Contacts of the helix formed by residues 415 - 438 (chain B) in PDB entry 5ITZ
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 GLU 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B PHE* 4.0 22.9 - - + -
402B LYS* 5.5 5.5 - - - +
405B LEU* 4.4 15.0 - - + +
409B THR* 4.0 20.6 - - + +
413B MET 3.5 2.4 + - - -
414B ASP* 1.3 75.6 + - - +
416B MET* 1.3 75.4 + - + +
418B PHE* 2.9 33.6 + - + +
419B THR* 3.7 4.9 + - + +
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Residues in contact with MET 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ASP* 3.1 16.5 + - - +
415B GLU* 1.3 98.5 - - + +
417B GLU* 1.3 56.9 + - - +
419B THR* 3.1 24.8 + - + +
420B GLU* 2.8 30.5 + - - +
375D PHE* 3.6 22.7 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TRP* 3.5 19.3 - - - -
108B TYR* 2.5 37.6 + - - -
189B LEU* 4.0 7.6 - - + +
192B HIS* 5.0 7.8 - - + -
193B GLN* 3.9 12.0 + - - -
413B MET* 3.5 21.9 - - + +
414B ASP* 3.3 14.3 + - + +
415B GLU 3.1 0.8 - - - -
416B MET* 1.3 79.7 - - - +
418B PHE* 1.3 57.4 + - - +
420B GLU* 3.6 1.0 - - - +
421B ALA* 2.9 28.4 + - - +
373D GLN 5.4 0.5 - - - +
375D PHE* 3.1 38.9 - - + +
376D LEU 4.6 0.5 + - - -
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Residues in contact with PHE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.8 29.2 - + + -
189B LEU* 4.3 13.2 - - + -
395B PHE* 3.7 27.2 - + + -
399B PHE* 3.6 25.4 - + + -
405B LEU* 3.9 17.3 - - + -
408B TYR* 3.4 46.2 - + + -
409B THR* 5.2 2.9 - - + -
413B MET* 3.5 22.0 - - + -
414B ASP 4.9 0.7 - - - -
415B GLU* 2.9 26.4 + - + +
417B GLU* 1.3 78.6 - - - +
419B THR* 1.3 62.6 + - - +
421B ALA* 3.8 1.2 - - - +
422B GLU* 3.0 23.4 + - - +
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Residues in contact with THR 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PHE* 3.7 29.2 - - + -
415B GLU* 3.7 8.0 + - - +
416B MET* 3.1 31.8 + - + -
418B PHE* 1.3 75.2 - - - +
420B GLU* 1.3 58.8 + - - +
422B GLU* 3.9 13.0 - - - +
423B SER* 3.0 34.8 + - - -
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B HIS* 3.8 7.4 - - + +
416B MET 2.8 17.8 + - - +
417B GLU* 3.6 5.8 - - - +
419B THR* 1.3 78.2 + - - +
421B ALA* 1.3 57.3 + - - +
423B SER* 3.3 6.6 + - - -
424B ASN* 3.0 27.0 + - - +
375D PHE* 3.7 20.8 - - + -
376D LEU 3.6 20.2 - - - +
377D LYS* 3.4 9.1 - - - +
378D ARG* 2.8 42.3 + - - +
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 3.6 19.9 - - + +
189B LEU* 4.0 14.4 - - + -
192B HIS* 3.5 35.8 - - + +
417B GLU 2.9 17.7 + - - +
418B PHE 3.8 3.1 - - - +
420B GLU* 1.3 76.4 - - - +
422B GLU* 1.3 58.7 + - - +
424B ASN* 3.2 2.3 + - - +
425B MET* 2.9 30.3 + - - +
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 3.9 9.7 - - - +
392B SER* 5.0 4.0 - - - +
395B PHE* 3.4 35.9 - - + -
396B THR* 3.2 28.1 + - - +
399B PHE* 4.6 11.4 - - - -
418B PHE 3.0 10.9 + - - +
419B THR* 3.9 15.2 - - - +
421B ALA* 1.3 76.0 - - - +
