Contacts of the helix formed by residues 496 - 501 (chain C) in PDB entry 4AY6
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 HIS 496 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494C SER 3.4 5.2 + - - +
495C VAL* 1.3 76.8 - - - +
497C PRO* 1.3 80.1 - - + +
498C HIS* 3.0 25.1 + - - +
499C HIS* 2.8 47.7 + - + +
500C SER 3.0 8.8 + - - -
517C HIS* 4.6 12.7 + + - -
632C TYR* 3.4 27.8 - - + +
1397G ALA* 3.7 13.2 - - + +
1398G GLN* 3.4 27.5 + - - +
1399G SER* 4.5 11.7 - - - -
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Residues in contact with PRO 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C VAL 3.7 0.9 - - - +
496C HIS* 1.3 99.3 - - + +
498C HIS* 1.3 63.4 + - - +
500C SER* 2.7 28.6 + - - +
501C MET* 4.3 3.1 + - - +
510C ARG 6.0 0.2 - - - +
513C ILE* 4.0 9.2 - - + -
514C ALA* 4.3 17.9 - - + +
517C HIS* 3.4 34.1 - - + +
632C TYR* 3.7 25.4 - - + -
655C TYR* 3.5 18.3 + - - +
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Residues in contact with HIS 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C HIS* 3.0 23.3 + - + +
497C PRO* 1.3 79.3 - - - +
499C HIS* 1.3 67.7 + + - +
501C MET* 3.2 26.5 - - + +
632C TYR 4.1 4.5 - - - +
633C THR* 3.9 22.0 - - + +
655C TYR* 3.6 24.2 + - + -
656C PRO* 4.2 16.4 - - + +
841C TYR* 5.0 6.4 + + - -
1200C 12V 3.3 29.4 + - - +
1395G DNP 4.4 9.5 + - - -
1396G SER* 4.7 5.4 - - - -
1397G ALA* 4.1 18.4 - - + -
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Residues in contact with HIS 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LYS* 5.1 3.1 - - - -
458C ASN* 5.9 2.9 - - - -
461C HIS* 3.2 52.1 - + + +
495C VAL* 4.5 1.1 - - + -
496C HIS* 2.8 34.0 + + + +
498C HIS* 1.3 90.6 - + - +
500C SER* 1.3 59.6 + - - +
501C MET 3.0 2.9 - - - -
502C LEU* 2.8 38.3 + - + +
503C TYR* 4.0 22.9 + - + +
841C TYR* 6.5 0.7 - + - -
1397G ALA* 3.5 23.7 + - + +
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Residues in contact with SER 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C VAL* 3.9 9.2 - - - -
496C HIS 3.0 9.7 + - - -
497C PRO* 2.7 24.5 + - - +
499C HIS* 1.3 77.0 - - - +
501C MET* 1.3 62.4 + - - +
502C LEU 3.2 0.7 + - - -
503C TYR* 3.3 10.9 + - - +
505C LEU* 3.5 15.7 - - - +
510C ARG* 3.0 42.9 + - - +
513C ILE* 4.3 13.5 - - - -
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Residues in contact with MET 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C PRO 4.3 2.4 + - - +
498C HIS* 3.2 35.0 - - + +
499C HIS 2.9 1.4 + - - -
500C SER* 1.3 81.1 + - - +
502C LEU* 1.3 75.9 + - + +
503C TYR 3.4 4.1 + - - +
510C ARG* 3.7 13.0 + - - +
655C TYR* 6.0 2.2 - - + +
656C PRO* 3.9 33.4 - - + +
841C TYR* 5.7 2.7 - - - -
916C LEU* 4.2 14.4 - - - +
917C CYS* 4.2 22.4 - - + -
940C THR* 4.5 23.0 - - + +
942C ALA* 4.1 20.0 - - + -
1200C 12V 4.9 5.2 - - + -
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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