Contacts of the helix formed by residues 460 - 468 (chain C) in PDB entry 6AH0
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 ASP 460 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459C SER* 1.3 79.6 - - - +
461C LEU* 1.3 60.6 + - - +
462C GLY 3.3 3.0 - - - +
463C GLU* 3.2 5.1 + - - +
464C ALA* 2.9 26.3 + - - -
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Residues in contact with LEU 461 (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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460C ASP* 1.3 74.7 - - - +
462C GLY* 1.3 63.4 + - - +
464C ALA* 3.2 2.0 + - - +
465C MET* 2.9 22.2 + - - -
573C GLU 6.1 1.8 - - - -
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Residues in contact with GLY 462 (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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456C GLY 5.0 0.2 - - - -
457C VAL* 3.3 33.4 - - - +
458C ASP 4.8 0.2 - - - +
460C ASP 3.3 1.4 - - - +
461C LEU* 1.3 75.2 - - - +
463C GLU* 1.3 61.9 + - - +
465C MET* 3.4 1.8 + - - -
466C SER* 3.3 17.5 + - - -
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Residues in contact with GLU 463 (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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457C VAL* 4.7 1.8 - - - +
458C ASP 4.9 4.2 - - - +
459C SER 5.6 1.3 - - - -
460C ASP* 3.2 8.5 + - - +
462C GLY* 1.3 75.8 - - - +
464C ALA* 1.3 62.8 + - - +
466C SER* 3.2 10.7 + - - +
467C ASP* 3.4 9.9 + - - -
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Residues in contact with ALA 464 (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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460C ASP 2.9 14.6 + - - -
461C LEU* 3.2 3.6 + - - +
463C GLU* 1.3 76.3 - - - +
465C MET* 1.3 62.5 - - - +
467C ASP* 3.4 10.3 + - - +
468C CYS* 3.6 8.1 + - - -
469C ASP 4.8 2.8 + - - +
498C SER* 5.5 2.3 - - - -
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Residues in contact with MET 465 (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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445C ALA* 5.1 8.0 + - - -
461C LEU 2.9 15.6 + - - -
462C GLY* 3.9 2.2 - - - -
464C ALA* 1.3 77.4 - - - +
466C SER* 1.3 60.4 + - - +
468C CYS* 3.2 16.3 + - - +
474C LEU 6.1 0.9 - - - -
497C LEU 4.4 9.3 - - - +
498C SER* 5.6 5.2 - - - +
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Residues in contact with SER 466 (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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441C PRO 5.3 1.2 - - - +
442C LYS 3.9 17.7 - - - +
445C ALA* 5.0 14.4 + - - +
446C LYS* 5.0 5.8 - - - +
462C GLY 3.3 10.6 + - - -
463C GLU* 3.2 7.7 + - - +
464C ALA 3.2 0.8 - - - -
465C MET* 1.3 73.1 - - - +
467C ASP* 1.3 64.2 + - - +
468C CYS* 3.4 0.7 + - - -
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Residues in contact with ASP 467 (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 LYS* 5.5 5.9 - - - -
463C GLU 3.4 8.1 + - - -
464C ALA 3.4 6.7 + - - -
465C MET 3.3 0.8 - - - -
466C SER* 1.3 78.3 - - - +
468C CYS* 1.3 58.4 + - - +
469C ASP* 3.2 7.2 + - - +
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Residues in contact with CYS 468 (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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441C PRO 5.7 5.6 - - - -
442C LYS* 6.5 0.2 - - - +
464C ALA 3.6 5.9 + - - -
465C MET 3.2 16.3 + - - -
466C SER 4.4 0.7 - - - -
467C ASP* 1.3 75.2 - - - +
469C ASP* 1.3 64.0 + - - +
470C PRO 4.0 0.5 - - - -
497C LEU 4.0 17.6 - - - +
498C SER* 4.7 2.0 - - - +
499C GLY 4.5 2.1 + - - +
546C ALA* 4.6 13.0 + - - +
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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