Contacts of the helix formed by residues 406 - 426 (chain a) in PDB entry 5W97
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 ASN 406 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405a LEU* 1.3 75.4 - - - +
407a ASP* 1.3 57.5 - - - +
408a THR* 3.1 14.0 + - - -
409a TRP* 3.1 41.8 + - + +
410a ALA* 3.1 25.5 + - - +
471a ILE* 4.9 5.7 + - + +
474a GLU* 3.7 20.4 + - - +
480a ARG* 3.4 15.1 - - - +
607a PGV 3.4 34.7 + - - +
15m GLN* 5.9 0.8 + - - -
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Residues in contact with ASP 407 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335a SER* 5.7 1.8 - - - -
336a PRO* 3.7 23.3 - - + +
394a VAL* 5.4 1.6 - - - +
405a LEU* 3.4 12.8 + - - +
406a ASN* 1.3 70.4 + - - +
408a THR* 1.3 60.9 + - - +
410a ALA* 3.3 6.8 + - - +
411a LYS* 2.9 47.1 + - - +
77d GLU* 4.9 2.2 - - - +
1m ILE* 5.5 7.4 - - - +
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Residues in contact with THR 408 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406a ASN* 3.1 8.7 + - - -
407a ASP* 1.3 77.8 - - - +
409a TRP* 1.3 59.1 + - - +
411a LYS* 3.3 6.2 + - - +
412a ILE* 3.0 29.5 + - + +
607a PGV 2.9 47.0 + - + -
77d GLU* 2.7 24.6 + - - +
80d THR* 3.9 20.2 - - + -
81d VAL* 4.1 10.6 - - + +
10k HIS* 3.8 6.8 + - + -
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Residues in contact with TRP 409 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406a ASN* 3.1 41.5 + - + +
408a THR* 1.3 76.1 - - - +
410a ALA* 1.3 51.8 + - - +
412a ILE* 2.9 33.2 + - + +
413a HIS* 2.7 34.3 + - - +
467a LEU* 3.9 19.7 - - + -
470a PHE* 3.7 23.7 - + - -
471a ILE* 3.7 20.1 - - + +
474a GLU* 5.1 5.8 - - + -
607a PGV 3.5 51.7 - - + +
88d PHE* 3.7 26.9 - + - -
15m GLN* 3.1 30.8 - - - +
19m LEU* 4.1 16.8 - - + -
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Residues in contact with ALA 410 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336a PRO* 3.5 28.2 - - + +
340a TRP* 4.6 3.8 + - - -
394a VAL* 4.8 13.2 - - + -
405a LEU* 5.2 7.4 - - + -
406a ASN 3.1 14.0 + - - +
407a ASP* 3.5 9.9 - - - +
409a TRP* 1.3 75.3 - - - +
411a LYS* 1.3 57.2 + - - +
413a HIS* 3.5 6.1 + - - +
414a PHE* 3.0 25.6 + - - +
471a ILE* 4.1 14.5 - - + +
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Residues in contact with LYS 411 (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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334a TRP 3.0 26.2 + - - -
335a SER* 4.9 0.4 - - - +
336a PRO* 4.5 12.1 - - + -
339a MET* 3.9 22.5 - - + +
407a ASP* 2.9 32.4 + - - +
408a THR 3.5 7.0 - - - +
409a TRP 3.2 0.2 - - - -
410a ALA* 1.3 75.7 - - - +
412a ILE* 1.3 64.5 + - - +
414a PHE* 3.3 8.1 + - - +
415a ALA* 3.0 23.4 + - - +
606a TGL 3.9 30.9 + - + +
77d GLU* 3.2 32.6 + - - +
81d VAL* 3.8 15.6 - - + +
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Residues in contact with ILE 412 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408a THR* 3.0 26.0 + - + +
409a TRP* 2.9 34.1 + - + +
411a LYS* 1.3 73.5 - - - +
413a HIS* 1.3 63.9 + - - +
415a ALA* 3.1 13.5 + - - +
416a ILE* 3.1 32.1 + - + +
467a LEU* 3.9 10.3 - - + -
607a PGV 4.2 13.2 - - + -
80d THR 4.6 1.3 - - - +
81d VAL* 3.9 20.4 - - - +
84d ALA* 3.7 24.5 - - + -
85d ALA 4.0 15.3 - - - +
88d PHE* 4.2 8.7 - - + -
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Residues in contact with HIS 413 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340a TRP* 4.0 14.2 + + - -
