Contacts of the helix formed by residues 342 - 366 (chain A) in PDB entry 2VF8
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 ARG 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP* 5.4 5.5 + - - -
338A ARG* 2.8 63.3 + - - +
339A VAL 3.4 2.7 - - - +
340A LYS 3.4 0.4 - - - -
341A ASN* 1.3 95.9 - - - +
343A PRO* 1.3 71.0 - - - +
344A GLU* 3.4 12.1 - - - +
345A GLN* 3.4 38.7 + - + +
346A ALA* 3.3 12.4 + - - +
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Residues in contact with PRO 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL 3.6 12.6 - - - +
340A LYS 4.8 4.7 - - - +
341A ASN 4.5 1.8 - - - +
342A ARG* 1.3 76.0 - - - +
344A GLU* 1.3 98.5 + - + +
345A GLN 3.1 2.2 - - - -
346A ALA* 2.8 17.5 + - + -
347A ILE* 3.1 28.7 + - + +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.5 25.3 + - - +
342A ARG* 3.4 17.5 - - - +
343A PRO* 1.3 112.2 - - + +
345A GLN* 1.3 63.7 + - + +
347A ILE* 3.8 6.2 + - - +
348A ALA* 3.5 13.5 + - - +
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Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 4.1 38.3 + - + +
127A ALA* 4.2 13.7 - - - +
128A GLY 5.1 2.9 + - - +
338A ARG* 3.0 30.2 + - - +
342A ARG* 3.4 49.8 + - + +
343A PRO 2.8 2.4 + - - -
344A GLU* 1.3 77.7 - - + +
346A ALA* 1.3 63.4 + - + +
347A ILE 3.1 2.0 - - - -
348A ALA* 2.9 4.1 + - - +
349A LEU* 2.4 38.8 + - + +
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLU* 5.3 2.4 - - - +
335A HIS* 4.9 12.9 + - + +
338A ARG* 4.0 14.8 - - + +
339A VAL* 4.4 18.6 - - + -
342A ARG 3.3 20.2 - - - +
343A PRO* 2.8 8.3 + - + +
345A GLN* 1.3 80.5 - - + +
347A ILE* 1.3 62.6 + - + +
349A LEU* 4.1 7.6 - - - +
350A GLN* 3.4 20.3 + - - +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL 5.9 0.2 - - - +
343A PRO* 3.1 42.2 + - + +
344A GLU* 4.1 6.5 - - - +
345A GLN 3.1 0.6 - - - -
346A ALA* 1.3 81.4 - - + +
348A ALA* 1.3 63.8 + - - +
350A GLN* 3.5 6.1 + - - +
351A ARG* 3.3 19.8 + - + +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 4.2 27.8 - - + +
344A GLU 3.5 12.6 + - - +
345A GLN 2.9 5.6 + - - +
347A ILE* 1.3 77.1 - - - +
349A LEU* 1.3 54.8 + - - +
351A ARG* 3.0 30.4 + - - +
352A MET* 2.7 42.1 + - + +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 5.5 4.5 - - + -
126A ARG* 5.6 1.2 - - - +
127A ALA* 3.8 30.1 - - + -
304A PHE* 4.2 13.5 - - + -
327A TYR* 3.8 41.1 - - + +
332A GLU* 5.7 1.8 - - - +
338A ARG* 3.3 33.2 - - - +
345A GLN* 2.4 34.7 + - + +
346A ALA* 4.3 6.3 - - - +
348A ALA* 1.3 66.1 - - - +
350A GLN* 1.3 68.5 + - - +
352A MET* 3.2 7.5 + - - +
353A ALA* 3.0 18.3 + - + -
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Residues in contact with GLN 350 (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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327A TYR 3.8 13.0 - - - +
328A ALA* 2.6 30.1 + - - +
330A GLU* 3.7 32.4 + - + +
346A ALA 3.4 13.8 + - - +
347A ILE* 3.6 10.3 - - - +
348A ALA 3.2 0.6 - - - -
349A LEU* 1.3 79.9 - - - +
351A ARG* 1.3 75.0 + - - +
353A ALA* 3.0 2.3 + - - +
354A ALA* 2.5 49.4 + - - +
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A MET* 5.3 7.3 - - - +
126A ARG* 5.3 4.0 - - - +
347A ILE* 3.3 11.3 + - + +
348A ALA* 3.0 31.4 + - - +
350A GLN* 1.3 88.6 + - - +
352A MET* 1.3 74.6 + - - +
354A ALA* 3.4 4.4 - - - +
