Contacts of the helix formed by residues 376 - 397 (chain A) in PDB entry 3F9C
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 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LYS* 5.8 0.9 + - - -
374A ASP 3.9 1.2 + - - -
375A ILE* 1.3 76.1 - - - +
377A SER* 1.3 57.5 + - - +
378A ASN* 3.2 17.7 + - - +
379A VAL* 3.1 41.1 + - + +
380A ALA* 2.8 33.4 + - - +
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Residues in contact with SER 377 (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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353A ASN* 3.7 15.5 + - - +
358A THR* 2.7 39.2 + - - -
359A PHE* 3.5 23.6 - - - -
372A LYS* 3.4 21.8 + - - +
375A ILE 3.7 1.4 + - - -
376A ASP* 1.3 74.6 + - - +
378A ASN* 1.3 59.5 + - - +
380A ALA* 3.9 1.3 - - - +
381A ILE* 3.0 31.4 + - - +
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Residues in contact with ASN 378 (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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55A LYS 4.7 4.0 + - - -
57A PRO* 3.5 23.6 - - - +
359A PHE* 3.2 27.5 - - - -
376A ASP* 3.2 18.3 + - - +
377A SER* 1.3 78.2 - - - +
379A VAL* 1.3 62.3 + - + +
381A ILE* 4.1 4.2 - - - +
382A ASP* 3.0 38.8 + - - +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 4.2 9.6 - - + -
376A ASP* 3.1 33.1 + - + +
378A ASN* 1.3 78.4 - - + +
380A ALA* 1.3 61.6 - - - +
382A ASP* 3.4 5.6 + - - +
383A LEU* 3.1 33.6 + - + +
415A ASN* 4.0 21.3 - - - +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 3.9 17.9 - - + +
349A SER* 4.9 0.2 - - - -
353A ASN* 3.9 22.0 - - + +
375A ILE* 3.8 28.9 - - + +
376A ASP 2.8 18.8 + - - +
377A SER 3.9 4.3 - - - +
379A VAL* 1.3 73.2 - - - +
381A ILE* 1.3 58.0 + - - +
383A LEU* 3.1 5.5 + - - +
384A SER* 3.0 28.3 + - - -
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Residues in contact with ILE 381 (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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57A PRO* 4.4 12.3 - - + -
162A ALA* 4.4 16.2 - - + -
163A ILE* 4.0 15.5 - - + -
353A ASN 3.6 21.3 - - - +
354A PHE* 3.9 20.4 - - + +
359A PHE* 3.6 20.4 - - + -
377A SER 3.0 21.1 + - - +
378A ASN* 3.8 8.1 - - - +
380A ALA* 1.3 77.2 - - - +
382A ASP* 1.3 67.6 + - - +
384A SER* 4.0 10.5 - - - -
385A ASN* 3.0 52.3 + - - +
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Residues in contact with ASP 382 (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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57A PRO* 6.0 0.9 - - - +
60A ASN* 3.7 23.6 + - - +
166A ASP* 6.0 0.3 - - - -
378A ASN* 3.0 29.8 + - - +
379A VAL* 3.7 5.8 - - - +
381A ILE* 1.3 85.6 - - - +
383A LEU* 1.3 60.7 + - + +
385A ASN* 4.5 5.1 + - - -
386A LYS* 2.9 57.6 + - - +
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Residues in contact with LEU 383 (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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344A ILE* 5.0 3.2 - - - +
346A ILE* 4.5 5.6 - - + -
375A ILE* 4.3 7.9 - - + -
379A VAL* 3.1 29.1 + - + +
380A ALA* 3.1 7.2 + - - +
382A ASP* 1.3 78.1 - - + +
384A SER* 1.3 60.4 + - - +
386A LYS* 5.8 3.1 - - + +
387A ALA* 3.0 27.2 + - - +
408A LEU* 4.0 23.4 - - + +
413A ASP* 3.7 28.5 - - + +
415A ASN* 3.4 33.0 - - + +
416A LEU* 4.1 22.8 - - + +
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Residues in contact with SER 384 (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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163A ILE* 5.4 0.3 - - - +
