286A LEU* 3.9 20.2 - - + -
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Residues in contact with GLY 241 (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 HIS* 4.2 13.6 - - - -
237A ARG 3.1 9.2 + - - -
238A GLN* 3.3 4.2 + - - -
240A PHE* 1.3 79.4 - - - +
242A GLU* 1.3 57.5 + - - +
244A LEU* 3.1 10.1 + - - +
245A GLN* 2.8 32.1 + - - +
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Residues in contact with GLU 242 (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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193A ARG* 3.3 40.5 + - - +
238A GLN* 2.7 38.4 + - + +
239A GLY* 3.1 10.3 + - - +
241A GLY* 1.3 72.8 - - - +
243A LEU* 1.3 56.7 + - - +
245A GLN* 4.8 11.4 - - - +
246A ALA* 2.8 39.2 + - - +
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Residues in contact with LEU 243 (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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192A PHE* 5.0 9.4 - - + -
193A ARG* 4.2 20.8 - - + +
196A LEU* 3.8 19.7 - - + -
207A LEU* 4.3 9.2 - - + -
211A LEU* 4.7 7.6 - - + -
239A GLY 2.8 11.4 + - - +
240A PHE* 3.1 20.9 - - + +
242A GLU* 1.3 76.9 - - - +
244A LEU* 1.3 60.0 + - - +
247A VAL* 3.3 51.7 + - + +
249A LEU* 3.9 11.1 + - + +
286A LEU* 3.9 22.9 - - + -
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Residues in contact with LEU 244 (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 HIS* 3.8 17.3 - - + +
240A PHE* 2.9 46.5 + - + +
241A GLY* 3.1 9.6 + - - +
243A LEU* 1.3 76.0 - - - +
245A GLN* 1.3 59.2 + - - +
248A PRO* 3.3 6.6 - - - +
249A LEU* 3.2 53.5 + - + +
250A ALA* 4.1 2.9 - - - +
251A ASP* 4.2 11.4 - - + +
286A LEU* 4.2 17.7 - - + -
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Residues in contact with GLN 245 (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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241A GLY 2.8 20.1 + - - +
242A GLU* 4.1 11.7 - - - +
244A LEU* 1.3 74.5 - - - +
246A ALA* 1.3 67.7 + - - +
247A VAL 3.5 0.2 - - - -
248A PRO* 3.5 13.7 - - - +
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Residues in contact with ALA 246 (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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193A ARG* 3.6 27.1 - - + -
197A LYS* 3.0 37.9 + - + +
242A GLU* 2.8 27.5 + - - +
245A GLN* 1.3 78.7 - - + +
247A VAL* 1.3 63.6 + - - +
248A PRO* 3.5 1.6 - - - +
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Residues in contact with VAL 247 (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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193A ARG* 4.1 11.4 - - + +
196A LEU* 3.8 21.5 - - + -
197A LYS* 4.0 18.1 + - - +
200A ALA* 3.8 26.2 - - + +
201A SER* 5.3 1.9 + - - -
205A LEU* 4.4 2.0 - - + -
243A LEU* 3.3 35.0 + - + +
246A ALA* 1.3 78.2 - - - +
248A PRO* 1.3 80.1 - - + +
249A LEU* 3.6 22.2 - - + -
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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