Contacts of the helix formed by residues 469 - 488 (chain G) in PDB entry 6CM9
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 GLN 469 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426G LEU 3.7 16.6 - - - +
427G THR 4.0 13.2 + - - +
428G THR 5.5 1.0 + - - -
429G ALA 4.9 2.8 + - - -
430G GLY* 3.7 32.1 - - - -
431G SER* 4.3 6.9 - - - +
466G ASP* 3.1 27.2 + - + +
467G TYR 3.2 6.6 - - - +
468G SER* 1.3 82.8 - - - +
470G GLN* 1.3 67.1 + - - +
471G PRO* 3.6 2.2 - - - -
472G LEU* 3.3 29.4 + - + +
473G VAL* 3.5 4.7 + - - +
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Residues in contact with GLN 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G GLY 4.8 0.6 + - - -
431G SER* 5.6 1.4 - - - +
435G ASP* 4.8 7.4 - - - +
467G TYR 4.2 3.6 + - - -
468G SER* 4.0 20.4 + - - +
469G GLN* 1.3 70.8 - - - +
471G PRO* 1.4 67.4 - - + +
472G LEU 3.2 0.3 + - - -
473G VAL* 3.3 10.0 + - - +
474G GLN* 2.9 30.1 + - + +
517G MET* 2.9 35.6 + - - +
518G SER* 3.5 15.5 + - - -
519G THR* 3.5 23.5 + - + +
522G THR* 3.3 25.7 + - + +
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Residues in contact with PRO 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426G LEU* 4.9 7.9 - - + -
430G GLY 3.7 15.0 - - - +
431G SER* 5.5 1.3 - - - -
433G VAL* 3.7 37.0 - - + +
434G ARG 4.5 3.6 - - - +
435G ASP* 3.3 19.5 - - - +
438G VAL* 3.7 15.3 - - + -
470G GLN* 1.4 92.1 - - + +
472G LEU* 1.3 55.7 + - - +
474G GLN* 3.3 11.9 - - + +
475G VAL* 3.0 34.8 + - - +
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Residues in contact with LEU 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G MET* 3.6 30.3 - - + -
426G LEU* 4.2 29.0 - - + +
427G THR* 5.0 5.2 - - + -
430G GLY* 5.7 0.8 + - - -
459G LEU* 4.4 3.8 - - + -
462G ALA* 4.1 11.9 - - + +
463G ILE* 3.8 15.9 - - + -
466G ASP* 3.6 27.1 - - - +
467G TYR* 6.2 0.4 - - - -
469G GLN* 3.3 32.2 + - + +
470G GLN 3.1 0.8 - - - -
471G PRO* 1.3 78.7 - - - +
473G VAL* 1.3 59.6 + - + +
475G VAL* 3.3 4.9 + - - +
476G ALA* 2.9 27.2 + - - +
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Residues in contact with VAL 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463G ILE* 4.3 17.3 - - + -
466G ASP 4.5 0.7 - - - +
467G TYR* 3.7 39.5 - - + +
469G GLN 3.5 4.5 + - - +
470G GLN* 3.3 18.8 + - - +
472G LEU* 1.3 74.9 - - + +
474G GLN* 1.3 60.6 + - - +
476G ALA* 4.0 6.3 - - - -
477G ALA* 2.9 33.9 + - + +
512G VAL* 4.8 20.4 - - + -
518G SER* 5.8 1.1 - - - +
522G THR* 3.8 25.4 - - + +
525G TYR* 5.2 0.3 - - - +
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Residues in contact with GLN 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G ASP* 5.0 13.4 + - - +
438G VAL* 3.8 22.3 - - + +
442G ILE* 4.0 4.2 - - - +
470G GLN* 2.9 24.0 + - + +
471G PRO* 3.3 17.3 - - + +
473G VAL* 1.3 77.9 - - - +
475G VAL* 1.3 61.9 + - - +
478G TRP 3.9 6.6 + - - -
521G VAL* 3.2 21.5 - - - +
522G THR* 3.1 36.9 + - + -
525G TYR* 3.2 50.4 + - - -
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Residues in contact with VAL 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G MET* 6.0 0.4 - - - -
426G LEU* 4.0 24.2 - - + -
438G VAL* 4.1 15.7 - - + -
441G LEU* 4.2 21.5 - - + -
442G ILE* 4.3 13.6 - - + +
445G ILE* 5.4 7.0 - - + -
459G LEU* 4.3 13.0 - - + -
471G PRO 3.0 17.3 + - - +