390a MET* 3.6 33.8 - - + +
394a VAL* 5.9 2.2 - - - +
409a TRP 2.7 15.7 + - - +
410a ALA* 3.5 10.8 + - - +
412a ILE* 1.3 73.0 - - - +
414a PHE* 1.3 62.3 + - - +
416a ILE* 3.4 2.7 + - - +
417a MET* 3.1 34.1 + - + +
464a ALA* 3.1 36.9 + - + -
467a LEU* 4.4 10.0 - - + +
468a MET* 3.7 24.1 - - + +
471a ILE* 3.6 20.2 - - + +
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Residues in contact with PHE 414 (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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336a PRO* 5.5 1.6 - - + +
339a MET* 3.2 58.6 - - + -
340a TRP* 3.6 52.5 - + + +
343a GLY* 4.7 2.7 - - - -
387a PHE* 4.1 13.0 - + - -
410a ALA 3.0 16.4 + - - +
411a LYS* 3.6 9.0 - - - +
412a ILE 3.3 0.4 - - - -
413a HIS* 1.3 77.4 - - - +
415a ALA* 1.3 61.3 + - - +
417a MET* 3.2 1.6 + - - +
418a PHE* 2.9 51.4 + + + +
606a TGL 4.1 32.3 - - + -
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Residues in contact with ALA 415 (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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411a LYS 3.0 12.3 + - - +
412a ILE 3.1 8.7 + - - +
414a PHE* 1.3 81.9 - - - +
416a ILE* 1.3 62.2 + - - +
418a PHE* 3.6 5.3 + - - +
419a VAL* 3.3 28.2 + - - +
606a TGL 4.5 26.6 - - + +
81d VAL* 4.6 10.1 - - + -
82d VAL* 5.9 0.7 - - - -
85d ALA* 3.8 22.2 - - + -
89d ILE* 5.5 0.2 - - - -
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Residues in contact with ILE 416 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412a ILE* 3.1 18.5 + - + +
413a HIS* 3.9 4.7 - - - +
415a ALA* 1.3 73.2 - - - +
417a MET* 1.3 61.3 + - - +
419a VAL* 3.2 3.1 + - - -
420a GLY* 2.9 24.6 + - - -
460a ILE* 3.5 38.3 - - + +
463a THR* 4.6 6.3 - - + -
464a ALA* 3.9 14.4 - - + +
467a LEU* 3.5 32.5 - - + -
85d ALA* 4.1 20.2 - - - +
88d PHE* 3.7 21.8 - - + -
89d ILE* 4.4 11.9 - - + +
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Residues in contact with MET 417 (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 TRP* 3.7 28.3 - - + -
386a VAL* 5.2 7.4 - - - -
387a PHE* 4.3 10.8 - - + -
390a MET* 5.3 2.5 - - - +
413a HIS* 3.1 33.7 + - + +
414a PHE 3.6 3.1 - - - +
416a ILE* 1.3 72.6 - - - +
418a PHE* 1.3 66.8 + - - +
420a GLY* 3.2 1.4 + - - -
421a VAL* 3.0 42.1 + - + +
461a SER* 3.6 42.2 - - - +
464a ALA* 3.8 8.9 - - + +
465a VAL* 4.7 4.5 - - + -
468a MET* 6.1 0.4 - - - -
601a HEA 4.1 27.8 - - + -
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Residues in contact with PHE 418 (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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343a GLY* 4.9 3.4 - - - -
346a PHE* 5.7 4.0 - + - -
347a LEU* 3.9 31.4 - - + -
387a PHE* 4.3 7.6 - + - -
414a PHE* 2.9 42.2 + + + +
415a ALA* 3.7 7.4 - - - +
417a MET* 1.3 79.1 - - - +
419a VAL* 1.3 67.0 + - + +
421a VAL* 3.7 4.4 - - - +
422a ASN* 3.0 46.1 + - + +
606a TGL 4.4 42.8 - - + -
101i TGL 4.8 14.1 - - + -
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Residues in contact with VAL 419 (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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415a ALA 3.3 15.7 + - - +
416a ILE 3.2 7.6 + - - +
418a PHE* 1.3 78.4 - - + +
420a GLY* 1.3 65.5 + - - +
422a ASN* 4.1 2.5 - - - +
423a MET* 3.0 33.0 + - + +
460a ILE* 4.2 14.8 - - + -
606a TGL 4.5 36.6 - - + -
89d ILE* 4.1 26.7 - - + -
