Contacts of the helix formed by residues 435 - 457 (chain G) in PDB entry 5X8X
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 435 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343G GLU 4.8 1.0 - - - +
344G LEU* 3.9 9.7 - - + +
345G CYS* 3.3 32.8 + - - +
348G ASP* 3.1 14.3 + - - +
433G LEU* 5.1 0.4 - - - -
434G GLN* 1.3 81.2 - - + +
436G LYS* 1.3 63.1 + - - +
437G ARG 3.3 3.6 + - - -
438G LYS* 3.3 44.1 + - + +
439G VAL* 3.4 16.2 + - - +
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Residues in contact with LYS 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ALA* 4.4 14.2 - - - +
430G ARG 5.9 0.4 - - - +
433G LEU* 3.9 35.8 - - + +
434G GLN 3.3 12.6 + - - -
435G GLU* 1.3 72.8 - - - +
437G ARG* 1.3 59.5 + - + +
439G VAL* 3.2 9.2 + - - +
440G GLU* 2.9 35.9 + - + +
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Residues in contact with ARG 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G GLU 3.3 1.0 - - - -
436G LYS* 1.3 79.0 - - + +
438G LYS* 1.3 66.2 + - - +
440G GLU* 3.1 38.8 + - - +
441G GLN* 3.0 37.2 + - + +
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Residues in contact with LYS 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G GLY 5.8 0.2 - - - +
343G GLU* 4.8 17.5 + - + +
344G LEU* 3.9 25.8 - - + -
435G GLU* 3.3 41.1 + - + +
437G ARG* 1.3 75.4 - - - +
439G VAL* 1.3 61.6 + - - +
441G GLN* 3.2 20.7 + - + +
442G LEU* 3.2 28.0 + - + +
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Residues in contact with VAL 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G LEU* 3.9 30.5 - - + -
348G ASP* 4.7 3.1 - - - +
352G LEU* 4.4 11.2 - - + -
426G ILE* 3.9 12.1 - - + +
427G ASN 3.9 7.9 - - - +
428G ALA* 3.6 29.8 - - + +
433G LEU* 4.2 17.9 - - + -
435G GLU 3.4 12.1 + - - +
436G LYS 3.2 8.9 + - - +
437G ARG 3.2 1.0 - - - -
438G LYS* 1.3 72.1 - - - +
440G GLU* 1.3 55.7 + - - +
442G LEU* 3.3 7.4 + - - +
443G GLN* 2.8 33.3 + - - +
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Residues in contact with GLU 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ALA* 3.8 19.4 - - + +
436G LYS* 2.9 20.3 + - + +
437G ARG* 3.2 47.4 + - - +
439G VAL* 1.3 72.9 - - - +
441G GLN* 1.3 64.0 + - - +
443G GLN* 3.9 3.8 - - - +
444G TYR* 2.8 35.4 + - + +
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Residues in contact with GLN 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437G ARG* 3.0 37.0 + - - +
438G LYS* 3.2 15.0 + - + +
440G GLU* 1.3 79.8 + - - +
442G LEU* 1.3 69.0 + - + +
444G TYR* 3.9 5.2 - - - +
445G ASN* 3.2 33.9 + - - +
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Residues in contact with LEU 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G SER* 6.2 0.2 - - - -
340G GLY* 3.6 43.5 - - - +
341G PHE* 4.3 1.8 - - - +
344G LEU* 4.2 21.3 - - + -
426G ILE* 4.0 18.8 - - + -
438G LYS* 3.2 24.5 + - + +
439G VAL* 3.8 6.3 - - - +
441G GLN* 1.3 77.9 - - + +
443G GLN* 1.3 67.6 + - - +
445G ASN* 3.4 11.1 + - - +
446G LEU* 3.1 27.3 + - + +
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Residues in contact with GLN 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G LEU* 4.2 7.0 - - + +
426G ILE* 3.5 28.2 - - + +
427G ASN* 4.4 3.6 - - - +
428G ALA* 3.0 35.1 + - - +
429G HIS* 4.4 16.3 - - - -
439G VAL 2.8 20.8 + - - +
440G GLU* 3.9 3.7 - - - +
442G LEU* 1.3 73.8 - - - +
444G TYR* 1.3 51.3 + - - +
446G LEU* 3.1 8.5 + - - +
447G GLU* 2.8 59.5 + - + +
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Residues in contact with TYR 444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440G GLU 2.8 21.5 + - - +
441G GLN* 3.9 5.8 - - - +
443G GLN* 1.3 74.8 - - - +
445G ASN* 1.3 68.2 + - - +
447G GLU* 3.1 14.7 + - + +
448G LEU* 2.9 69.1 + - + +
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Residues in contact with ASN 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 5.2 1.9 - - - +
273G LEU* 3.7 18.5 - - + +
441G GLN* 3.2 21.8 + - - +
442G LEU* 3.7 10.3 - - - +
444G TYR* 1.3 87.4 - - - +
446G LEU* 1.3 57.0 + - - +
448G LEU* 3.4 9.4 + - - +
449G ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273G LEU* 4.1 17.5 - - + -
277G VAL* 3.9 28.5 - - + -
338G LEU* 5.6 2.9 - - + -
419G LEU* 4.8 8.9 - - + +
422G ALA* 4.0 24.5 - - + +
423G LEU* 3.7 15.3 - - + -
426G ILE* 3.8 37.9 - - + -
442G LEU* 3.1 16.7 + - + +
443G GLN* 3.1 8.0 + - - +
