Contacts of the helix formed by residues 233 - 250 (chain A) in PDB entry 3QJQ
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 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A TRP* 3.3 8.9 + - - +
231A THR 3.1 0.2 - - - -
232A GLY* 1.3 78.5 - - - +
234A PRO* 1.3 77.1 - - + +
235A ILE 3.2 1.1 - - - -
236A VAL* 3.0 28.2 + - + +
237A TYR* 1.8 54.3 + + - -
276A SER 3.4 13.9 - - - -
279A VAL* 3.6 16.5 - - + +
280A GLY* 4.8 2.5 - - - -
282A HIS* 2.9 17.9 - + + +
283A HIS* 3.4 8.7 - - + +
305A VAL* 4.7 2.3 - - + +
563A CMO 3.3 9.8 + - - -
801A HAS 4.6 1.8 - + - -
803A CU1 1.9 32.0 - - - -
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Residues in contact with PRO 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A MET* 4.5 8.6 - - - +
193A TRP* 4.9 0.4 - - - -
196A ALA* 3.2 29.2 - - + -
229A TRP 4.4 0.2 - - - +
230A TRP 3.4 24.5 - - - +
231A THR 3.3 4.3 - - - +
233A HIS* 1.3 94.2 - - + +
235A ILE* 1.3 54.3 + - - +
237A TYR* 2.6 32.2 + - + +
238A PHE* 2.8 11.3 + - - +
276A SER* 3.4 26.2 - - - +
277A THR* 3.6 16.4 - - - +
280A GLY 5.9 0.2 - - - +
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 5.3 0.2 - - - +
78A ILE* 5.0 16.6 - - + -
153A VAL* 6.3 2.7 - - + -
193A TRP* 3.7 29.0 - - + -
200A LEU* 6.1 3.6 - - + -
231A THR* 2.8 20.1 + - + +
232A GLY* 3.6 26.2 - - - +
233A HIS 3.2 0.2 - - - -
234A PRO* 1.3 72.6 - - - +
236A VAL* 1.3 69.4 + - + +
238A PHE* 3.1 16.5 - - + +
239A TRP* 2.9 58.5 + - + +
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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
----------------------------------------------------------
232A GLY 4.2 7.4 - - - +
233A HIS* 3.0 40.3 + - + +
234A PRO 2.9 2.0 + - - -
235A ILE* 1.3 79.4 - - + +
237A TYR* 1.3 68.8 + - + +
239A TRP* 3.2 34.3 + - + -
240A LEU* 3.2 18.4 + - - +
283A HIS* 6.2 0.2 - - + -
563A CMO 4.2 1.3 - - - -
801A HAS 3.1 62.0 - - + +
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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
----------------------------------------------------------
192A MET* 4.8 5.4 - - + -
233A HIS* 1.8 55.9 + + - -
234A PRO 2.6 14.6 + - - +
236A VAL* 1.3 76.2 - - + +
238A PHE* 1.3 54.1 - - - -
240A LEU* 3.1 13.5 + - + +
241A LEU* 3.0 39.4 + - + +
272A PHE* 3.3 35.4 - + + -
276A SER* 4.1 21.5 - - - +
305A VAL* 3.4 22.9 - - + +
309A SER* 4.7 1.1 - - - -
801A HAS 2.6 51.2 + + + -
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLN* 3.8 35.9 - - + -
85A ALA* 3.8 24.0 - - + +
156A THR* 3.9 8.3 - - + -
189A PHE* 3.6 19.0 - + - -
190A TRP* 3.9 14.8 - + - -
192A MET* 4.6 5.7 - - + +
193A TRP* 3.3 57.2 - + + -
234A PRO 2.8 5.5 + - - +
235A ILE* 3.1 26.9 - - + +
237A TYR* 1.3 76.5 - - - +
239A TRP* 1.3 75.4 + + - -
240A LEU 3.2 0.2 - - - -
242A PRO* 3.2 19.9 - - - +
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Residues in contact with TRP 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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77A ALA* 3.1 41.5 + - + -
78A ILE* 5.3 1.5 + - + -
81A THR* 3.2 32.5 + - + -
82A GLN 5.1 0.2 - - - +
84A PHE* 5.4 2.3 - - - -
