Contacts of the helix formed by residues 327 - 350 (chain J) in PDB entry 2QJK
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 327 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I PRO* 4.2 19.3 - - + +
315J VAL* 4.5 2.5 - - - -
319J ASN* 4.5 15.0 - - - +
324J GLY 3.6 10.1 + - - +
325J ILE 2.7 14.9 + - - +
326J ILE* 1.3 75.1 - - - +
328J ALA* 1.3 66.2 + - - +
329J LYS* 3.1 21.0 + - - +
330J PHE* 3.1 13.4 + - - +
331J PHE* 2.9 20.8 + - - +
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Residues in contact with ALA 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I PRO* 4.2 12.3 - - + +
168I PRO* 6.2 1.1 - - + -
308J PHE 4.1 10.5 - - - +
309J THR 3.8 7.0 - - - +
310J ALA* 3.6 39.5 - - + +
315J VAL* 3.9 15.0 - - + +
319J ASN* 5.5 0.6 - - - +
327J ASP* 1.3 76.0 - - - +
329J LYS* 1.3 65.6 + - - +
331J PHE* 2.9 4.7 + - - +
332J GLY* 2.7 22.5 + - - -
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Residues in contact with LYS 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I THR 2.6 20.2 + - - +
131I HIS* 2.4 49.5 + - + +
132I LEU* 4.4 9.6 - - + -
166I PRO* 4.1 15.1 + - - +
168I PRO* 4.4 13.8 - - + +
164J GLY 5.5 0.7 - - - -
167J GLY 5.3 3.1 - - - -
168J ALA* 4.4 24.0 - - + +
305J LEU* 5.4 0.7 - - - +
327J ASP* 3.1 13.6 + - - +
328J ALA* 1.3 82.1 - - - +
330J PHE* 1.3 59.2 + - + +
332J GLY* 2.9 13.5 + - - -
333J VAL* 3.1 15.1 + - + +
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Residues in contact with PHE 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J ALA* 3.5 29.8 - - + +
169J ILE* 4.0 14.8 - - + -
170J PRO* 3.5 35.9 - - + -
325J ILE* 4.7 3.1 - - + +
326J ILE* 4.3 23.1 - - + -
327J ASP* 3.1 15.2 + - - +
329J LYS* 1.3 76.8 - - + +
331J PHE* 1.3 61.2 + - - +
333J VAL* 3.4 14.3 + - + -
334J LEU* 2.9 67.0 + - + +
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Residues in contact with PHE 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J PHE* 3.3 50.0 - + + -
314J VAL* 3.6 27.4 - - + -
315J VAL* 3.6 23.8 - - + -
318J ALA* 3.9 26.7 - - + -
326J ILE* 4.1 8.2 - - + +
327J ASP 2.9 20.1 + - - +
328J ALA* 2.9 8.6 + - - +
330J PHE* 1.3 75.9 - - - +
332J GLY* 1.3 52.2 + - - +
334J LEU* 2.9 13.5 + - + +
335J ALA* 2.6 39.9 + - + +
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Residues in contact with GLY 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305J LEU* 3.5 37.3 - - - +
308J PHE* 4.5 5.2 - - - -
328J ALA 2.7 12.8 + - - -
329J LYS 2.9 4.7 + - - -
331J PHE* 1.3 80.8 - - - +
333J VAL* 1.3 60.0 - - - +
335J ALA* 3.3 9.2 + - - +
336J MET* 3.0 18.5 + - - +
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Residues in contact with VAL 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I HIS* 6.2 0.7 - - - +
132I LEU* 5.5 2.7 - - + -
165J LEU* 4.1 31.6 - - + +
168J ALA* 3.5 26.9 - - + -
169J ILE* 6.1 2.7 - - + +
305J LEU* 3.8 9.4 - - + +
329J LYS* 3.1 12.2 + - + +
330J PHE* 3.5 19.3 - - + +
332J GLY* 1.3 76.1 - - - +
334J LEU* 1.3 64.7 + - + +
336J MET* 3.0 13.7 + - - +
337J PHE* 3.1 39.8 + - + -
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Residues in contact with LEU 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326J ILE* 4.4 15.7 - - + -
330J PHE* 2.9 64.1 + - + +
331J PHE* 3.3 11.7 - - + +
333J VAL* 1.3 76.2 - - + +
335J ALA* 1.3 55.8 + - - +
337J PHE* 5.1 3.4 - - - -
338J GLY* 2.7 35.7 + - - -