295A LEU* 3.7 16.1 - - - +
317A ILE* 3.8 10.3 - - - +
346A ILE* 4.2 7.5 - - - +
354A PHE* 3.5 35.1 - - - -
380A ALA 3.0 15.1 + - - -
381A ILE* 3.9 12.3 - - - +
383A LEU* 1.3 76.1 - - - +
385A ASN* 1.3 61.4 + - - +
387A ALA* 3.6 2.3 - - - +
388A SER* 2.9 34.1 + - - -
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Residues in contact with ASN 385 (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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162A ALA 3.7 9.5 + - - -
163A ILE* 3.7 27.9 - - - +
166A ASP* 3.2 44.1 + - - +
167A LEU* 5.3 5.4 - - + +
381A ILE* 3.0 42.4 + - - +
382A ASP* 4.1 5.4 + - - +
384A SER* 1.3 79.7 + - - +
386A LYS* 1.3 56.9 + - + +
388A SER* 3.4 7.3 + - - -
389A LEU* 2.9 36.0 + - + +
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Residues in contact with LYS 386 (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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60A ASN* 5.1 7.4 - - - -
166A ASP* 6.0 0.2 - - - +
382A ASP* 2.9 44.3 + - - +
383A LEU* 5.1 2.9 - - + +
385A ASN* 1.3 75.1 - - + +
387A ALA* 1.3 64.7 + - - +
389A LEU* 3.3 4.8 + - + -
390A ALA* 3.0 23.9 + - - +
405A TRP* 3.6 59.5 - - + +
408A LEU* 3.6 17.7 - - + -
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Residues in contact with ALA 387 (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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315A PHE* 3.4 26.4 - - + -
317A ILE* 4.2 2.0 - - + -
344A ILE* 4.1 14.1 - - + -
383A LEU 3.0 19.0 + - - +
384A SER 3.6 3.1 - - - +
386A LYS* 1.3 75.1 - - - +
388A SER* 1.3 57.9 + - - +
390A ALA* 3.5 5.5 + - - +
391A PHE* 2.9 29.8 + - - +
405A TRP 4.8 0.2 - - - -
408A LEU* 3.9 21.9 - - + +
409A ILE* 3.9 1.7 - - - +
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Residues in contact with SER 388 (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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167A LEU* 5.2 5.6 - - - -
270A ILE* 5.1 5.4 - - - +
293A ILE* 3.7 25.6 - - - +
295A LEU* 4.5 5.0 - - - +
315A PHE* 4.2 1.5 - - - -
317A ILE* 3.5 13.9 - - - +
384A SER* 2.9 23.9 + - - -
385A ASN* 3.4 9.4 + - - -
387A ALA* 1.3 72.0 - - - +
389A LEU* 1.3 62.0 + - - +
391A PHE* 3.1 4.1 + - - +
392A LEU* 2.8 40.8 + - - +
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Residues in contact with LEU 389 (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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166A ASP* 3.8 9.9 - - - +
167A LEU* 4.0 16.2 - - + -
170A HIS* 3.7 47.6 - - + +
172A PHE* 3.6 29.2 - - + -
385A ASN 2.9 25.6 + - - +
386A LYS* 3.3 7.4 + - + +
388A SER* 1.3 76.2 - - - +
390A ALA* 1.3 52.6 + - - +
392A LEU* 3.3 4.5 + - - +
393A GLN 2.8 31.0 + - - -
402A PHE* 3.4 27.2 - - + -
405A TRP* 3.9 17.9 - - + -
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Residues in contact with ALA 390 (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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386A LYS 3.0 16.5 + - - +
387A ALA 3.6 4.5 - - - +
389A LEU* 1.3 75.6 - - - +
391A PHE* 1.3 63.0 + - - +
393A GLN* 3.4 2.3 + - - +
394A LYS* 3.1 23.0 + - - +
402A PHE* 3.4 28.8 - - - +
405A TRP 3.7 23.3 - - - +
406A ASP* 3.7 12.8 - - - +
409A ILE* 3.7 10.0 - - + +
