Contacts of the helix formed by residues 229 - 243 (chain A) in PDB entry 2W5X
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 ASN 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A MET* 6.0 0.2 - - + -
227A ARG 3.7 0.2 + - - -
228A GLY* 1.3 71.0 - - - -
230A PHE* 1.3 63.4 + - - +
231A LEU 3.2 3.8 + - - +
232A SER* 3.4 20.7 + - - +
233A ALA* 2.9 28.3 + - - +
276A ASP* 4.3 9.2 - - - +
279A ASP* 5.6 6.1 - - + +
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Residues in contact with PHE 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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128A VAL* 4.2 9.4 - - + -
129A ALA 3.5 29.6 - - - -
130A THR* 4.2 13.5 - - + -
167A ALA* 3.9 13.7 - - + -
168A GLY* 3.9 18.4 - - - -
199A LEU* 4.0 17.5 - - + -
215A LEU* 3.7 18.4 - - + -
220A MET* 3.6 31.2 - - + -
227A ARG* 3.8 26.1 + - + +
228A GLY 3.2 4.8 + - - -
229A ASN* 1.3 75.3 - - - +
231A LEU* 1.3 59.1 + - - +
233A ALA* 3.7 4.7 - - - +
234A ALA* 2.7 51.3 + - + +
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Residues in contact with LEU 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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128A VAL* 3.8 21.5 - - + -
130A THR* 4.2 13.5 - - + -
227A ARG* 5.1 0.4 - - - +
228A GLY 4.9 0.2 + - - -
229A ASN 3.2 1.0 - - - -
230A PHE* 1.3 83.8 - - - +
232A SER* 1.3 57.5 + - - +
234A ALA* 4.0 1.3 - - - +
235A THR* 2.8 34.2 + - - +
253A SER* 4.3 11.2 - - - -
254A GLU 3.7 19.1 - - - +
255A GLY* 4.1 24.9 - - - +
276A ASP* 3.6 27.9 + - - +
277A PHE* 4.2 12.3 - - + -
280A ALA* 3.8 24.7 - - + -
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Residues in contact with SER 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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229A ASN* 3.4 22.9 + - - +
231A LEU* 1.3 75.4 - - - +
233A ALA* 1.3 61.4 + - - +
235A THR* 3.3 6.3 + - - -
236A ASP* 2.9 31.1 + - - +
276A ASP* 4.6 2.0 + - - -
279A ASP* 3.3 12.0 - - - +
280A ALA* 3.3 24.4 + - - +
283A THR* 3.2 29.8 + - - +
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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
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199A LEU* 3.4 22.0 - - + -
229A ASN* 2.9 29.9 + - - +
230A PHE* 4.4 0.2 - - - -
232A SER* 1.3 78.3 - - - +
234A ALA* 1.3 57.5 + - - +
236A ASP* 3.3 8.3 + - - +
237A LEU* 2.9 29.6 + - - +
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Residues in contact with ALA 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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128A VAL* 3.8 26.2 - - + -
165A PHE* 3.9 5.3 - - - -
167A ALA* 4.0 18.4 - - + -
199A LEU* 3.6 10.7 - - + +
230A PHE* 2.7 32.2 + - + +
233A ALA* 1.3 73.9 - - - +
235A THR* 1.3 57.3 + - - +
237A LEU* 3.4 7.5 + - - +
238A ALA* 2.9 28.1 + - - +
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Residues in contact with THR 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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38A ILE* 5.0 5.6 - - + -
40A LEU* 4.9 8.7 - - + -
128A VAL* 4.7 1.6 - - - +
231A LEU* 2.8 25.6 + - - +
232A SER* 3.6 6.5 - - - -
234A ALA* 1.3 75.5 - - - +
236A ASP* 1.3 64.0 + - - +
238A ALA* 3.2 6.9 + - - +
239A ILE* 2.9 43.4 + - + +
251A ILE* 4.9 7.6 - - + -
253A SER* 3.0 32.7 + - - +
280A ALA* 5.0 6.2 - - - +
283A THR* 4.8 7.9 - - + -
284A ALA* 5.0 5.8 - - + -
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Residues in contact with ASP 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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232A SER* 2.9 11.4 + - - +
233A ALA* 3.5 11.2 - - - +
235A THR* 1.3 76.8 - - - +
237A LEU* 1.3 62.4 + - - +