355A ASP* 2.9 37.7 + - + +
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Residues in contact with MET 352 (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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119A LEU* 3.7 9.8 - - + +
122A MET* 3.6 32.8 - - + -
123A LEU* 3.4 50.5 - - + +
126A ARG* 4.3 20.9 - - - -
127A ALA* 5.3 1.3 - - - -
348A ALA* 2.7 34.2 + - + +
349A LEU* 3.6 9.0 - - - +
351A ARG* 1.3 93.6 - - - +
353A ALA* 1.3 51.9 + - - +
355A ASP* 3.3 8.3 + - - +
356A LEU* 2.8 39.1 + - - +
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Residues in contact with ALA 353 (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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123A LEU* 4.5 5.7 - - + +
324A LEU* 4.5 16.2 - - + +
327A TYR* 3.9 14.4 - - + -
328A ALA* 3.8 21.5 - - + +
349A LEU* 3.0 13.2 + - + +
350A GLN 3.4 6.7 - - - +
352A MET* 1.3 76.0 - - - +
354A ALA* 1.3 66.7 + - - +
356A LEU* 3.5 7.7 - - - +
357A VAL* 2.9 28.8 + - - +
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Residues in contact with ALA 354 (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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328A ALA* 3.5 15.2 - - + +
350A GLN* 2.5 41.9 + - - +
351A ARG* 3.4 10.3 - - + +
353A ALA* 1.3 73.7 - - - +
355A ASP* 1.3 63.3 + - - +
357A VAL* 3.6 4.9 + - - +
358A LYS* 3.3 19.5 + - - +
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Residues in contact with ASP 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.6 24.8 - - - +
351A ARG* 2.9 22.7 + - + +
352A MET* 3.7 3.5 - - - +
354A ALA* 1.3 75.7 - - + +
356A LEU* 1.3 65.8 + - - +
358A LYS* 3.3 26.6 + - + +
359A ARG* 2.9 48.5 + - - +
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Residues in contact with LEU 356 (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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116A LEU* 3.8 31.0 - - + +
119A LEU* 4.3 23.6 - - + +
120A LEU* 4.0 20.2 - - + -
123A LEU* 3.6 30.3 - - + -
324A LEU* 3.7 20.4 - - + -
352A MET 2.8 16.1 + - - +
353A ALA* 3.1 7.6 + - - +
355A ASP* 1.3 79.9 + - - +
357A VAL* 1.3 56.7 + - - +
359A ARG* 3.6 3.2 + - - +
360A LEU* 3.1 39.8 + - + +
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Residues in contact with VAL 357 (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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321A SER* 4.1 13.0 + - - +
324A LEU* 4.0 16.4 - - + -
325A ARG* 4.0 42.4 - - + +
328A ALA* 4.5 8.7 - - + -
353A ALA 2.9 18.0 + - - +
354A ALA 3.7 6.1 - - - +
356A LEU* 1.3 72.8 - - - +
358A LYS* 1.3 62.9 + - - +
360A LEU* 3.4 7.7 - - - +
361A ASP* 2.8 35.6 + - + +
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Residues in contact with LYS 358 (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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354A ALA 3.3 12.3 + - - +
355A ASP* 3.3 22.5 + - + +
357A VAL* 1.3 81.3 - - - +
359A ARG* 1.3 69.5 + - + +
361A ASP* 3.7 12.8 - - - +
362A VAL* 3.9 10.2 + - - +
395A TYR* 5.1 13.3 - - - +
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Residues in contact with ARG 359 (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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115A THR* 5.1 2.0 + - - -
