Contacts of the helix formed by residues 453 - 458 (chain J) in PDB entry 6C6S
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 VAL 453 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363J LEU* 4.7 4.7 - - + +
435J GLN* 3.3 28.5 - - - +
437J PHE* 3.7 14.1 - - + -
449J LEU* 4.8 2.5 - - + -
450J HIS* 3.1 35.6 + - + +
452J LEU* 1.3 75.1 - - + +
454J CYS* 1.3 58.5 + - - +
455J ALA 3.3 1.1 - - - -
456J ALA* 2.9 24.2 + - - +
457J TYR* 3.1 34.4 + - + -
486J SER* 3.9 14.6 - - - +
500J ILE* 5.2 9.4 - - + -
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Residues in contact with CYS 454 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812I PHE* 4.5 9.2 - - + -
813I GLU* 4.9 4.3 - - + +
449J LEU* 4.3 11.9 - - - -
450J HIS 4.0 4.9 - - - -
451J PRO* 2.9 26.4 + - - +
453J VAL* 1.3 74.7 - - - +
455J ALA* 1.3 59.8 + - - +
457J TYR* 3.9 5.6 - - - +
458J ASN* 3.0 23.7 + - - -
459J ALA* 3.2 26.1 + - - +
461J PHE* 3.5 37.2 - - + -
503J SER* 5.7 0.4 - - - +
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Residues in contact with ALA 455 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430J HIS* 5.7 0.9 - - - -
451J PRO 4.4 0.6 + - - -
452J LEU 3.9 5.1 + - - +
453J VAL 3.3 0.6 - - - -
454J CYS* 1.3 77.2 - - - +
456J ALA* 1.3 63.0 + - - +
458J ASN* 3.8 8.3 + - - +
499J ILE* 4.2 25.9 - - + +
501J VAL* 4.7 13.5 - - + +
503J SER* 3.9 19.7 + - - +
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Residues in contact with ALA 456 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430J HIS* 3.7 24.8 + - - -
432J LEU* 4.1 11.1 - - + +
433J GLY* 5.0 0.7 + - - -
435J GLN* 3.5 29.8 - - - +
453J VAL* 2.9 15.9 + - + +
455J ALA* 1.3 80.9 - - - +
457J TYR* 1.3 62.2 + - - +
458J ASN* 3.3 1.7 + - - +
499J ILE* 4.0 28.6 + - + +
500J ILE* 6.0 1.3 - - + -
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Residues in contact with TYR 457 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423J LEU* 3.4 10.6 - - - +
425J ARG* 3.3 26.0 + - + +
427J PRO 5.4 2.3 - - - +
432J LEU 3.7 10.5 - - - -
433J GLY* 3.2 37.9 - - - -
435J GLN* 3.4 18.6 + - + +
437J PHE* 3.2 21.4 - + - -
449J LEU* 4.0 20.4 - - + -
453J VAL* 3.1 42.0 + - + +
454J CYS* 3.6 1.1 + - - +
456J ALA* 1.3 75.3 - - - +
458J ASN* 1.3 66.6 - - - +
459J ALA* 3.9 17.0 - - + +
466J MET* 3.5 31.2 - - + -
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Residues in contact with ASN 458 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425J ARG* 2.4 30.5 + - - +
430J HIS* 6.3 1.8 - - + -
454J CYS 3.0 9.4 + - - -
455J ALA* 3.8 7.4 + - - +
456J ALA 3.2 5.1 - - - +
457J TYR* 1.3 79.1 - - - +
459J ALA* 1.3 54.0 + - - +
460J ASP* 4.0 2.7 + - - +
925J GLU* 5.8 2.0 + - - -
928J THR* 6.3 1.6 - - - +
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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