Contacts of the helix formed by residues 230 - 246 (chain A) in PDB entry 1W6J
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 TRP 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LEU* 1.3 73.1 - - - +
231A CYS* 1.3 81.7 + - - +
232A HIS* 3.5 41.4 - + + -
233A CYS* 3.1 6.4 + - - +
234A ARG* 3.0 20.3 + - - +
502A THR* 3.4 18.7 + - - +
503A TYR* 5.1 0.7 - + - -
523A ASP 5.0 1.1 - - - -
524A ILE* 3.2 38.3 + - + +
525A MET 3.0 9.5 + - - -
526A ILE* 3.7 14.6 - - - +
527A ASP* 3.6 33.5 + - + +
530A TYR* 5.7 3.6 - - - -
581A TRP* 3.9 22.7 - + - -
697A ASN* 3.4 38.6 - - - -
1733A R71 3.7 21.8 - + - -
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Residues in contact with CYS 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU 3.4 2.4 + - - -
230A TRP* 1.3 79.1 - - - +
232A HIS* 1.3 66.7 + - - +
234A ARG* 3.5 14.8 - - - +
235A GLN* 2.9 35.0 + - - +
335A ILE* 3.6 10.1 - - - -
451A TRP* 3.6 22.4 - - + -
503A TYR* 3.3 48.5 - - - -
504A GLU* 3.8 17.7 + - - +
527A ASP* 5.0 0.9 - - - +
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Residues in contact with HIS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TRP* 3.3 37.3 - + + -
231A CYS* 1.3 80.7 - - - +
233A CYS* 1.3 63.5 + - - +
235A GLN* 4.3 2.7 - - - +
236A VAL* 3.4 17.0 + - - +
335A ILE* 3.6 40.4 - - + +
336A GLY* 4.9 4.6 - - - -
381A THR* 5.7 2.5 - - + -
503A TYR* 2.9 43.7 + + - -
1733A R71 3.3 62.0 + + + -
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Residues in contact with CYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 4.9 7.0 - - + -
230A TRP* 3.1 12.3 + - + +
232A HIS* 1.3 79.5 - - - +
234A ARG* 1.3 60.4 + - - +
236A VAL* 3.2 3.1 + - - -
237A TYR* 3.0 49.8 + - - -
524A ILE* 3.4 42.0 - - - +
525A MET* 4.2 14.1 - - - -
1733A R71 3.9 14.1 - - + -
1735A C14 4.6 10.5 - - - -
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Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 3.8 20.3 - - + -
226A PRO* 3.2 29.8 - - + +
227A SER 4.2 2.0 + - - -
229A LEU* 2.9 31.7 + - + -
230A TRP 3.0 10.2 + - - +
231A CYS* 3.5 20.3 - - - +
233A CYS* 1.3 78.6 - - - +
235A GLN* 1.3 70.9 + - - +
237A TYR* 4.5 5.4 - - - +
238A LEU* 2.9 32.6 + - - +
433A TYR 4.6 3.2 + - - -
434A TYR* 3.3 36.0 + - - +
435A ARG* 4.7 0.4 - - - +
451A TRP* 4.3 10.7 - - - -
504A GLU* 2.8 37.6 + - - -
507A ARG* 3.9 10.0 - - - +
1735A C14 6.2 0.7 - - - -
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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
----------------------------------------------------------
216A TRP* 6.3 0.4 - - - -
231A CYS 2.9 19.4 + - - +
232A HIS 4.3 1.8 - - - +
234A ARG* 1.3 91.8 - - - +
236A VAL* 1.3 56.6 + - - +
238A LEU* 3.7 21.5 - - - +
239A PRO* 3.0 19.5 - - - +
322A HIS 4.7 0.7 - - - +
326A ASP* 3.6 22.3 - - - +
334A SER* 4.1 6.5 - - - +
335A ILE* 3.9 27.6 - - + -
339A SER* 3.2 21.4 - - - -
343A ASN* 4.7 2.7 + - - +
433A TYR 5.8 1.6 + - - -
451A TRP* 3.4 31.9 - - + -
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A TRP* 4.1 13.2 - - + -
232A HIS* 3.4 18.1 + - - +
233A CYS 3.2 3.9 + - - +
235A GLN* 1.3 78.0 - - - +
237A TYR* 1.3 67.2 + - + +
238A LEU 3.2 0.2 - - - -
239A PRO* 3.2 14.7 - - - +
240A MET* 3.3 43.6 + - + +
335A ILE* 6.2 1.1 - - + -
338A ILE* 3.8 30.5 - - + -
339A SER* 4.1 11.0 - - - +
342A ILE* 4.2 0.6 - - + +
1733A R71 3.8 20.4 - - + -
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Residues in contact with TYR 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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191A SER* 4.7 1.6 + - - -
192A TRP* 3.1 39.7 + + - -
211A LEU* 3.9 31.0 - - + -
216A TRP* 5.0 4.5 - - + +
233A CYS* 3.0 45.1 + - - +
234A ARG* 4.3 3.6 - - - +
236A VAL* 1.3 81.5 - - + +
238A LEU* 1.3 57.0 + - - +
239A PRO 3.6 0.2 - - - -
240A MET* 3.8 12.0 - - - +
241A SER* 2.8 39.0 + - - +
297A TYR* 5.7 0.9 - - - -
517A PRO* 3.6 30.6 + - + +
518A SER* 3.8 11.1 - - - -
524A ILE* 4.9 2.5 - - + -
1733A R71 4.6 4.9 - - + -
1735A C14 4.2 22.4 - - + -
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Residues in contact with LEU 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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216A TRP* 3.6 31.3 - - + +
