Contacts of the helix formed by residues 492 - 509 (chain C) in PDB entry 6CP3
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 492 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488C LYS* 5.9 2.8 - - - +
491C LEU* 1.3 73.7 - - - +
493C LYS* 1.3 55.5 + - - +
494C GLU* 3.1 20.0 - - - -
495C LEU* 3.0 26.8 + - - +
496C LEU* 2.6 39.6 + - - +
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Residues in contact with LYS 493 (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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492C SER* 1.3 72.5 - - - +
494C GLU* 1.3 64.9 + - - +
496C LEU* 3.7 15.4 - - + +
497C ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492C SER* 3.3 18.9 - - - -
493C LYS* 1.3 82.6 + - - +
495C LEU* 1.3 58.8 + - + +
497C ALA* 3.8 5.2 - - - +
498C SER* 2.9 35.1 + - - +
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Residues in contact with LEU 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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481C LEU* 3.7 26.9 - - + +
484C GLU* 4.0 32.5 - - + +
485C ILE 5.4 0.4 - - - +
488C LYS* 4.8 11.2 - - + -
490C GLU 4.2 4.9 - - - +
491C LEU* 3.8 27.7 - - + +
492C SER* 3.0 36.5 + - - +
494C GLU* 1.3 78.0 - - + +
496C LEU* 1.3 58.5 + - - +
498C SER* 3.8 4.1 - - - +
499C LEU* 2.8 31.4 + - - +
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Residues in contact with LEU 496 (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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387C GLN* 5.0 13.2 - - + +
388C VAL* 5.3 2.7 - - + -
448C TYR* 3.9 27.9 + - + +
491C LEU* 3.7 31.0 - - + +
492C SER 2.6 23.9 + - - +
493C LYS* 3.7 16.8 - - + +
495C LEU* 1.3 73.4 - - - +
497C ALA* 1.3 56.7 + - - +
499C LEU* 3.7 6.8 - - + +
500C LYS* 2.9 30.0 + - - +
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Residues in contact with ALA 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C LYS 2.9 18.3 + - - +
494C GLU* 3.8 6.1 - - - +
495C LEU 3.3 0.2 - - - -
496C LEU* 1.3 77.7 - - - +
498C SER* 1.3 55.7 + - - +
500C LYS* 3.3 9.2 + - - +
501C SER* 2.8 34.3 + - - +
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Residues in contact with SER 498 (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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478C HIS* 5.7 3.3 - - - -
481C LEU* 4.6 14.9 - - - +
494C GLU* 2.9 19.9 + - - +
495C LEU* 3.8 7.7 - - - +
497C ALA* 1.3 73.4 - - - +
499C LEU* 1.3 60.2 + - - +
501C SER* 3.3 6.7 + - - -
502C ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 499 (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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444C VAL* 4.8 5.2 - - + -
445C PRO* 3.8 34.8 - - + -
448C TYR* 3.6 41.1 - - + -
470C PHE* 5.6 0.7 - - + -
474C LEU* 5.3 2.9 - - + -
481C LEU* 4.1 22.6 - - + +
485C ILE* 5.3 4.0 - - + -
491C LEU* 4.6 22.9 - - + -
495C LEU 2.8 18.4 + - - +
496C LEU* 3.7 6.1 - - + +
498C SER* 1.3 75.2 - - - +
500C LYS* 1.3 56.3 + - - +
502C ALA* 3.5 2.1 + - + -
503C THR* 2.5 43.3 + - - +
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Residues in contact with LYS 500 (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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448C TYR* 3.3 28.6 + - - +
452C ASN* 6.0 0.8 - - - +
454C HIS* 4.4 15.9 + - - +
496C LEU 2.9 14.5 + - - +
497C ALA* 3.6 9.0 - - - +
499C LEU* 1.3 76.4 - - - +
501C SER* 1.3 58.2 + - - +
503C THR* 3.7 1.2 - - - -
504C GLU* 2.9 61.0 + - - +
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Residues in contact with SER 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ALA* 2.8 24.6 + - - +
498C SER* 3.6 8.0 - - - -
