Contacts of the helix formed by residues 230 - 249 (chain A) in PDB entry 4WNF
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 ASP 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A ARG* 4.8 3.5 + - - -
225A ALA* 3.1 17.6 + - - +
228A PHE* 4.3 11.4 - - + -
229A GLY* 1.3 75.5 - - - +
231A LYS* 1.3 60.4 + - - +
232A ALA* 3.1 7.9 + - - +
233A ALA* 2.6 37.9 + - + +
234A GLU* 3.1 29.4 + - - +
236A ARG* 5.0 2.3 + - - -
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Residues in contact with LYS 231 (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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229A GLY* 4.2 14.6 + - - +
230A ASP* 1.3 72.1 + - - +
232A ALA* 1.3 56.4 + - - +
234A GLU* 3.1 24.7 + - - +
235A ARG* 2.5 37.5 + - - +
264A LEU* 5.6 1.8 - - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASP* 3.1 4.9 + - - +
231A LYS* 1.3 78.1 - - - +
233A ALA* 1.3 57.0 + - - +
235A ARG* 2.9 16.6 - - - +
236A ARG* 2.9 47.2 + - - +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ARG* 3.6 36.2 - - - +
225A ALA* 3.6 9.8 - - + +
230A ASP* 2.6 33.6 + - - +
232A ALA* 1.3 70.4 - - - +
234A GLU* 1.3 59.8 + - - +
236A ARG* 3.5 18.2 + - - +
237A ALA* 3.0 29.6 + - - +
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Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.7 25.4 - - + -
225A ALA* 3.7 5.7 - - + +
226A LYS* 3.7 29.1 - - + +
229A GLY* 5.2 0.3 - - - -
230A ASP 3.1 22.0 + - - +
231A LYS* 3.1 31.6 + - + +
233A ALA* 1.3 74.7 - - - +
235A ARG* 1.3 68.2 + - - +
237A ALA* 3.2 0.9 + - - +
238A TYR* 3.1 47.1 + - + -
264A LEU* 5.7 2.9 - - + -
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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 LYS 2.5 17.2 + - - +
232A ALA* 2.9 22.2 - - - +
234A GLU* 1.3 74.3 - - - +
236A ARG* 1.3 62.0 + - - +
238A TYR* 3.7 1.4 + - - +
239A SER* 3.3 16.6 + - - -
261A THR* 3.5 35.0 - - + +
264A LEU* 4.8 9.9 - - + -
265A ALA* 4.1 34.0 - - + +
996B GLU* 2.7 28.4 + - - -
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Residues in contact with ARG 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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221A ARG* 3.8 2.2 - - - +
230A ASP* 5.0 2.0 + - - -
232A ALA* 2.9 42.2 + - - +
233A ALA* 3.7 23.1 - - - +
234A GLU 3.2 0.2 - - - -
235A ARG* 1.3 78.0 - - - +
237A ALA* 1.3 56.7 + - - +
239A SER* 2.8 10.3 + - - -
240A ASN* 2.7 48.1 + - - +
996B GLU* 4.1 28.0 - - + +
997B MET 3.7 20.5 + - - -
998B GLU* 2.7 46.3 + - - +
999B PRO* 4.1 13.6 - - - +
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Residues in contact with ALA 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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218A HIS* 4.1 13.0 - - - +
221A ARG* 4.5 7.8 - - + +
222A LEU* 3.7 39.5 - - + +
233A ALA 3.0 15.1 + - - +
234A GLU 3.2 4.4 + - - +
236A ARG* 1.3 78.5 - - - +
238A TYR* 1.3 53.3 + - - +
240A ASN* 3.1 5.6 + - - +
241A LEU* 2.8 42.6 + - + +
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Residues in contact with TYR 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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222A LEU* 3.6 37.0 - - + +
226A LYS* 5.0 2.1 - - - +
234A GLU* 3.1 43.6 + - + +
235A ARG* 3.9 4.5 - - - +
236A ARG 3.2 0.4 - - - -
237A ALA* 1.3 73.6 - - - +
239A SER* 1.3 68.0 + - - +
241A LEU* 3.2 4.8 + - - +
242A GLY* 2.8 23.0 + - - -
257A TYR* 3.5 37.4 - + - +
258A TYR* 5.5 0.2 - - - -
260A LYS* 3.5 51.8 + - + -
261A THR* 3.3 19.6 + - - +
264A LEU* 4.8 6.7 - - + -
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Residues in contact with SER 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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235A ARG* 3.3 15.4 + - - -
236A ARG* 2.8 18.3 + - - -
238A TYR* 1.3 77.9 - - - +
240A ASN* 1.3 65.4 + - - -
242A GLY* 2.9 8.9 + - - -
243A ASN* 3.0 24.1 + - - +
258A TYR* 6.1 1.1 - - - +
261A THR* 3.4 17.0 + - - -
994B HIS 5.4 2.6 + - - -
996B GLU* 4.3 16.8 - - - +
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Residues in contact with ASN 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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199A GLY* 6.1 0.4 - - - -
203A ASN* 2.9 20.5 - - - +
206A TYR* 6.1 0.5 - - - -
218A HIS* 3.2 40.0 + - + +