423B SER* 1.3 59.0 + - - +
425B MET* 3.4 3.9 + - + +
426B ASN* 3.0 45.5 + - - +
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B THR* 3.0 20.2 + - - -
420B GLU* 3.6 4.7 - - - -
421B ALA 3.2 0.2 - - - -
422B GLU* 1.3 79.6 + - - +
424B ASN* 1.3 56.5 + - - +
426B ASN* 3.3 5.7 + - - +
427B ASP* 2.8 34.6 + - - +
378D ARG* 3.5 33.5 + - - -
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Residues in contact with ASN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B HIS* 2.8 38.3 + - + +
195B VAL* 3.2 18.8 - - - +
196B GLU* 2.8 24.2 + - - +
264B ARG* 2.8 40.6 + - - -
420B GLU 3.0 11.3 + - - +
421B ALA 3.2 2.4 + - - +
423B SER* 1.3 77.1 - - - +
425B MET* 1.3 58.7 + - - +
427B ASP* 3.3 3.0 + - - +
428B LEU* 2.9 24.4 + - - +
378D ARG* 3.6 19.3 - - + +
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Residues in contact with MET 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B THR* 3.4 32.5 - - + +
191B VAL* 3.7 41.3 - - + -
192B HIS* 5.8 0.8 - - - +
195B VAL* 5.8 0.9 - - - -
388B PHE* 3.8 26.7 - - + +
391B ILE* 3.6 9.2 - - + -
392B SER* 3.6 38.4 - - - +
395B PHE* 5.3 0.4 - - + -
421B ALA 2.9 16.9 + - - +
422B GLU* 3.9 5.8 - - + +
424B ASN* 1.3 75.9 - - - +
426B ASN* 1.3 63.8 + - - +
428B LEU* 3.1 10.2 + - + +
429B VAL* 3.1 22.5 + - + +
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B SER* 2.9 31.7 + - - -
396B THR* 5.6 1.0 + - - -
422B GLU* 3.0 35.0 + - - +
423B SER* 3.8 5.3 - - - +
425B MET* 1.3 74.2 - - - +
427B ASP* 1.3 65.4 + - - +
429B VAL* 3.3 13.5 + - - +
430B SER* 3.2 21.7 + - - -
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ARG* 3.7 13.4 - - - +
423B SER* 2.8 16.3 + - - +
424B ASN* 3.3 10.1 + - - +
426B ASN* 1.3 73.8 - - - +
428B LEU* 1.3 66.1 + - - +
430B SER* 3.1 9.3 + - - -
431B GLU* 3.0 25.3 + - - +
378D ARG* 2.6 34.8 + - - -
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.5 4.3 - - + -
195B VAL* 3.9 24.7 - - + -
264B ARG* 3.6 39.4 - - + +
265B LEU* 3.7 17.9 - - + -
267B PHE* 4.0 5.6 - - + -
388B PHE* 3.7 41.3 - - + -
424B ASN 2.9 13.1 + - - +
425B MET* 3.1 11.6 + - - +
427B ASP* 1.3 76.7 - - - +
429B VAL* 1.3 62.0 + - + +
431B GLU* 3.1 6.4 + - - +
432B TYR* 3.0 36.9 + - + -
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Residues in contact with VAL 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLN* 3.7 32.3 - - + +
388B PHE* 3.8 26.7 - - + -
389B LYS* 3.8 28.3 - - + +
392B SER* 5.8 0.2 - - - -
425B MET* 3.1 14.3 + - + +
426B ASN* 3.5 16.6 - - - +
427B ASP 3.3 0.2 - - - -
428B LEU* 1.3 74.6 - - - +
430B SER* 1.3 64.7 + - - +
432B TYR* 3.2 7.1 + - - +
433B GLN* 3.0 19.2 + - + +
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Residues in contact with SER 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ASN 3.2 9.9 + - - -
427B ASP* 3.1 18.4 + - - -
429B VAL* 1.3 81.5 - - - +
431B GLU* 1.3 55.8 + - - +
433B GLN* 3.0 10.8 + - - +