234A ARG 2.9 17.3 + - - +
235A GLN* 3.7 24.0 - - - +
237A TYR* 1.3 77.6 - - - +
239A PRO* 1.3 66.6 - - + +
241A SER* 3.4 3.7 + - - -
242A TYR* 3.2 23.2 + - - +
319A LEU* 3.5 44.1 - - + +
322A HIS* 3.8 24.0 - - + +
323A ILE* 3.7 15.7 - - + -
343A ASN* 5.7 0.7 - - - +
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Residues in contact with PRO 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN 3.0 24.2 - - - +
236A VAL* 3.2 15.0 - - - +
238A LEU* 1.3 89.1 - - + +
240A MET* 1.3 62.6 + - - +
242A TYR* 3.3 2.4 + - + +
243A CYS* 3.0 27.7 + - - -
323A ILE* 3.9 15.9 - - + -
339A SER* 4.4 3.4 - - - +
342A ILE* 3.5 33.0 - - + +
343A ASN* 3.4 25.4 - - - +
346A VAL* 4.3 1.1 - - + +
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Residues in contact with MET 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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192A TRP* 3.9 36.8 - - + +
195A PHE* 3.4 45.6 - - + -
196A TRP* 5.2 3.6 - - - +
211A LEU* 4.3 13.2 - - + -
236A VAL* 3.3 43.1 + - + +
237A TYR* 3.8 27.8 - - - +
239A PRO* 1.3 77.3 - - - +
241A SER* 1.3 57.6 + - - +
243A CYS 3.3 0.3 + - - -
244A TYR* 2.9 28.2 + - - +
338A ILE* 4.9 2.9 - - + -
342A ILE* 3.6 18.3 - - + +
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 2.8 37.1 + - - +
213A PRO* 4.3 11.7 - - - +
215A MET* 5.7 1.4 - - - +
216A TRP* 4.8 5.9 + - - -
237A TYR* 2.8 27.4 + - - +
238A LEU* 3.6 6.3 - - - -
239A PRO 3.2 0.2 - - - -
240A MET* 1.3 73.6 - - - +
242A TYR* 1.3 60.1 + - - +
244A TYR* 3.4 2.1 + - - +
245A ALA* 2.8 29.8 + - - +
319A LEU* 3.8 16.2 - - - +
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Residues in contact with TYR 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 LEU 3.2 11.1 + - - +
239A PRO 3.3 8.0 + - - +
241A SER* 1.3 79.5 - - - +
243A CYS* 1.3 67.3 + - - +
245A ALA* 3.1 14.5 + - - +
246A VAL* 3.1 37.6 + - + +
248A LEU* 5.5 0.9 - - + -
316A VAL* 3.5 40.7 - - + +
319A LEU* 3.4 16.5 - - + +
320A TYR* 4.1 17.3 - - + -
323A ILE* 4.2 10.5 - - + -
346A VAL* 4.0 26.9 - - + -
349A TYR* 3.8 19.8 - + - -
350A VAL* 3.0 26.0 - - + +
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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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195A PHE* 3.8 14.8 - - + -
199A VAL* 4.8 1.1 - - + -
205A TRP* 3.8 8.0 - - + -
239A PRO 3.0 18.3 + - - +
240A MET 3.7 7.0 - - - +
242A TYR* 1.3 78.5 - - - +
244A TYR* 1.3 60.8 + - - +
246A VAL* 3.6 5.6 + - - -
247A ARG* 3.1 3.5 + - - -
248A LEU* 3.0 50.7 + - + -
342A ILE* 3.7 20.4 - - - -
345A LEU* 4.1 12.3 - - - -
346A VAL* 4.1 13.7 - - - -
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Residues in contact with TYR 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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205A TRP* 3.5 38.9 + + + -
206A GLU* 5.1 0.7 + - - -
208A LEU* 3.7 26.9 + - + -
210A THR* 3.5 21.2 + - - -
211A LEU* 3.7 27.8 - - + -
212A PHE 4.4 0.7 - - - -
213A PRO* 4.3 10.8 - - + -
240A MET 2.9 16.9 + - - +
241A SER 3.6 3.8 - - - +
242A TYR 3.2 0.2 - - - -
243A CYS* 1.3 74.8 - - - +
245A ALA* 1.3 65.2 + - - +
247A ARG* 2.9 55.5 + - - -
277A ARG* 5.9 1.2 + - - -
301A ASN* 5.2 0.2 + - - -
304A GLU* 3.1 43.1 + - - +
312A ARG* 4.2 2.2 - - - -
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Residues in contact with ALA 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 PRO* 4.0 16.4 - - + -
241A SER 2.8 17.4 + - - +
242A TYR* 3.1 11.4 + - - +
244A TYR* 1.3 80.1 - - - +
246A VAL* 1.3 59.7 + - - +
247A ARG* 3.6 7.4 + - - +
312A ARG* 4.2 20.8 + - - +
316A VAL* 3.5 29.6 - - + -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR* 3.1 45.4 + - + +
243A CYS* 3.7 2.5 - - - +
245A ALA* 1.3 79.6 - - + +
247A ARG* 1.3 68.9 + - - +
248A LEU* 3.2 22.4 + - + +
316A VAL* 4.5 12.3 - - + -
349A TYR* 3.8 35.6 + - + +
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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
------------------------------------------------------------
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