Contacts of the helix formed by residues 480 - 499 (chain G) in PDB entry 3SRF
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 ALA 480 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478G GLN* 4.0 2.6 - - - +
479G GLU* 1.3 77.9 - - - +
481G TRP* 1.3 54.6 + - - +
482G ALA* 4.6 3.4 - - + +
483G GLU* 3.1 27.6 + - + +
484G ASP* 2.8 34.7 + - - +
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Residues in contact with TRP 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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432G GLU* 4.1 19.5 - - - -
479G GLU 3.6 4.4 + - - -
480G ALA* 1.3 71.5 - - - +
482G ALA* 1.3 55.9 + - + +
484G ASP* 3.1 26.7 + - + +
485G VAL* 2.7 53.4 + - + +
488G ARG* 3.6 15.7 - - - -
513G GLY* 3.0 35.0 + - - -
514G TRP 3.5 14.6 - - - -
515G ARG* 3.3 25.2 - - + +
516G PRO* 3.5 42.2 - - + -
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Residues in contact with ALA 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C TRP* 6.2 5.2 - - + -
480G ALA* 3.3 3.0 - - + +
481G TRP* 1.3 82.3 - - + +
483G GLU* 1.3 67.0 + - + +
485G VAL* 4.1 5.7 - - - +
486G ASP* 3.3 32.5 + - - +
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Residues in contact with GLU 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478G GLN* 4.2 16.9 - - + +
480G ALA* 3.1 27.7 + - + +
482G ALA* 1.3 79.8 - - + +
484G ASP* 1.3 64.1 + - - +
486G ASP* 3.7 4.1 + - - +
487G LEU* 3.2 23.4 + - - +
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Residues in contact with ASP 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454G ARG* 2.8 40.1 + - - -
476G PRO 4.5 0.5 - - - +
477G VAL* 4.4 6.0 - - - +
478G GLN* 3.6 33.4 + - + +
480G ALA 2.8 16.2 + - - +
481G TRP* 3.1 22.0 + - + +
483G GLU* 1.3 74.5 - - - +
485G VAL* 1.3 65.0 + - - +
487G LEU* 3.2 13.0 + - - +
488G ARG* 3.3 28.6 + - - +
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Residues in contact with VAL 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C TRP* 5.9 2.7 - - + -
430G LEU* 3.6 11.3 - - + +
481G TRP* 2.7 61.4 + - + +
482G ALA* 4.1 5.4 - - - +
484G ASP* 1.3 73.3 - - - +
486G ASP* 1.3 67.6 + - - +
487G LEU 3.3 0.2 + - - -
488G ARG* 3.3 9.9 + - - +
489G VAL* 3.1 28.0 + - + +
512G THR* 3.6 34.5 - - + +
513G GLY 4.3 4.5 - - - +
525G ARG* 4.4 4.3 - - - +
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Residues in contact with ASP 486 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C TRP* 4.5 18.8 + - - -
515C ARG* 5.8 1.9 + - - -
482G ALA* 3.3 20.2 + - - +
483G GLU* 4.2 4.3 - - - +
485G VAL* 1.3 86.2 - - - +
487G LEU* 1.3 59.3 + - - +
489G VAL* 3.9 7.3 - - - +
490G ASN* 3.0 40.5 + - - +
525G ARG* 4.2 11.6 + - - -
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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
----------------------------------------------------------
454G ARG* 4.4 9.9 - - - +
473G CYS* 4.4 2.9 - - - -
475G ASP* 3.7 37.9 - - + +
476G PRO 4.7 2.5 - - - +
478G GLN* 4.0 28.9 - - + +
483G GLU 3.2 12.9 + - - +
484G ASP* 3.4 11.9 - - - +
485G VAL 3.2 0.6 - - - -
486G ASP* 1.3 78.0 - - - +
488G ARG* 1.3 70.2 + - + +
490G ASN* 3.6 4.8 + - - +
491G PHE* 3.0 27.8 + - + +
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Residues in contact with ARG 488 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G LEU* 3.7 50.4 - - + +
431G THR 4.9 0.8 - - - +
432G GLU* 4.7 18.0 + - - +
452G VAL* 3.6 33.9 + - + +
453G THR* 5.8 1.2 - - - +
454G ARG* 3.4 30.9 - - - +
473G CYS* 3.8 25.8 - - - -
481G TRP* 3.6 24.2 - - - -
484G ASP* 3.3 26.4 + - - +
485G VAL* 3.3 8.9 + - - +
487G LEU* 1.3 81.1 - - + +
489G VAL* 1.3 64.7 + - - +
491G PHE* 3.5 8.3 - - - +
492G ALA 3.2 14.7 + - - -
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Residues in contact with VAL 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ILE* 4.3 3.8 - - + +
430G LEU* 3.7 20.9 - - + -
485G VAL 3.1 21.9 + - - +
486G ASP* 4.1 8.3 - - - +
488G ARG* 1.3 75.0 - - - +
490G ASN* 1.3 63.9 + - - +
492G ALA* 3.1 9.6 + - - +
493G MET* 3.0 39.4 + - + +
510G VAL* 3.8 37.0 - - + -
512G THR* 3.9 10.3 - - + -
525G ARG* 4.0 9.9 - - - +
527G VAL* 5.7 2.2 - - + -
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Residues in contact with ASN 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486G ASP* 3.0 28.2 + - - +