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Residues in contact with PHE 391 (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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291A CYS* 4.1 19.3 - - + -
292A GLY 3.6 17.9 - - - -
293A ILE* 3.8 18.2 - - + -
313A PRO* 3.8 2.9 - - + -
314A LEU 3.7 21.8 - - - -
315A PHE* 3.4 37.2 - + + -
340A GLU* 4.8 2.0 - - + -
342A LYS* 4.2 16.4 - - + -
387A ALA 2.9 21.2 + - - +
388A SER 3.1 4.2 + - - +
390A ALA* 1.3 74.0 - - - +
392A LEU* 1.3 55.0 - - - +
394A LYS* 3.3 1.3 + - - -
395A HIS* 3.0 67.0 + + - +
409A ILE* 3.7 19.2 - - + +
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Residues in contact with LEU 392 (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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147A VAL* 4.4 2.2 - - + -
167A LEU* 3.8 23.1 - - + -
172A PHE* 3.7 34.5 - - + -
268A ALA* 3.7 30.1 - - + -
270A ILE* 4.3 13.9 - - + -
291A CYS* 4.0 11.4 - - - -
293A ILE* 3.9 14.4 - - + -
388A SER* 2.8 27.0 + - - +
389A LEU* 3.6 4.5 - - - +
391A PHE* 1.3 67.8 - - - +
393A GLN* 1.3 61.7 + - - +
396A LEU* 2.7 45.7 + - + +
398A LEU* 4.4 1.3 - - - -
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Residues in contact with GLN 393 (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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389A LEU 2.8 20.2 + - - +
390A ALA* 3.8 4.3 - - - +
392A LEU* 1.3 73.2 - - - +
394A LYS* 1.3 58.7 + - - +
397A GLY* 3.0 9.0 + - - -
398A LEU* 3.0 52.8 + - + +
399A HIS* 4.9 0.4 - - - +
400A LYS* 2.8 37.6 + - - +
402A PHE* 3.1 33.7 + - + +
403A ASP* 3.6 29.8 + - + +
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Residues in contact with LYS 394 (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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340A GLU* 4.5 10.5 - - - +
390A ALA 3.1 13.2 + - - +
391A PHE* 3.7 9.2 - - - +
392A LEU 3.2 0.2 - - - -
393A GLN* 1.3 79.4 - - - +
395A HIS* 1.3 90.3 + - + +
397A GLY* 3.8 6.6 + - - -
406A ASP* 5.4 7.6 - - - +
409A ILE* 5.3 9.6 - - + -
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Residues in contact with HIS 395 (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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290A ARG* 4.7 9.4 - - - +
291A CYS* 4.0 21.3 - - + -
313A PRO* 3.4 21.5 - - + +
340A GLU* 3.7 25.2 + - + +
391A PHE* 3.0 57.6 + + - +
394A LYS* 1.3 116.4 + - + +
396A LEU* 1.3 68.5 + - - +
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Residues in contact with LEU 396 (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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145A PRO* 4.7 0.9 - - + -
146A LEU 5.4 0.7 - - - +
172A PHE* 4.3 14.8 - - + -
265A GLU 4.6 1.1 - - - +
266A LYS* 3.3 48.2 - - + +
267A ILE 3.6 33.0 - - - +
268A ALA* 4.2 7.4 - - + -
290A ARG* 3.8 16.6 - - + -
291A CYS* 4.2 11.2 - - - -
392A LEU* 2.7 46.3 + - + +
395A HIS* 1.3 75.7 - - - +
397A GLY* 1.3 60.5 + - - +
398A LEU* 3.4 6.7 - - + -
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Residues in contact with GLY 397 (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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266A LYS* 3.5 12.4 - - - -
393A GLN 3.0 10.0 + - - -
394A LYS 3.8 5.4 + - - -
395A HIS 3.5 2.6 - - - -
396A LEU* 1.3 81.1 - - - +
398A LEU* 1.3 64.9 + - - +
399A HIS* 3.8 17.8 + - - -
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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