Contacts of the helix formed by residues 240 - 257 (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 ASP 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A CYS* 1.3 85.2 - - - +
241A PRO* 1.3 69.0 - - - +
242A ASP* 2.6 52.8 + - - +
243A CYS* 3.2 31.9 + - - +
244A LEU 3.6 1.7 + - - -
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Residues in contact with PRO 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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230A THR* 3.5 20.8 - - + +
231A ARG* 4.5 15.5 - - + +
234A SER* 3.3 24.2 - - - +
239A CYS 3.4 9.6 - - - +
240A ASP* 1.3 88.0 - - - +
242A ASP* 1.3 63.6 + - - +
243A CYS 3.4 0.2 - - - -
244A LEU* 3.5 2.6 + - + -
245A ARG* 3.1 35.0 + - - +
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Residues in contact with ASP 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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240A ASP* 2.6 31.6 + - - +
241A PRO* 1.3 77.6 - - - +
243A CYS* 1.3 55.8 + - - +
245A ARG* 3.3 18.5 + - - +
246A ALA* 2.8 34.1 + - - +
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Residues in contact with CYS 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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202A MET* 3.7 21.2 - - + +
239A CYS* 5.2 1.6 - - - -
240A ASP* 3.2 37.9 - - - +
242A ASP* 1.3 77.3 - - - +
244A LEU* 1.3 53.9 + - - +
246A ALA* 3.1 7.1 + - - +
247A CYS* 2.5 37.4 + - - +
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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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202A MET* 4.1 14.8 - - - +
205A ALA* 3.3 21.8 - - + -
206A GLY* 3.2 33.9 - - - +
209A VAL* 4.7 4.0 - - + -
230A THR* 3.5 41.1 - - + +
233A LEU* 4.2 9.9 - - + -
234A SER* 3.8 9.2 - - - +
237A ILE* 5.6 1.1 - - + -
239A CYS* 5.0 4.5 - - - -
240A ASP 3.6 4.1 + - - +
241A PRO* 3.5 14.1 + - + +
242A ASP 3.2 0.4 - - - -
243A CYS* 1.3 81.6 - - - +
245A ARG* 1.3 56.5 + - - +
247A CYS* 4.3 4.9 - - + -
248A GLN* 2.9 27.0 + - - +
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Residues in contact with ARG 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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230A THR* 3.7 28.4 + - + +
231A ARG* 5.6 0.8 - - - +
241A PRO* 3.1 23.4 + - - +
242A ASP* 3.7 21.5 + - - +
244A LEU* 1.3 75.6 - - - +
246A ALA* 1.3 60.1 + - - +
248A GLN* 3.6 15.7 - - - +
249A GLU* 2.9 51.3 + - + +
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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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242A ASP 2.8 18.3 + - - +
243A CYS* 3.3 9.4 - - - +
245A ARG* 1.3 76.5 - - - +
247A CYS* 1.3 62.9 + - - +
249A GLU* 3.2 15.0 + - - +
250A GLN* 3.1 33.1 + - - +
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Residues in contact with CYS 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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194A LYS* 3.4 24.3 + - - +
198A ASN* 3.6 21.1 - - - +
202A MET* 3.7 33.4 - - + -
203A VAL* 4.5 1.8 - - - -
206A GLY* 4.4 9.6 - - - -
243A CYS 2.5 21.1 + - - +
244A LEU* 3.9 4.5 - - - +
246A ALA* 1.3 72.6 - - - +
248A GLN* 1.3 61.8 + - - +
250A GLN* 3.4 10.8 + - - +
251A ILE* 3.2 24.9 + - - +
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Residues in contact with GLN 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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206A GLY* 3.9 28.0 - - - +
209A VAL* 3.2 23.2 - - + +
210A ALA* 4.3 4.5 - - + +
213A GLN* 3.1 28.5 + - - +
230A THR* 4.0 7.6 + - - -
244A LEU 2.9 18.4 + - - +
245A ARG* 3.6 16.6 - - - +
246A ALA 3.2 0.2 - - - -
247A CYS* 1.3 76.6 - - - +
249A GLU* 1.3 68.5 + - - +
251A ILE* 3.1 14.4 + - - +
252A GLU* 2.7 41.5 + - - +
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Residues in contact with GLU 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 ARG* 2.9 43.1 + - + +