472G LEU 3.8 3.6 - - - +
474G GLN* 1.3 76.6 - - - +
476G ALA* 1.3 58.2 + - - +
478G TRP* 3.4 4.5 + - - +
479G CYS* 3.0 48.2 + - - -
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Residues in contact with ALA 476 (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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459G LEU* 3.7 23.7 - - + +
463G ILE* 3.7 37.7 - - + -
472G LEU 2.9 17.6 + - - +
473G VAL* 3.3 4.7 + - - +
475G VAL* 1.3 78.4 - - - +
477G ALA* 1.3 58.3 + - - +
479G CYS* 3.2 2.1 + - - +
480G ILE* 2.9 35.6 + - + +
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Residues in contact with ALA 477 (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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463G ILE* 6.1 0.4 - - - -
473G VAL* 2.9 18.6 + - + +
476G ALA* 1.3 76.6 - - - +
478G TRP* 1.3 57.2 + - - +
480G ILE* 3.4 5.5 + - - +
481G GLY 2.9 22.5 + - - -
509G LEU* 4.7 13.0 - - + -
512G VAL* 6.2 1.6 - - + -
522G THR 4.9 1.8 - - - +
525G TYR* 3.9 31.4 - - + +
526G ALA* 4.2 9.6 - - + +
529G ALA* 3.3 16.8 - - + +
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Residues in contact with TRP 478 (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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517B PRO* 3.9 19.3 + - + +
521B ASP* 3.3 31.7 + - - -
442G ILE* 3.6 46.2 - - + -
445G ILE* 3.7 28.7 - - + -
446G THR* 3.9 24.9 - - + -
474G GLN 3.9 5.5 + - - +
475G VAL 3.4 3.0 + - - +
476G ALA 3.3 0.4 - - - -
477G ALA* 1.3 79.0 - - - +
479G CYS* 1.3 60.1 + - - +
481G GLY* 3.3 2.1 + - - +
482G GLU* 3.0 54.2 + - + +
483G TYR* 4.0 13.7 - + - -
525G TYR* 4.8 13.5 - + + +
528G THR* 5.8 0.9 - - + -
529G ALA* 5.4 0.2 - - - -
532G LYS* 5.2 2.5 - - - -
584G MET* 5.1 12.3 - - + +
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Residues in contact with CYS 479 (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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442G ILE* 5.6 0.2 - - - -
445G ILE* 3.7 28.5 - - - -
455G THR* 4.5 6.7 - - - -
456G VAL* 3.9 17.1 - - + +
459G LEU* 4.3 19.3 - - + -
475G VAL* 3.0 40.5 + - - +
476G ALA* 3.2 7.1 + - - +
478G TRP* 1.3 79.6 - - - +
480G ILE* 1.3 59.9 + - + +
483G TYR* 2.9 38.4 + - + +
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Residues in contact with ILE 480 (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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456G VAL* 3.8 17.7 - - + +
459G LEU* 5.8 2.2 - - + -
460G TYR* 4.7 16.6 - - + +
463G ILE* 5.3 8.7 - - + -
476G ALA* 2.9 23.0 + - + +
477G ALA* 3.7 6.5 - - - +
479G CYS* 1.3 74.4 - - + +
481G GLY* 1.3 59.4 + - - +
484G GLY* 2.9 30.3 + - - +
487G LEU* 3.8 26.5 - - + -
505G VAL* 4.4 13.7 - - + -
508G ILE* 6.6 0.2 - - + -
509G LEU* 4.4 15.0 - - + -
529G ALA* 5.0 0.9 - - + -
533G LEU* 3.8 29.7 - - + +
537G PHE* 5.9 0.2 - - + -
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Residues in contact with GLY 481 (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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477G ALA 2.9 16.9 + - - -
478G TRP* 3.3 2.4 + - - -
480G ILE* 1.3 77.8 - - - +
482G GLU* 1.3 58.0 + - - +
529G ALA* 3.9 20.0 - - - -
532G LYS* 3.3 36.7 - - - +
533G LEU* 5.0 1.8 - - - -
536G ARG* 3.5 15.4 + - - +