85A ALA* 5.7 1.3 - - - -
133A TYR* 4.4 10.5 - + - -
235A ILE* 2.9 48.1 + - + +
236A VAL* 3.2 30.7 - - + +
237A TYR 3.2 0.2 - - - -
238A PHE* 1.3 88.4 - + - +
240A LEU* 1.3 61.1 + - - +
242A PRO* 3.6 9.1 - - - +
243A ALA 4.6 1.7 + - - -
389A VAL* 3.7 15.3 - - + -
393A VAL* 3.4 23.1 - - + +
800A HEM 5.6 0.2 - - + -
801A HAS 3.3 49.6 - - + -
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Residues in contact with LEU 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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236A VAL 3.3 14.4 - - - +
237A TYR* 3.1 21.4 + - + +
239A TRP* 1.3 76.7 - - - +
241A LEU* 1.3 59.7 + - + +
242A PRO* 3.2 2.0 - - - -
243A ALA* 2.8 29.4 + - + +
244A TYR* 2.8 57.5 + - + +
272A PHE* 4.7 0.4 - - + -
309A SER* 4.6 3.4 - - - +
356A PHE* 3.8 21.5 - - + -
392A LEU* 3.8 14.8 - - + -
393A VAL* 3.8 14.4 - - + -
801A HAS 4.0 20.0 - - + -
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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
----------------------------------------------------------
89A MET* 3.8 3.6 - - - +
188A VAL* 6.3 0.2 - - + -
189A PHE* 3.4 30.5 - - + -
192A MET* 4.2 12.8 - - + -
237A TYR* 3.0 18.2 + - + +
240A LEU* 1.3 82.7 - - + +
242A PRO* 1.3 59.3 - - - +
244A TYR* 2.8 31.9 + - + +
245A ALA* 2.7 30.1 + - - +
269A PHE* 3.5 25.1 - - + +
272A PHE* 4.0 45.3 - - + -
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Residues in contact with PRO 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.4 12.1 - - + -
85A ALA* 3.6 32.3 - - + -
88A ILE* 3.7 17.4 - - + +
89A MET* 3.7 15.5 - - + -
189A PHE* 3.6 14.1 - - + -
238A PHE 3.2 24.5 - - - +
239A TRP 3.6 7.6 - - - +
240A LEU 3.4 4.0 - - - -
241A LEU* 1.3 87.9 - - - +
243A ALA* 1.3 61.1 + - - +
245A ALA* 3.4 3.8 - - - +
246A ILE* 3.3 22.7 + - - +
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Residues in contact with ALA 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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84A PHE* 4.6 4.7 - - + -
239A TRP 4.6 2.1 + - - +
240A LEU* 2.8 19.5 + - + +
242A PRO* 1.3 73.9 - - - +
244A TYR* 1.3 52.5 + - + +
246A ILE* 2.9 8.7 + - - +
247A ILE* 2.7 45.4 + - + +
392A LEU* 5.2 0.9 - - + -
393A VAL* 4.4 21.5 - - + +
396A THR* 3.9 30.1 - - + +
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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
----------------------------------------------------------
240A LEU* 2.8 37.9 + - + -
241A LEU* 2.8 38.9 + - + +
243A ALA* 1.3 70.9 - - - +
245A ALA* 1.3 61.2 + - - +
247A ILE* 3.3 16.8 + - + +
248A TYR* 3.0 41.0 + + - -
268A ALA* 6.1 0.2 - - + -
269A PHE* 4.0 7.4 - + + -
272A PHE* 4.0 20.4 - + - -
309A SER* 3.2 27.6 + - - -
312A THR* 3.4 39.4 - - + +
353A LEU* 5.7 2.9 - - + -
356A PHE* 3.5 18.0 - + - -
392A LEU* 4.7 4.3 - - + -
801A HAS 4.1 3.7 - - + +
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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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88A ILE* 4.6 5.8 - - + -
89A MET* 3.7 24.2 - - + -
92A LEU* 4.8 7.0 - - + -
182A VAL* 5.8 4.9 - - + -
185A MET* 4.3 21.3 - - + -