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Residues in contact with ALA 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304J ILE* 4.0 7.4 - - + +
308J PHE* 3.3 37.5 - - + -
331J PHE* 2.6 21.7 + - + +
332J GLY 3.4 9.4 - - - +
334J LEU* 1.3 73.7 - - - +
336J MET* 1.3 57.0 + - - +
338J GLY* 4.9 0.2 - - - -
339J ALA* 2.8 26.0 + - - +
401J PHE* 3.3 18.0 - - + -
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Residues in contact with MET 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J LEU* 3.7 24.5 - - + -
301J PHE* 3.4 39.4 - - + +
304J ILE* 4.1 7.4 - - - +
305J LEU* 4.0 11.9 - - + -
332J GLY 3.0 11.2 + - - +
333J VAL* 3.0 8.3 + - - +
335J ALA* 1.3 73.1 - - - +
337J PHE* 1.3 88.4 + - + +
338J GLY 2.9 0.7 - - - -
339J ALA* 2.8 20.6 + - - +
340J ILE* 3.3 8.1 + - - +
503J SMA 3.3 56.3 - - - +
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Residues in contact with PHE 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J LEU* 5.7 6.1 - - + -
165J LEU* 4.6 15.3 - - + -
166J PHE* 4.6 20.4 - + - -
333J VAL* 3.1 41.3 + - + +
334J LEU* 4.3 3.4 - - + +
336J MET* 1.3 93.8 - - + +
338J GLY* 1.3 57.1 + - - +
340J ILE* 3.1 12.5 + - + +
341J LEU* 2.8 29.1 + - - +
503J SMA 4.0 41.1 - - + -
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Residues in contact with GLY 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J LEU 2.7 24.1 + - - -
335J ALA* 3.7 1.3 - - - -
337J PHE* 1.3 70.2 - - - +
339J ALA* 1.3 64.2 + - - +
340J ILE 2.9 2.5 + - - -
341J LEU* 3.0 11.6 + - - +
342J VAL* 2.8 30.6 + - - +
401J PHE* 4.0 9.2 - - - -
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Residues in contact with ALA 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J PHE* 4.5 8.7 - - + -
304J ILE* 3.8 17.9 - - + -
335J ALA 2.8 14.9 + - - +
336J MET* 2.8 15.1 + - - +
338J GLY* 1.3 72.1 - - - -
340J ILE* 1.3 59.2 + - - +
342J VAL* 3.2 11.2 - - - +
343J MET* 3.9 1.6 + - - +
400J TRP* 2.9 38.6 + - + +
401J PHE* 3.6 21.4 - - + -
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Residues in contact with ILE 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J MET* 3.8 22.9 - - + +
136J TYR* 4.6 9.2 - - + -
137J LEU* 5.7 11.2 - - + -
140J MET* 3.9 13.5 - - + -
301J PHE* 3.2 35.4 - - + -
336J MET 3.8 7.6 - - - +
337J PHE* 3.1 15.2 + - + +
338J GLY 2.9 0.6 - - - -
339J ALA* 1.3 75.9 - - - +
341J LEU* 1.3 68.3 + - - +
343J MET* 2.9 28.6 + - + +
344J ALA 3.2 4.2 + - - -
503J SMA 3.6 31.4 - - - -
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Residues in contact with LEU 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J PHE 2.8 20.4 + - - +
338J GLY* 3.5 10.3 - - - +
340J ILE* 1.3 75.0 - - - +
342J VAL* 1.3 66.0 + - + +
344J ALA* 2.9 20.4 + - + +
345J LEU* 3.1 36.6 + - + +
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Residues in contact with VAL 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338J GLY* 2.8 21.7 + - - +
339J ALA* 3.2 20.9 - - - +
341J LEU* 1.3 73.8 - - + +
343J MET* 1.3 67.3 + - - +
345J LEU* 2.8 34.4 + - + +
346J VAL* 3.0 10.7 + - - -
349J LEU* 4.7 4.0 - - + +
400J TRP* 4.0 5.8 - - + +
401J PHE* 4.1 20.9 - - + -
404J PHE* 3.9 36.7 - - + -
405J LEU* 4.3 21.8 - - + -
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Residues in contact with MET 343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J TYR* 6.5 0.2 - - + -