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Residues in contact with GLU 482 (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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478G TRP* 3.0 48.3 + - + +
481G GLY* 1.3 78.6 - - - +
483G TYR* 1.3 65.7 + - + +
484G GLY 3.8 0.7 - - - -
532G LYS* 2.5 34.5 + - - +
536G ARG* 3.1 28.2 + - - +
582G GLU 4.2 0.2 - - - +
583G ARG* 2.4 56.3 + - - +
584G MET* 3.7 21.2 + - - +
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Residues in contact with TYR 483 (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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445G ILE* 4.5 8.7 - - + -
446G THR* 3.4 23.4 + - - -
448G SER 4.5 0.3 + - - -
452G HIS* 3.4 52.2 + + + -
456G VAL* 3.8 22.7 - - + +
478G TRP* 4.0 23.8 - + - -
479G CYS* 2.9 21.9 + - + +
480G ILE 3.7 1.3 - - - -
482G GLU* 1.3 85.6 - - + +
484G GLY* 1.3 64.9 + - - +
485G ASP* 3.2 12.2 + - - +
486G LEU* 3.4 17.3 + - + +
487G LEU 3.8 5.5 + - - -
583G ARG* 3.2 34.3 - - - -
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Residues in contact with GLY 484 (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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480G ILE* 2.9 22.2 + - - -
482G GLU 3.8 1.2 - - - -
483G TYR* 1.3 74.6 - - - +
485G ASP* 1.3 62.0 + - - +
486G LEU 3.2 1.4 + - - -
487G LEU* 3.6 17.0 + - - +
488G VAL 3.7 5.9 + - - +
533G LEU* 4.5 11.4 - - - -
536G ARG* 4.4 8.2 - - - +
537G PHE* 3.2 26.3 - - - -
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Residues in contact with ASP 485 (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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483G TYR* 3.6 11.0 - - - +
484G GLY* 1.3 73.9 - - - +
486G LEU* 1.3 79.8 + - - +
488G VAL 3.4 14.9 - - - +
489G SER* 4.1 5.9 + - - -
536G ARG* 4.3 26.9 - - + +
583G ARG* 2.6 32.8 + - - -
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Residues in contact with LEU 486 (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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452G HIS* 4.2 28.7 - - + +
453G ALA* 4.3 31.4 - - + +
456G VAL* 5.6 0.9 - - + -
457G GLN* 4.4 3.8 + - - -
483G TYR* 3.4 12.0 + - + +
484G GLY 3.2 0.2 - - - -
485G ASP* 1.3 97.5 + - - +
487G LEU* 1.3 65.8 + - - +
488G VAL 3.6 0.2 - - - -
489G SER* 3.8 13.5 + - - +
583G ARG* 5.7 2.0 - - - +
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Residues in contact with LEU 487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456G VAL* 3.8 26.4 - - + +
457G GLN* 3.4 35.4 + - - +
460G TYR* 4.1 18.8 - - + -
480G ILE* 3.8 20.9 - - + -
483G TYR 3.8 3.6 + - - -
484G GLY* 3.6 11.8 + - - +
486G LEU* 1.3 79.7 - - - +
488G VAL* 1.3 61.5 + - + +
489G SER* 4.1 1.7 + - - -
500G VAL* 3.3 33.0 - - + +
505G VAL* 3.7 38.6 - - + -
537G PHE* 5.0 2.7 - - + -
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Residues in contact with VAL 488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484G GLY 3.7 4.8 + - - +
485G ASP* 3.4 16.0 - - - +
487G LEU* 1.3 84.5 - - + +
489G SER* 1.3 62.3 + - - +
490G GLY 4.0 1.4 + - - -
491G GLN* 3.5 33.9 - - + +
500G VAL* 3.8 24.2 - - + -
502G GLU* 3.7 35.4 - - + +
505G VAL* 4.5 3.4 - - + -
537G PHE* 4.1 24.4 - - + -
539G CYS* 5.3 2.9 - - - -
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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