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Residues in contact with GLY 420 (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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416a ILE 2.9 11.9 + - - -
417a MET 3.2 2.0 + - - -
419a VAL* 1.3 77.0 - - - +
421a VAL* 1.3 52.1 + - - +
423a MET* 3.2 4.8 + - - +
424a THR* 2.6 38.4 + - - -
457a GLY 3.7 2.0 - - - +
460a ILE* 3.7 22.4 - - - +
461a SER* 3.2 19.1 - - - -
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Residues in contact with VAL 421 (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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382a SER* 3.8 23.3 - - - +
383a MET* 3.5 32.0 - - + +
387a PHE* 4.2 12.1 - - + -
417a MET* 3.0 43.5 + - + +
418a PHE 3.7 6.3 - - - +
420a GLY* 1.3 70.7 - - - -
422a ASN* 1.3 63.7 + - - +
424a THR* 3.4 6.2 + - - -
425a PHE* 2.9 37.0 + - + +
461a SER* 3.2 10.2 + - - +
601a HEA 4.2 10.8 - - + -
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Residues in contact with ASN 422 (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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347a LEU* 3.7 8.8 - - - +
379a TYR* 3.0 35.9 + - - +
383a MET* 4.2 3.1 - - - -
418a PHE* 3.0 51.0 + - + +
419a VAL* 4.2 2.2 - - - +
420a GLY 3.3 0.6 - - - -
421a VAL* 1.3 84.6 - - - +
423a MET* 1.3 61.8 + - - +
426a PHE* 2.9 35.9 + - - +
101i TGL 3.7 35.9 - - + +
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Residues in contact with MET 423 (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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419a VAL* 3.0 25.1 + - + +
420a GLY 3.5 3.4 - - - +
422a ASN* 1.3 77.2 - - - +
424a THR* 1.3 61.5 + - - +
427a PRO* 3.1 22.9 - - - +
453a ILE* 3.6 39.4 - - + +
454a SER* 3.9 5.4 - - - -
456a MET* 3.8 17.5 - - + -
457a GLY* 4.1 7.4 - - - -
460a ILE* 3.6 27.6 - - - -
101i TGL 5.5 6.0 - - - +
29k TRP* 4.1 17.3 - - + -
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Residues in contact with THR 424 (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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38a ARG* 4.1 5.8 - - - -
420a GLY 2.6 27.3 + - - -
421a VAL* 3.5 6.0 - - - -
423a MET* 1.3 74.2 - - - +
425a PHE* 1.3 76.2 + - + +
427a PRO* 3.9 1.0 - - - +
428a GLN* 3.5 6.8 + - - +
454a SER* 2.6 50.0 + - - +
457a GLY* 3.1 17.7 + - - -
458a SER* 3.4 2.5 + - - +
461a SER* 4.3 1.2 + - - -
601a HEA 3.8 29.0 - - + +
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Residues in contact with PHE 425 (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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374a VAL 4.8 0.2 - - - -
375a ALA* 4.1 5.7 - - - +
378a HIS* 3.1 39.0 - + + -
379a TYR* 3.8 9.0 - - + -
382a SER* 3.3 27.6 - - - -
383a MET* 3.8 16.8 - - + -
421a VAL* 2.9 28.4 + - - +
424a THR* 1.3 80.2 - - + +
426a PHE* 1.3 67.6 + - - +
427a PRO* 3.4 2.9 - - - -
428a GLN* 3.1 44.0 + - - +
429a HIS* 3.9 5.5 + - - -
601a HEA 3.3 54.3 - + + -
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Residues in contact with PHE 426 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379a TYR* 3.4 22.8 + + - +
422a ASN* 2.9 20.8 + - + +
425a PHE* 1.3 78.0 - - - +
427a PRO* 1.3 67.9 - - + +
429a HIS* 2.8 38.4 + + - +
430a PHE* 3.5 32.7 - + - -
101i TGL 4.0 112.8 - - + -
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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