112J ILE* 4.3 35.0 - - + -
116J LEU* 4.8 7.4 - - + -
129J TRP* 3.2 17.5 + - + -
133J MET* 3.9 20.4 - - + -
136J TYR* 4.4 14.6 - - + -
301J PHE* 4.7 10.3 - - + -
339J ALA 4.1 6.5 - - - +
340J ILE* 2.9 22.6 + - + +
342J VAL* 1.3 81.3 - - - +
344J ALA* 1.3 55.5 + - - +
346J VAL* 2.9 27.4 - - - +
400J TRP* 4.2 20.4 - - + -
404J PHE* 3.9 23.6 - - + -
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Residues in contact with ALA 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J TRP* 3.6 15.6 + - - +
130J ILE* 5.2 3.3 - - + +
133J MET* 3.9 28.0 - - + +
340J ILE 3.2 3.8 + - - +
341J LEU* 2.9 24.2 + - + +
343J MET* 1.3 76.3 - - - +
345J LEU* 1.3 60.9 + - + +
346J VAL 3.2 0.4 - - - -
347J PRO* 3.1 16.3 - - - +
348J TRP* 3.6 8.0 - - - -
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Residues in contact with LEU 345 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341J LEU* 3.3 42.4 - - + +
342J VAL* 2.8 12.8 + - + +
344J ALA* 1.3 77.6 - - + +
346J VAL* 1.3 52.3 + - - +
347J PRO* 3.0 4.3 - - - -
348J TRP* 2.6 48.0 + - + -
349J LEU* 3.2 24.5 + - + -
405J LEU* 6.5 0.4 - - + -
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Residues in contact with VAL 346 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J LEU* 4.1 5.6 - - + -
121J TYR* 3.6 32.2 - - + +
129J TRP* 3.4 21.3 - - + +
342J VAL 3.0 6.1 + - - -
343J MET 2.9 24.9 - - - +
345J LEU* 1.3 75.8 - - - +
347J PRO* 1.3 72.5 - - + +
348J TRP 3.0 1.0 + - - -
349J LEU* 3.7 8.7 - - - +
350J ASP* 3.2 20.9 + - + +
404J PHE* 4.0 28.3 - - + -
408J LEU* 4.3 12.6 - - + -
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Residues in contact with PRO 347 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J TYR* 3.7 33.8 - - + +
122J LYS* 5.3 4.5 - - - +
123J ALA 5.7 0.2 - - - +
126J GLU* 4.1 15.9 - - + +
129J TRP* 3.7 20.9 - - + -
344J ALA 3.1 12.6 - - - +
345J LEU 3.0 7.0 - - - -
346J VAL* 1.3 98.4 - - + +
348J TRP* 1.3 80.4 + - + +
350J ASP* 3.9 11.7 - - - +
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Residues in contact with TRP 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TRP* 4.8 11.1 - + - -
126J GLU* 4.4 21.7 + - + +
130J ILE* 3.8 29.2 - - + -
344J ALA 3.6 18.8 - - - -
345J LEU* 2.6 46.2 + - + +
347J PRO* 1.3 92.7 - - + +
349J LEU* 1.3 67.8 + - + +
350J ASP 3.3 4.4 - - - +
351J THR* 4.7 8.1 - - - +
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Residues in contact with LEU 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342J VAL* 4.7 9.2 - - + +
345J LEU* 3.2 26.3 + - + +
346J VAL* 3.4 6.2 + - - +
348J TRP* 1.3 86.3 - - + +
350J ASP* 1.3 61.3 + - - +
351J THR* 3.2 3.7 + - - +
404J PHE* 2.9 44.2 - - + +
405J LEU* 3.5 23.8 - - + -
408J LEU* 4.3 4.9 - - + -
409J PRO* 3.1 40.6 - - + +
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Residues in contact with ASP 350 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J TYR* 2.8 28.9 + - + +
122J LYS* 3.1 15.7 - - - +
346J VAL* 3.2 17.0 + - - +
347J PRO 3.9 12.0 - - - +
348J TRP 4.5 1.8 - - - -
349J LEU* 1.3 78.8 - - - +
351J THR* 1.3 60.0 + - - +
352J SER* 3.0 29.5 + - - +
360J ARG* 3.1 20.2 + - - -
408J LEU* 3.4 26.6 - - + +
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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
------------------------------------------------------------
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