Contacts of the helix formed by residues 479 - 495 (chain C) in PDB entry 6GYS
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 SER 479 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428C LEU* 5.2 6.4 - - - +
432C ILE* 5.7 0.2 - - - +
473C TYR* 4.4 7.2 - - - -
474C GLN* 2.5 25.3 + - - +
477C VAL* 2.9 14.8 + - - +
478C GLU* 1.3 72.5 - - - +
480C ALA* 1.3 54.5 + - - +
481C ALA* 3.6 13.0 + - - +
482C VAL* 3.1 24.5 + - - +
483C LYS* 2.6 17.4 + - - -
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Residues in contact with ALA 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLU 3.7 3.4 + - - +
479C SER* 1.3 71.5 + - - +
481C ALA* 1.3 60.3 + - - +
483C LYS* 3.6 12.4 - - + +
484C GLN* 2.8 27.2 + - - +
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Residues in contact with ALA 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 4.4 23.2 - - + +
479C SER* 3.2 9.4 + - - +
480C ALA* 1.3 76.6 - - - +
482C VAL* 1.3 59.1 + - - +
484C GLN* 3.1 8.6 + - - +
485C LEU* 2.9 27.2 + - - +
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Residues in contact with VAL 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C LEU* 3.9 17.9 - - + -
432C ILE* 3.9 17.0 - - + -
470C ILE* 3.7 21.5 - - + +
473C TYR* 3.7 28.9 - - + -
474C GLN* 3.6 23.8 - - + +
479C SER* 3.1 24.7 + - - +
481C ALA* 1.3 76.2 - - - +
483C LYS* 1.3 57.1 + - - +
485C LEU* 3.3 8.3 + - - +
486C LEU* 2.8 26.3 + - - +
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Residues in contact with LYS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C GLN* 3.0 27.7 + - + +
478C GLU* 5.4 7.9 + - + -
479C SER 2.6 19.9 + - - +
480C ALA* 3.8 12.6 - - + +
482C VAL* 1.3 71.4 - - - +
484C GLN* 1.3 58.6 + - - +
486C LEU* 3.2 13.8 + - + +
487C VAL* 2.9 38.1 + - + +
518C LYS* 4.9 12.0 - - - +
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Residues in contact with GLN 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ALA 2.8 19.4 + - - +
481C ALA* 3.1 8.5 + - - +
483C LYS* 1.3 74.3 - - - +
485C LEU* 1.3 59.9 + - - +
487C VAL* 3.2 18.0 + - - +
488C ASP* 2.9 62.8 + - - +
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Residues in contact with LEU 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C ILE* 4.2 25.1 - - + +
435C SER* 3.7 28.7 - - - +
436C LYS* 5.0 4.7 - - + +
439C ILE* 3.7 30.1 - - + -
470C ILE* 3.7 32.8 - - + -
481C ALA 2.9 12.6 + - - +
482C VAL* 3.5 9.6 - - - +
484C GLN* 1.3 74.7 - - - +
486C LEU* 1.3 59.1 + - - +
488C ASP* 3.3 8.3 + - - +
489C LEU* 2.9 45.3 + - + +
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C VAL* 5.3 7.4 - - + -
470C ILE* 4.0 10.7 - - + +
471C SER* 4.2 26.7 - - - +
474C GLN* 3.7 25.6 - - + -
482C VAL 2.8 14.3 + - - +
483C LYS* 3.2 16.8 - - + +
484C GLN 3.2 0.2 - - - -
485C LEU* 1.3 76.6 - - - +
487C VAL* 1.3 56.5 + - + +
489C LEU* 3.4 3.6 + - - +
490C THR* 2.3 47.1 + - - +
511C THR* 5.6 5.8 - - + -
515C SER* 6.1 5.6 - - - -
518C LYS* 4.3 17.9 - - + -
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Residues in contact with VAL 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C LYS* 2.9 27.9 + - + +
484C GLN* 3.5 24.7 - - - +
486C LEU* 1.3 78.0 - - + +
488C ASP* 1.3 58.8 + - - +
490C THR* 3.2 9.4 + - - -
491C GLU* 2.9 28.4 + - + +
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Residues in contact with ASP 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ILE* 4.0 21.7 - - + +
484C GLN* 2.9 48.1 + - - +
485C LEU* 3.6 11.5 - - - +
487C VAL* 1.3 77.7 - - - +
489C LEU* 1.3 57.0 + - - +
491C GLU* 3.3 14.9 + - - +
492C LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C SER* 5.5 0.7 - - - -
439C ILE* 3.7 23.6 - - + -
463C ILE* 4.2 20.4 - - + -
466C VAL* 4.8 15.3 - - + -
467C VAL* 3.8 34.5 - - + +
470C ILE* 5.6 2.9 - - + -
485C LEU* 2.9 40.5 + - + +
486C LEU* 4.0 4.3 - - - +
488C ASP* 1.3 74.3 - - - +
490C THR* 1.3 59.9 + - - +
492C LEU* 3.5 33.9 - - + +
493C THR* 2.8 30.6 + - - -
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Residues in contact with THR 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C VAL* 5.5 0.2 - - - +
486C LEU* 2.3 39.8 + - - +
487C VAL* 3.2 11.1 + - - -
489C LEU* 1.3 74.0 - - - +
491C GLU* 1.3 64.2 + - - +
493C THR* 3.3 21.4 - - - +
494C ALA* 4.0 2.9 + - - +
511C THR* 5.0 12.3 - - + +
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Residues in contact with GLU 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C VAL* 2.9 12.6 + - + +
488C ASP* 3.5 14.6 - - - +
490C THR* 1.3 77.5 - - - +
492C LEU* 1.3 56.0 + - - +
494C ALA* 3.0 23.4 + - - +
495C ASN* 3.1 30.1 + - - +
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Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ILE* 3.7 38.8 - - + -
442C ILE* 3.7 40.6 - - + -
463C ILE* 3.8 16.2 - - + -
488C ASP 2.9 16.0 + - - +
489C LEU* 3.1 26.6 + - + +
491C GLU* 1.3 72.3 - - - +
493C THR* 1.3 65.8 + - - +
495C ASN* 3.2 23.7 + - + +
496C LEU* 3.3 25.1 - - + +
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Residues in contact with THR 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C VAL* 5.4 1.9 - - - +
489C LEU 2.8 17.3 + - - -
490C THR* 3.3 17.0 + - - -
492C LEU* 1.3 77.7 - - - +
494C ALA* 1.3 60.3 + - + +
495C ASN 3.3 0.7 + - - -
496C LEU* 3.3 25.7 - - + +
504C LEU* 4.3 6.2 - - + +
507C LEU* 5.6 6.8 - - + +
508C VAL* 3.8 35.0 - - + +
511C THR* 4.4 19.5 + - + +
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Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490C THR 4.0 2.7 + - - +
491C GLU* 3.0 10.9 + - + +
493C THR* 1.3 76.5 - - + +
495C ASN* 1.3 58.5 + - - +
496C LEU 3.2 14.2 + - - +
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Residues in contact with ASN 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C ILE* 5.5 0.2 - - + -
446C PHE* 3.4 43.5 - - + -
454C ASN* 4.8 2.4 + - - -
491C GLU* 3.1 41.3 + - - +
492C LEU* 3.4 23.1 - - + +
493C THR 3.2 2.0 - - - -
494C ALA* 1.3 80.3 - - - +
496C LEU* 1.3 65.1 + - + +
497C PRO* 4.5 2.3 - - - +
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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
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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