246A ALA* 3.2 12.6 + - - +
248A GLN* 1.3 75.1 - - - +
250A GLN* 1.3 63.9 + - + +
252A GLU* 3.0 17.2 + - - +
253A ALA* 2.9 23.3 + - - +
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Residues in contact with GLN 250 (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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194A LYS* 3.1 39.1 + - + +
198A ASN* 4.4 6.6 + - - +
246A ALA* 3.1 21.5 + - - +
247A CYS* 3.5 11.5 - - - +
248A GLN 3.2 0.2 - - - -
249A GLU* 1.3 81.4 - - + +
251A ILE* 1.3 56.5 + - - +
253A ALA* 3.8 6.4 - - - +
254A LEU* 2.8 33.1 + - - +
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Residues in contact with ILE 251 (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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185A PHE* 3.0 39.3 - - + +
188A LEU* 4.8 3.1 - - + +
189A CYS* 3.5 28.0 - - - -
194A LYS* 3.8 5.6 - - - -
203A VAL 4.0 6.1 - - - +
206A GLY* 3.8 8.7 - - - -
207A SER* 3.5 36.6 - - - +
210A ALA* 4.9 4.3 - - + -
247A CYS* 3.3 19.7 - - - +
248A GLN* 3.1 7.3 + - - +
250A GLN* 1.3 75.4 - - - +
252A GLU* 1.3 57.8 + - + +
254A LEU* 3.5 7.0 + - + +
255A LEU* 2.9 28.1 + - - +
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Residues in contact with GLU 252 (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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185A PHE* 5.1 4.9 - - + -
210A ALA* 4.0 20.6 - - + +
213A GLN* 3.9 9.2 + - - -
248A GLN* 2.7 45.9 + - - +
249A GLU* 3.0 15.3 + - - +
251A ILE* 1.3 74.8 - - - +
253A ALA* 1.3 63.7 + - - +
255A LEU* 3.4 9.8 + - + +
256A GLU* 3.3 24.4 + - - +
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Residues in contact with ALA 253 (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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249A GLU 2.9 15.2 + - - +
250A GLN* 3.8 6.7 - - - +
252A GLU* 1.3 73.7 - - - +
254A LEU* 1.3 57.7 + - - +
256A GLU* 2.7 35.5 + - - +
257A SER* 3.3 7.8 + - - -
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Residues in contact with LEU 254 (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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58A LYS* 5.3 8.1 - - - +
188A LEU* 3.3 29.4 - - + +
189A CYS* 4.1 13.0 - - - -
192A ASP* 3.4 46.2 - - + +
194A LYS* 4.3 12.1 - - + -
250A GLN 2.8 20.9 + - - +
251A ILE* 3.7 5.4 - - + +
253A ALA* 1.3 72.7 - - - +
255A LEU* 1.3 58.0 + - - +
257A SER* 3.5 17.9 + - - -
258A SER* 2.8 17.4 + - - +
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Residues in contact with LEU 255 (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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184A THR* 5.4 9.2 - - + -
185A PHE* 3.3 32.3 - - + -
188A LEU* 3.2 24.0 - - + -
251A ILE 2.9 17.5 + - - +
252A GLU* 3.6 9.2 - - + +
253A ALA 3.0 0.4 - - - -
254A LEU* 1.3 75.3 - - - +
256A GLU* 1.3 62.9 + - - +
257A SER 3.2 0.4 - - - -
258A SER* 2.9 28.6 + - - -
259A LEU* 3.5 6.4 + - - +
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Residues in contact with GLU 256 (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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252A GLU 3.3 13.6 + - - +
253A ALA* 2.7 15.3 + - - +
255A LEU* 1.3 80.5 - - - +
257A SER* 1.3 54.8 + - - +
258A SER 3.1 0.9 - - - -
259A LEU* 3.0 55.8 - - - +
260A ARG* 4.3 0.7 + - - +
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Residues in contact with SER 257 (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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253A ALA 3.3 9.2 + - - -
254A LEU* 3.7 17.9 + - - +
255A LEU 3.2 0.8 - - - -
256A GLU* 1.3 77.0 - - - +
258A SER* 1.3 58.9 + - - +
259A LEU 3.4 1.1 - - - -
260A ARG* 3.4 37.7 + - - +
261A GLN* 3.1 14.0 - - - +
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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