241A LEU 2.7 14.0 + - - +
242A PRO 3.4 11.4 - - - +
244A TYR* 1.3 73.6 - - - +
246A ILE* 1.3 63.6 + - - +
248A TYR 3.2 0.2 + - - -
249A THR* 3.0 32.2 + - - +
269A PHE* 3.9 1.6 - - - -
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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
----------------------------------------------------------
84A PHE* 3.9 13.5 - - + -
88A ILE* 3.7 38.4 - - + -
92A LEU* 4.4 4.7 - - + -
242A PRO 3.3 12.3 + - - +
243A ALA 2.9 10.9 + - - +
245A ALA* 1.3 76.3 - - - +
247A ILE* 1.3 65.0 + - + +
249A THR* 4.6 0.7 - - - -
250A ILE* 3.2 18.1 + - + -
251A LEU* 3.1 26.3 + - + +
349A PRO* 5.8 3.6 - - + -
396A THR* 3.9 21.5 - - + -
400A SER* 4.2 7.9 - - - +
403A TRP* 3.9 35.0 - - + +
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Residues in contact with ILE 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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243A ALA* 2.7 43.4 + - + +
244A TYR* 3.8 20.9 - - + +
245A ALA 3.2 0.4 - - - -
246A ILE* 1.3 73.9 - - + +
248A TYR* 1.3 56.8 + - + +
251A LEU* 3.4 18.5 - - + +
252A PRO* 3.0 22.2 - - - +
312A THR* 5.7 2.5 - - + -
316A VAL* 3.7 39.2 - - + +
349A PRO* 4.5 18.8 - - + -
353A LEU* 4.3 14.1 - - + -
392A LEU* 4.4 19.7 - - + -
396A THR* 4.4 4.7 - - + +
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Residues in contact with TYR 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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185A MET* 4.0 8.3 - - + -
244A TYR* 3.0 34.1 + + - +
245A ALA 3.7 2.5 - - - +
247A ILE* 1.3 77.3 - - + +
249A THR* 1.3 68.5 + - + +
250A ILE 3.8 0.4 - - - -
252A PRO* 3.4 18.6 - - - +
259A LEU* 3.4 38.4 - - + +
265A ALA* 4.1 19.0 - - + -
268A ALA* 3.8 11.9 - - + +
269A PHE* 4.1 24.5 - + - -
312A THR* 2.8 49.6 + - + -
315A THR* 3.7 28.6 + - + -
316A VAL* 4.3 11.0 - - + -
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Residues in contact with THR 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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92A LEU* 4.6 3.3 - - - +
181A LEU* 3.8 27.8 - - + -
182A VAL* 4.1 23.7 - - + +
185A MET* 3.9 14.4 - - + -
245A ALA* 3.0 18.7 + - - +
248A TYR* 1.3 90.2 - - + +
250A ILE* 1.3 73.3 + - - +
259A LEU* 5.1 0.9 - - - -
508A PHE* 3.4 6.4 - - - -
509A ALA* 3.0 32.3 + - - -
511A VAL* 6.3 1.3 - - - -
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Residues in contact with ILE 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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92A LEU* 3.7 26.0 - - + -
246A ILE* 3.2 13.8 + - + +
248A TYR 3.8 0.4 - - - -
249A THR* 1.3 93.1 - - - +
251A LEU* 1.3 66.5 + - - +
252A PRO* 3.4 1.7 - - - +
253A LYS* 3.2 15.5 + - - +
254A GLN* 3.2 26.3 - - - +
403A TRP* 3.7 40.4 - - + +
506A LEU* 4.6 7.0 - - + -
507A PRO* 3.6 30.1 - - + +
508A PHE* 4.0 15.7 - - + -
509A ALA 4.8 0.2 - - - +
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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
------------------------------------------------------------
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