116A LEU* 4.1 11.7 - - + -
119A LEU* 3.7 27.8 - - - +
355A ASP* 2.9 38.8 + - - +
356A LEU* 3.9 4.7 - - - +
357A VAL 3.2 0.4 - - - -
358A LYS* 1.3 84.6 - - + +
360A LEU* 1.3 57.7 + - - +
362A VAL* 2.6 32.0 + - - +
363A LEU* 3.3 10.8 + - - +
395A TYR* 3.0 73.1 + - + +
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Residues in contact with LEU 360 (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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116A LEU* 4.3 17.2 - - + +
317A LEU* 3.4 44.6 - - + +
320A VAL* 4.2 9.4 - - + -
321A SER* 4.1 20.2 - - - +
324A LEU* 3.9 27.6 - - + -
356A LEU* 3.1 28.2 + - + +
357A VAL* 3.4 8.1 - - - +
359A ARG* 1.3 76.5 - - - +
361A ASP* 1.3 58.1 + - - +
363A LEU* 2.9 31.7 + - + +
364A LEU* 2.9 16.2 + - + +
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Residues in contact with ASP 361 (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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321A SER* 4.7 1.5 + - - +
325A ARG* 5.1 7.7 + - - +
357A VAL* 2.8 25.2 + - + +
358A LYS* 3.7 9.6 - - - +
360A LEU* 1.3 72.1 - - - +
362A VAL* 1.3 59.9 + - - +
364A LEU* 3.6 17.2 - - + +
365A HIS* 2.7 67.3 + - - -
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LYS 3.9 8.3 + - - +
359A ARG 2.6 17.6 + - - +
361A ASP* 1.3 75.1 - - - +
363A LEU* 1.3 70.3 + - - +
365A HIS* 3.2 17.2 + - + +
366A LEU* 3.2 12.3 + - + +
391A ALA* 3.9 31.0 - - + +
394A LEU* 4.0 26.9 - - + +
395A TYR* 4.3 10.8 - - + -
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Residues in contact with LEU 363 (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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114A THR* 4.3 5.4 - - + -
116A LEU* 3.4 33.7 - - + -
317A LEU* 3.9 22.2 - - + -
359A ARG 3.3 10.1 + - - +
360A LEU* 2.9 13.0 + - + +
362A VAL* 1.3 78.1 - - - +
364A LEU* 1.3 54.6 + - + +
366A LEU* 2.7 33.6 + - - +
367A GLY 3.3 2.8 + - - -
368A LEU* 3.5 12.3 + - + +
388A LEU* 3.3 32.8 - - + +
391A ALA* 3.3 24.5 - - + -
395A TYR* 3.9 15.0 - - + +
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 3.9 24.7 - - + +
318A ALA* 3.9 8.7 - - + +
321A SER* 3.3 30.5 - - - +
322A GLU* 5.9 0.2 - - - +
325A ARG* 4.8 11.0 - - - +
360A LEU* 2.9 13.1 + - + +
361A ASP* 3.6 21.5 - - - +
363A LEU* 1.3 75.1 - - - +
365A HIS* 1.3 58.5 + - + +
367A GLY* 2.6 26.7 + - - +
369A GLY* 3.6 29.3 - - - +
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Residues in contact with HIS 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ASP* 2.7 52.6 + - - +
362A VAL* 3.2 11.6 + - + +
364A LEU* 1.3 78.1 - - + +
366A LEU* 1.3 56.9 + - - +
367A GLY 3.2 1.1 + - - -
419A ALA* 3.5 21.3 - - - +
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Residues in contact with LEU 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 3.2 6.6 + - + +
363A LEU 2.7 17.6 + - - +
365A HIS* 1.3 72.2 - - - +
367A GLY* 1.3 64.6 + - - +
368A LEU* 3.1 19.6 + - + +
387A ARG* 3.8 45.1 + - + +
390A LEU* 4.3 5.4 - - + -
391A ALA* 4.0 20.9 - - + +
394A LEU* 5.3 1.3 - - + -
412A LEU* 5.3 6.1 - - + +
416A ASP* 6.0 1.9 - - - +
419A ALA* 4.2 9.8 - - + +
420A LEU* 3.9 32.3 - - + +
423A ALA* 4.1 21.3 - - + -
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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