236A ARG* 2.7 33.7 + - - +
239A SER* 1.3 72.8 + - - +
241A LEU* 1.3 62.3 + - - +
243A ASN* 3.2 21.6 + - - +
244A ALA* 3.5 11.8 + - - +
995B MET* 3.8 6.1 - - - +
996B GLU* 3.1 44.9 + - - +
998B GLU* 5.4 2.2 + - - -
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Residues in contact with LEU 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 VAL* 3.7 37.0 - - + +
218A HIS* 3.6 28.9 - - + +
219A GLU* 4.1 8.1 - - + +
222A LEU* 4.4 18.4 - - + -
237A ALA* 2.8 34.3 + - + +
238A TYR* 3.6 8.3 - - - +
240A ASN* 1.3 75.9 - - - +
242A GLY* 1.3 67.5 + - - +
243A ASN 3.3 0.3 + - - -
244A ALA* 3.3 12.1 + - - +
245A TYR* 3.4 25.1 + - + -
257A TYR* 4.3 24.0 - - + +
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Residues in contact with GLY 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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238A TYR 2.8 18.4 + - - -
239A SER 2.9 4.9 + - - -
241A LEU* 1.3 74.5 - - - +
243A ASN* 1.3 64.0 + - - +
244A ALA 3.2 0.2 + - - -
245A TYR* 3.3 0.7 + - - +
246A ILE* 3.2 28.4 + - - +
254A ALA* 3.6 16.3 - - - +
257A TYR* 4.0 14.7 - - - +
258A TYR* 4.9 4.9 - - - -
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Residues in contact with ASN 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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206A TYR* 4.3 26.9 + - + +
239A SER* 3.0 22.2 + - - +
240A ASN* 3.2 18.6 + - - +
241A LEU 3.2 0.6 - - - -
242A GLY* 1.3 75.6 - - - +
244A ALA* 1.3 61.7 + - - +
246A ILE* 3.2 29.2 - - - +
247A PHE* 3.3 15.7 + - + -
994B HIS* 4.4 29.9 + - - -
995B MET* 4.7 4.6 - - - +
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Residues in contact with ALA 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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206A TYR* 4.8 6.0 - - + -
211A PHE* 4.1 33.6 - - + +
214A ALA* 4.2 13.9 - - + -
215A VAL* 4.3 11.0 - - + +
218A HIS* 6.2 0.7 - - - +
240A ASN 3.5 7.2 + - - +
241A LEU* 3.3 8.4 + - - +
242A GLY 3.2 0.8 + - - -
243A ASN* 1.3 76.4 - - - +
245A TYR* 1.3 61.6 + - - +
247A PHE* 2.8 19.9 + - - +
248A LEU* 3.0 17.3 + - - +
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Residues in contact with TYR 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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215A VAL* 3.7 37.4 - - + +
219A GLU* 4.4 6.2 + - - -
241A LEU* 3.4 20.5 + - + -
242A GLY* 3.3 6.5 + - - +
244A ALA* 1.3 75.2 - - - +
246A ILE* 1.3 67.9 + - - +
248A LEU* 2.7 28.7 + - + +
249A GLY 2.7 10.6 + - - -
250A GLU* 3.0 45.7 + - + +
253A THR* 3.7 19.7 - - + -
254A ALA 4.2 5.6 - - - +
257A TYR* 3.5 31.9 + + - -
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Residues in contact with ILE 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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242A GLY 3.2 13.2 + - - +
243A ASN* 3.2 21.8 - - - +
245A TYR* 1.3 76.1 - - - +
247A PHE* 1.3 70.7 + - + +
249A GLY* 3.0 18.6 + - - +
250A GLU 4.8 0.7 - - - -
251A PHE* 4.6 23.7 - - + -
254A ALA* 3.5 22.8 - - + +
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Residues in contact with PHE 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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157A PRO* 4.4 32.3 - - + -
160A VAL* 4.9 9.0 - - + -
206A TYR* 3.5 29.2 - + - -
211A PHE* 3.4 46.8 - + + -
243A ASN* 3.4 13.7 - - + -
244A ALA 2.8 14.7 + - - +
246A ILE* 1.3 87.1 - - + +
248A LEU* 1.3 60.1 + - - +
249A GLY 3.2 0.4 + - - -
994B HIS* 6.2 1.1 - + - -
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Residues in contact with LEU 248 (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 PHE* 4.1 27.4 - - + +
212A ARG* 4.6 17.7 - - + +
215A VAL* 4.7 4.9 - - + -
244A ALA 3.0 16.8 + - - +
245A TYR* 2.7 32.5 + - + +
247A PHE* 1.3 73.7 - - - +
249A GLY* 1.3 56.8 + - - +
250A GLU* 3.1 24.3 - - - +
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Residues in contact with GLY 249 (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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245A TYR 2.7 3.3 + - - -
246A ILE 3.0 12.3 + - - -
247A PHE 3.2 0.8 - - - -
248A LEU* 1.3 78.4 - - - +
250A GLU* 1.3 54.1 + - - +
251A PHE* 2.5 41.3 + - - -
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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