434B GLN* 2.9 35.7 + - - +
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 4.3 10.9 - - - +
263B PRO* 5.9 0.3 - - - +
264B ARG* 2.9 43.7 + - - +
265B LEU* 3.9 24.8 - - + +
427B ASP* 3.0 16.9 + - - +
428B LEU* 3.1 6.3 + - - +
430B SER* 1.3 78.8 + - - +
432B TYR* 1.3 60.7 + - - +
434B GLN* 3.2 21.3 - - - +
435B TYR* 3.2 38.6 + - + +
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Residues in contact with TYR 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 3.7 38.9 - - + +
267B PHE* 3.5 36.2 + - - +
313B LEU* 5.0 1.6 - - + -
380B ASN* 4.3 8.5 - - - -
381B SER 4.1 5.4 - - - -
382B THR* 3.5 42.7 - - + +
384B ILE* 3.4 25.8 - - + +
385B GLN* 4.0 13.5 - - + -
388B PHE* 3.9 6.5 - + - -
428B LEU* 3.0 46.6 + - + -
429B VAL* 3.5 6.3 - - - +
431B GLU* 1.3 75.1 - - - +
433B GLN* 1.3 63.8 + - - +
434B GLN 3.3 0.2 + - - -
435B TYR* 3.3 2.0 + - - -
436B GLN* 2.9 22.3 + - - +
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLN* 3.0 31.4 + - - +
389B LYS* 5.2 1.9 + - - -
429B VAL* 3.0 13.5 + - + +
430B SER* 3.0 15.5 + - - +
432B TYR* 1.3 77.1 - - - +
434B GLN* 1.3 62.4 + - - +
436B GLN* 3.3 19.0 + - - +
437B ASP* 2.6 52.4 + - - +
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B SER* 2.9 17.3 + - - +
431B GLU* 3.2 28.7 - - - +
433B GLN* 1.3 78.9 - - - +
435B TYR* 1.3 83.5 + - + +
437B ASP* 3.3 5.6 + - - +
438B ALA* 2.9 27.2 + - - +
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Residues in contact with TYR 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LYS* 4.5 12.5 + - + -
262B PHE* 3.4 50.0 - + - -
265B LEU* 3.5 20.4 - - + -
311B ARG* 3.6 12.5 + - - -
313B LEU* 4.0 18.6 - - + -
344B VAL* 4.0 5.2 - - - +
346B TRP* 3.8 25.8 - + + -
382B THR* 4.2 4.9 - - + -
431B GLU* 3.2 34.7 + - + +
432B TYR 3.3 5.7 + - - +
434B GLN* 1.3 93.6 + - + +
436B GLN* 1.3 66.0 + - - +
437B ASP 3.4 0.2 + - - -
438B ALA* 3.6 9.8 + - + -
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B HIS 3.3 20.4 + - - +
310B GLY* 3.3 13.9 - - - -
311B ARG* 2.8 34.8 + - + +
382B THR* 2.7 34.8 + - - +
383B ALA* 4.6 0.3 - - - -
385B GLN* 3.0 19.2 + - - +
432B TYR 2.9 10.1 + - - +
433B GLN* 3.3 32.5 + - - +
435B TYR* 1.3 78.9 - - - +
437B ASP* 1.3 65.0 + - - +
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Residues in contact with ASP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ARG* 4.3 0.7 - - - +
433B GLN* 2.6 38.6 + - - +
434B GLN* 3.3 6.7 + - - +
435B TYR 3.2 0.4 - - - -
436B GLN* 1.3 89.1 + - - +
438B ALA* 1.3 65.1 + - - +
439B THR* 3.4 14.7 - - - +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS* 3.9 15.0 - - + -
311B ARG* 2.7 30.1 + - - -
346B TRP* 3.4 22.2 + - + +
434B GLN 2.9 16.4 + - - +
435B TYR* 4.0 16.2 - - + +
436B GLN 3.5 1.6 - - - -
437B ASP* 1.3 77.0 - - - +
439B THR* 1.3 60.1 + - - +
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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