Contacts of the helix formed by residues 235 - 250 (chain A) in PDB entry 1WG8
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 HIS 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLN* 3.5 26.1 + - - +
202A ARG* 3.6 24.1 + - - -
203A ILE* 3.5 26.2 - - + +
208A GLU* 4.3 2.0 + - - -
209A LEU* 4.4 3.5 - - + +
234A PHE* 1.3 79.9 - - + +
236A SER* 1.3 63.5 + - - +
237A LEU* 3.2 23.2 + - + +
238A GLU* 3.0 51.0 + - + +
239A ASP* 3.0 24.8 + - - +
276A LYS* 6.5 0.4 - - - -
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Residues in contact with SER 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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151A GLU* 3.7 23.1 + - - -
235A HIS* 1.3 73.3 - - - +
237A LEU* 1.3 64.4 + - - +
239A ASP* 3.9 4.8 - - - +
240A ARG* 3.1 29.7 + - - +
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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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148A GLU 3.4 20.9 - - - +
149A LEU* 3.3 31.9 - - - +
151A GLU* 3.5 28.2 + - + +
199A GLN* 4.4 3.8 - - - +
203A ILE* 4.3 4.3 - - + -
209A LEU* 4.2 23.6 - - + -
235A HIS* 3.2 14.7 + - + +
236A SER* 1.3 78.6 - - - +
238A GLU* 1.3 63.2 + - - +
240A ARG* 3.2 34.1 + - - +
241A VAL* 3.2 25.1 + - - +
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.7 28.1 - - + +
98A GLY* 5.2 2.5 + - - -
202A ARG* 5.4 0.2 + - - -
208A GLU* 4.2 10.4 - - - +
209A LEU* 4.1 10.5 - - + +
212A LEU* 3.9 17.4 - - + +
233A ALA* 3.7 6.8 - - + -
234A PHE* 2.7 30.4 + - - +
235A HIS* 3.0 47.1 + - + +
237A LEU* 1.3 73.8 - - - +
239A ASP* 1.3 69.5 + - - +
241A VAL* 3.2 3.6 + - - +
242A VAL* 3.0 26.9 + - - +
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Residues in contact with ASP 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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233A ALA* 3.6 18.8 - - + +
234A PHE 5.9 0.2 - - - -
235A HIS 3.0 19.6 + - - +
236A SER* 4.0 4.7 - - - +
238A GLU* 1.3 77.9 - - - +
240A ARG* 1.3 58.9 + - - +
242A VAL* 3.4 1.8 + - - +
243A LYS* 2.8 29.1 + - - +
276A LYS* 3.4 38.0 - - + +
278A ARG* 2.9 41.8 + - - +
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 4.0 14.3 + - - -
236A SER* 3.1 22.7 + - - +
237A LEU* 3.2 33.6 + - - +
238A GLU 3.1 0.2 - - - -
239A ASP* 1.3 73.4 - - - +
241A VAL* 1.3 67.2 + - + +
243A LYS* 3.8 19.8 - - - +
244A ARG* 2.9 48.5 + - + +
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Residues in contact with VAL 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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209A LEU* 4.1 20.9 - - + -
212A LEU* 3.9 17.9 - - + -
213A LYS* 3.6 45.8 - - + +
216A LEU* 4.0 9.6 - - + -
237A LEU 3.2 14.5 + - - +
238A GLU 3.2 7.3 + - - +
240A ARG* 1.3 78.9 - - + +
242A VAL* 1.3 58.5 + - - +
244A ARG* 4.1 5.2 - - - +
245A PHE* 2.9 29.7 + - + +
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Residues in contact with VAL 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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97A LEU* 4.4 3.8 - - + -
212A LEU* 4.0 19.3 - - + -
216A LEU* 4.2 11.2 - - + -
231A VAL* 3.8 42.2 - - + +
233A ALA* 4.5 5.4 - - + -
238A GLU 3.0 20.7 + - - +
239A ASP* 3.7 7.9 - - - +
241A VAL* 1.3 77.2 - - - +
243A LYS* 1.3 64.2 + - - +
245A PHE* 3.7 0.7 - - - +