239A ILE* 3.3 13.7 + - - +
240A GLN* 3.0 39.7 + - - +
283A THR* 3.3 28.0 + - - +
287A PHE* 5.3 4.0 - - - +
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Residues in contact with LEU 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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165A PHE* 4.2 5.2 - - + -
199A LEU* 3.8 18.4 - - + -
200A THR* 3.6 26.7 - - - +
201A ASP 4.1 0.2 - - - -
202A PHE* 3.8 32.5 - - + +
205A ILE* 3.9 14.9 - - + +
213A PHE* 3.6 32.8 - - + -
233A ALA 2.9 16.3 + - - +
234A ALA 3.5 5.6 - - - +
235A THR 3.2 0.2 - - - -
236A ASP* 1.3 74.3 - - - +
238A ALA* 1.3 58.1 + - - +
240A GLN* 3.4 7.9 + - - +
241A PHE* 2.9 32.1 + - - +
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Residues in contact with ALA 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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126A GLY* 5.5 1.1 - - - -
128A VAL* 4.6 6.5 - - + -
165A PHE* 3.7 31.3 - - + -
234A ALA 2.9 14.7 + - - +
235A THR* 3.5 11.4 - - - +
237A LEU* 1.3 75.3 - - - +
239A ILE* 1.3 60.3 + - - +
242A LEU* 2.8 38.4 + - + +
251A ILE* 3.6 21.3 - - + -
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Residues in contact with ILE 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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38A ILE* 3.9 24.2 - - + -
235A THR* 2.9 30.3 + - + +
236A ASP* 3.3 16.4 + - - +
238A ALA* 1.3 76.6 - - - +
240A GLN* 1.3 64.4 + - + +
242A LEU 4.0 0.2 - - - -
243A SER* 2.7 31.4 + - - +
249A PHE* 3.9 8.4 - - + -
251A ILE* 3.6 20.0 - - + -
283A THR* 5.1 0.7 - - + +
284A ALA* 4.8 5.4 - - - -
287A PHE* 3.5 56.5 - - + -
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Residues in contact with GLN 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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202A PHE* 3.4 55.8 - - + +
236A ASP* 3.0 31.9 + - + +
237A LEU* 3.9 6.2 - - - +
239A ILE* 1.3 82.7 - - + +
241A PHE* 1.3 62.2 + - - +
243A SER* 3.6 6.9 + - - -
244A LYS* 3.5 13.7 + - - +
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Residues in contact with PHE 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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124A LYS* 6.1 1.6 - - + -
164A ASP* 3.6 21.3 - - + -
165A PHE* 3.7 20.4 - + + -
202A PHE* 3.8 7.6 - + + -
205A ILE* 3.5 37.2 - - + -
208A ASN 3.4 21.3 - - - -
209A ARG 3.6 22.7 - - - -
210A LYS* 3.8 9.9 - - - -
211A MET* 3.9 11.4 - - + -
237A LEU 2.9 19.3 + - - +
238A ALA 3.8 2.0 - - - +
240A GLN* 1.3 78.3 - - - +
242A LEU* 1.3 78.4 + - + +
244A LYS* 3.2 36.4 - - + +
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Residues in contact with LEU 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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124A LYS* 3.7 21.8 - - + +
125A THR 3.4 17.9 - - - +
126A GLY* 3.5 27.4 - - - +
164A ASP* 3.6 19.7 - - + -
165A PHE* 3.9 6.1 - - + -
238A ALA* 2.8 21.8 + - + +
241A PHE* 1.3 87.5 - - + +
243A SER* 1.3 58.8 + - - +
244A LYS* 3.2 2.7 + - - +
247A SER* 3.6 21.7 - - - +
249A PHE* 3.6 22.5 - - + +
250A PHE 4.1 2.5 - - - +
251A ILE* 3.5 26.2 - - + -
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Residues in contact with SER 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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239A ILE* 2.7 26.9 + - - +
240A GLN* 3.6 8.3 + - - -
241A PHE 3.3 0.2 - - - -
242A LEU* 1.3 76.2 - - - +
244A LYS* 1.3 66.4 + - - +
245A ASP 3.5 0.3 + - - -
246A ASN* 3.2 13.2 + - - -
247A SER 3.7 11.2 - - - -
249A PHE* 3.9 20.0 - - - -
287A PHE* 5.2 5.5 - - - -
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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