487G LEU* 3.9 5.1 - - - +
489G VAL* 1.3 77.0 - - - +
491G PHE* 1.3 63.4 + - - +
493G MET* 3.1 11.1 + - - +
494G ASN* 2.9 33.5 + - - +
530G PRO* 4.0 24.0 - - - +
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Residues in contact with PHE 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G PRO* 3.9 25.8 - - + -
102G ILE* 4.0 25.6 - - + -
452G VAL* 3.9 19.3 - - + -
471G VAL* 4.0 22.4 - - + -
472G LEU 3.8 15.5 - - - -
473G CYS* 3.8 30.3 - - + -
474G LYS 5.2 1.3 - - - -
475G ASP* 4.5 17.3 - - - +
487G LEU 3.0 18.6 + - - +
488G ARG* 3.5 7.0 - - - +
490G ASN* 1.3 76.3 - - - +
492G ALA* 1.3 60.0 + - - +
494G ASN* 3.4 9.5 + - - +
495G VAL* 3.3 28.7 + - + +
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Residues in contact with ALA 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ILE* 3.8 22.7 - - + -
450G ILE* 4.0 15.4 - - + +
452G VAL* 3.5 28.9 - - + -
471G VAL* 5.2 0.2 - - - -
488G ARG 3.2 3.5 + - - +
489G VAL 3.1 10.2 + - - +
491G PHE* 1.3 77.3 - - - +
493G MET* 1.3 63.6 + - - +
495G VAL* 3.4 8.5 + - - +
496G GLY 3.1 18.4 + - - -
502G PHE* 3.7 7.4 - - - -
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Residues in contact with MET 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428G ILE* 3.4 22.0 - - + -
489G VAL* 3.0 26.7 + - + +
490G ASN* 3.1 24.2 + - - +
492G ALA* 1.3 76.7 - - - +
494G ASN* 1.3 62.1 + - - +
497G LYS* 3.3 21.5 - - - +
502G PHE* 3.3 45.4 - - + -
508G VAL* 3.5 22.4 - - + -
527G VAL* 4.9 7.2 - - - -
529G VAL* 3.8 5.6 - - + -
530G PRO* 3.5 31.4 - - + -
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Residues in contact with ASN 494 (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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102G ILE* 4.1 23.0 - - + +
490G ASN* 2.9 26.6 + - - +
491G PHE* 3.7 10.5 - - - +
492G ALA 3.2 0.2 - - - -
493G MET* 1.3 77.3 - - - +
495G VAL* 1.3 65.7 + - - +
497G LYS* 3.2 19.6 + - - +
498G ALA* 3.0 24.9 + - - +
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Residues in contact with VAL 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G PRO 4.9 0.2 - - - +
102G ILE* 3.4 30.9 - - + +
450G ILE* 4.7 8.7 - - + -
469G PHE* 6.4 0.9 - - + -
471G VAL* 3.5 33.7 - - + -
491G PHE* 3.3 25.2 + - + +
492G ALA* 3.7 10.3 - - - +
494G ASN* 1.3 77.8 - - - +
496G GLY* 1.3 57.5 + - - +
498G ALA* 3.9 0.5 - - - +
499G ARG* 3.1 56.7 + - - +
501G PHE* 5.3 2.2 - - + -
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Residues in contact with GLY 496 (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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450G ILE* 4.4 1.8 - - - +
492G ALA 3.1 10.5 + - - -
494G ASN 3.2 0.2 - - - -
495G VAL* 1.3 75.4 - - - +
497G LYS* 1.3 63.0 + - - +
500G GLY 3.1 3.5 + - - -
501G PHE* 2.9 41.8 + - - -
502G PHE* 3.3 32.9 + - - -
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Residues in contact with LYS 497 (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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493G MET* 3.3 24.2 + - - +
494G ASN* 3.2 19.6 + - - +
496G GLY* 1.3 74.8 - - - +
498G ALA* 1.3 62.0 + - - +
500G GLY* 3.5 10.7 + - - -
502G PHE* 3.3 23.6 - - + +
503G LYS* 4.5 7.4 - - - -
504G LYS* 5.0 4.9 - - - +
529G VAL* 3.7 13.5 - - - -
530G PRO* 2.8 32.0 + - - +
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Residues in contact with ALA 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G ILE* 3.8 22.2 - - + -
103G LEU* 3.8 19.9 - - + +
494G ASN 3.0 15.3 + - - +
495G VAL 3.9 1.6 - - - +
497G LYS* 1.3 78.2 - - - +
499G ARG* 1.3 60.6 + - - +
500G GLY* 3.6 0.5 + - - -
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Residues in contact with ARG 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G THR* 3.8 15.1 + - - -
101G PRO 5.3 0.2 + - - -
102G ILE 3.7 13.9 + - - -
103G LEU* 3.7 23.4 + - + +
104G TYR 3.0 28.3 + - - -
105G ARG* 3.1 36.7 - - - +
469G PHE* 3.9 17.6 - - - +
471G VAL* 3.6 19.8 - - - +
495G VAL* 3.1 30.7 + - + +
498G ALA* 1.3 74.8 - - - +
500G GLY* 1.3 59.6 - - - +
501G PHE* 3.5 33.9 + - + -
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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
------------------------------------------------------------
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