499C LEU 3.2 0.2 - - - -
500C LYS* 1.3 77.6 - - - +
502C ALA* 1.3 56.5 + - - +
504C GLU* 3.4 10.2 + - - +
505C SER* 2.9 29.2 + - - -
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Residues in contact with ALA 502 (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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470C PHE* 4.6 2.4 - - + -
473C TYR* 3.6 23.2 - - + -
474C LEU* 4.8 6.3 - - + -
478C HIS* 3.6 35.2 - - + +
481C LEU* 5.1 3.1 - - + -
498C SER 2.9 17.1 + - - +
499C LEU* 4.0 6.3 - - + +
501C SER* 1.3 76.3 - - - +
503C THR* 1.3 56.6 + - - +
505C SER* 3.3 2.7 + - - -
506C PHE* 3.0 25.3 + - - +
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Residues in contact with THR 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C PRO 5.1 1.4 + - - -
448C TYR* 3.9 10.2 - - + -
449C ALA* 4.3 17.5 - - + -
454C HIS* 3.5 38.4 - - + +
470C PHE* 4.1 21.1 - - + -
499C LEU* 2.5 31.6 + - - +
500C LYS* 3.7 6.5 - - - -
502C ALA* 1.3 76.8 - - - +
504C GLU* 1.3 56.7 + - - +
506C PHE* 3.2 4.0 + - - +
507C VAL* 2.8 32.6 + - + +
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Residues in contact with GLU 504 (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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454C HIS* 3.9 18.1 + - + -
500C LYS* 2.9 58.0 + - - +
501C SER* 3.9 7.6 + - - +
503C THR* 1.3 74.7 - - - +
505C SER* 1.3 57.7 + - - +
507C VAL* 3.3 11.2 + - + +
508C ALA* 2.9 27.0 + - - +
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Residues in contact with SER 505 (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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473C TYR* 3.1 28.4 + - - -
501C SER 2.9 18.7 + - - -
502C ALA* 3.4 1.3 - - - -
503C THR 3.2 0.2 - - - -
504C GLU* 1.3 77.8 - - - +
506C PHE* 1.3 60.2 + - - +
508C ALA* 3.3 21.2 + - - +
509C THR* 3.3 10.9 + - - -
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Residues in contact with PHE 506 (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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466C PHE* 3.5 31.1 - + - -
469C SER* 3.3 32.8 - - - -
470C PHE* 3.4 45.5 - + + -
472C SER* 5.6 0.7 - - - -
473C TYR* 3.4 32.5 - + + -
502C ALA 3.0 16.2 + - - +
503C THR 4.0 0.4 - - - +
505C SER* 1.3 74.2 - - - +
507C VAL* 1.3 61.5 + - - +
508C ALA 3.2 0.2 - - - -
509C THR* 2.8 43.1 + - + +
510C PHE* 5.2 7.0 - - + -
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Residues in contact with VAL 507 (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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454C HIS* 3.3 45.8 - - + +
455C LEU* 5.6 2.9 - - + -
458C ILE* 5.8 2.7 - - + -
466C PHE* 5.6 6.5 - - + -
503C THR* 2.8 21.4 + - + +
504C GLU* 3.3 14.3 + - + +
506C PHE* 1.3 77.0 - - - +
508C ALA* 1.3 59.4 + - - +
509C THR 2.9 12.4 - - - +
510C PHE* 4.1 5.4 - - - +
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Residues in contact with ALA 508 (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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504C GLU 2.9 12.5 + - - +
505C SER* 3.3 13.9 - - - +
506C PHE 3.2 0.2 - - - -
507C VAL* 1.3 78.1 - - - +
509C THR* 1.3 59.7 + - - +
510C PHE 3.9 1.7 + - - -
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Residues in contact with THR 509 (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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466C PHE* 5.2 0.9 - - - -
473C TYR* 5.8 1.4 - - - -
505C SER 3.3 10.8 + - - -
506C PHE* 2.8 42.1 + - + +
507C VAL* 2.9 6.6 - - - +
508C ALA* 1.3 76.8 - - - +
510C PHE* 1.3 80.5 + - + +
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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