246A LEU* 3.0 44.1 + - + +
278A ARG* 4.1 13.7 - - + -
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Residues in contact with LYS 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 ASP* 2.8 17.8 + - - +
240A ARG* 3.3 23.1 + - - +
242A VAL* 1.3 78.3 - - - +
244A ARG* 1.3 62.3 + - - +
246A LEU* 3.5 3.6 + - - +
247A ARG* 3.2 60.1 + - + +
256A LYS 5.8 1.3 - - - +
278A ARG* 3.7 43.7 - - - +
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Residues in contact with ARG 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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213A LYS* 5.2 12.5 - - - +
240A ARG* 2.9 40.4 + - + +
241A VAL* 4.1 4.3 - - - +
243A LYS* 1.3 69.2 - - - +
245A PHE* 1.3 67.2 + - - +
247A ARG* 3.2 35.5 + - - +
248A GLU* 3.0 43.2 + - - +
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Residues in contact with PHE 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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213A LYS* 5.1 4.0 - - + -
216A LEU* 3.2 51.8 - - + -
217A GLU* 3.7 24.9 - - + -
220A ALA* 4.0 9.0 - - + -
229A LEU* 4.2 7.9 - - + -
241A VAL* 2.9 21.1 + - + +
242A VAL 3.7 2.7 - - - +
244A ARG* 1.3 77.9 - - - +
246A LEU* 1.3 77.5 + - + +
248A GLU* 3.6 3.2 - - - -
249A SER* 2.8 56.3 + - - -
251A LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 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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216A LEU* 5.5 0.4 - - + -
229A LEU* 3.9 22.2 - - + +
231A VAL* 6.0 1.6 - - + -
242A VAL* 3.0 24.3 + - + +
243A LYS* 3.9 3.4 - - - +
245A PHE* 1.3 98.5 - - + +
247A ARG* 1.3 61.1 + - - +
249A SER* 2.7 21.8 + - - -
250A GLY 4.2 1.4 + - - -
251A LEU* 4.4 4.5 - - + +
253A VAL* 3.7 21.1 - - + +
255A THR* 5.2 0.9 - - - +
278A ARG* 3.6 35.0 - - + +
279A ALA* 4.2 13.0 - - - +
280A ALA* 3.8 24.7 - - + +
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Residues in contact with ARG 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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240A ARG* 5.6 0.2 - - - +
243A LYS* 3.2 51.0 + - - +
244A ARG* 3.2 44.8 - - - +
246A LEU* 1.3 78.7 - - - +
248A GLU* 1.3 77.1 + - + +
249A SER 3.8 0.2 + - - -
250A GLY* 4.6 3.5 + - - -
253A VAL* 4.1 13.2 - - + +
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Residues in contact with GLU 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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244A ARG* 3.0 36.3 + - - +
245A PHE* 4.0 3.1 - - - +
247A ARG* 1.3 92.2 + - + +
249A SER* 1.3 62.0 + - - +
250A GLY* 3.5 1.9 + - - -
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Residues in contact with SER 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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220A ALA* 5.4 1.8 - - - -
245A PHE* 2.8 44.2 + - - -
246A LEU 2.7 17.7 + - - -
248A GLU* 1.3 81.0 - - - +
250A GLY* 1.3 58.7 + - - +
251A LEU* 2.8 27.5 + - - +
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Residues in contact with GLY 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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246A LEU 4.2 2.0 + - - -
247A ARG 4.6 3.2 + - - -
248A GLU 3.5 3.0 - - - -
249A SER* 1.3 78.6 + - - +
251A LEU* 1.3 67.2 + - - +
283A GLU* 5.0 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