445G ASN* 1.3 72.7 - - - +
447G GLU* 1.3 60.9 + - - +
449G ALA* 3.4 1.8 + - - +
450G PHE* 2.9 32.2 + - - +
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Residues in contact with GLU 447 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G LEU* 3.8 22.5 - - + +
443G GLN* 2.8 48.3 + - + +
444G TYR* 3.1 16.1 + - + +
446G LEU* 1.3 73.2 - - - +
448G LEU* 1.3 58.7 + - + +
450G PHE* 4.2 1.3 - - - +
451G HIS* 2.9 32.1 + - - +
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Residues in contact with LEU 448 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.9 24.9 - - + +
444G TYR* 2.9 56.8 + - + +
445G ASN* 3.5 13.0 - - - +
447G GLU* 1.3 77.0 - - + +
449G ALA* 1.3 64.8 + - - +
451G HIS* 3.7 10.7 - - - +
452G HIS* 3.0 23.9 + - - +
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Residues in contact with ALA 449 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.9 25.5 - - + +
273G LEU* 4.4 13.7 - - + -
274G VAL* 3.7 26.6 - - + +
419G LEU* 5.0 5.6 - - + -
445G ASN 3.0 13.3 + - - +
446G LEU* 4.0 3.6 - - - +
448G LEU* 1.3 78.3 - - - +
450G PHE* 1.3 62.7 + - - +
452G HIS* 3.4 3.3 + - - +
453G HIS* 3.1 23.0 + - - +
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Residues in contact with PHE 450 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G PHE* 5.8 0.2 - + - -
416G GLU* 3.8 30.7 - - + -
419G LEU* 3.4 39.2 - - + +
420G TYR* 4.0 15.7 - + + -
423G LEU* 3.7 24.5 - - + -
446G LEU 2.9 17.8 + - - +
447G GLU* 4.2 2.2 - - - +
449G ALA* 1.3 76.7 - - - +
451G HIS* 1.3 59.1 + - - +
453G HIS* 3.2 8.2 + + + -
454G LEU* 2.8 56.7 + - + +
462G ILE* 5.0 0.4 - - + -
463G LEU* 3.8 36.6 - - + -
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Residues in contact with HIS 451 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G GLU 2.9 20.7 + - - +
448G LEU* 3.7 11.3 - - + +
450G PHE* 1.3 75.6 - - - +
452G HIS* 1.3 61.7 + - - +
454G LEU* 3.3 10.3 + - + +
455G CYS* 3.0 42.2 + - - -
460G GLN* 5.1 8.1 - - + +
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Residues in contact with HIS 452 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267G LEU* 5.2 23.1 - - + +
270G ILE* 4.3 24.9 - - + -
271G GLU* 5.4 7.3 + - + -
274G VAL* 6.0 2.7 - - + -
448G LEU 3.0 13.3 + - - +
449G ALA 3.6 9.2 - - - +
451G HIS* 1.3 75.0 + - - +
453G HIS* 1.3 63.7 + - + +
455G CYS* 3.3 7.6 + - - +
456G LYS* 3.1 51.6 + - + +
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Residues in contact with HIS 453 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274G VAL* 4.6 18.2 - - + +
413G SER* 5.0 1.2 + - - -
415G ASP* 3.9 33.8 - - + +
416G GLU* 4.6 18.8 + - + +
419G LEU* 4.3 14.1 - - + -
449G ALA 3.1 13.9 + - - +
450G PHE* 3.6 15.3 - + + +
452G HIS* 1.3 76.5 - - + +
454G LEU* 1.3 67.1 + - + +
456G LYS* 3.4 17.4 - - + +
457G THR* 3.1 45.0 + - + +
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Residues in contact with LEU 454 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416G GLU* 4.4 5.4 - - + +
450G PHE* 2.8 48.1 + - + +
451G HIS* 3.3 10.5 + - + +
453G HIS* 1.3 79.6 - - + +
455G CYS* 1.3 61.1 - - - +
457G THR* 3.3 4.1 + - - +
458G HIS* 3.1 3.5 + - - -
459G ARG* 3.0 53.2 + - + +
460G GLN* 3.8 23.2 + - + +
462G ILE* 3.8 18.4 - - + -
463G LEU* 4.1 27.8 - - + -
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Residues in contact with CYS 455 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G HIS* 3.0 44.8 + - - +
452G HIS* 3.6 8.3 - - - +
453G HIS 3.3 0.2 - - - -
454G LEU* 1.3 74.2 - - - +
456G LYS* 1.3 65.8 + - - +
458G HIS* 3.0 22.3 + - - -
460G GLN* 3.7 27.1 + - - +
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Residues in contact with LYS 456 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G GLU* 5.1 10.5 + - - +
452G HIS* 3.1 39.6 + - + +
453G HIS* 3.4 27.1 - - - +
455G CYS* 1.3 76.0 - - - +
457G THR* 1.3 64.3 + - + +
458G HIS* 3.3 19.0 + - - -
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Residues in contact with THR 457 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416G GLU* 4.2 5.3 + - - +
453G HIS* 3.1 40.1 + - + +
454G LEU* 3.3 6.2 + - - -
455G CYS 3.2 0.6 - - - -
456G LYS* 1.3 83.8 - - + +
458G HIS* 1.3 69.9 + - - +
459G ARG* 3.3 29.1 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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