Contacts of the helix formed by residues 496 - 501 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B SER 3.5 5.0 + - - +
495B VAL* 1.3 73.7 - - - +
497B PRO* 1.3 78.9 - - + +
498B HIS* 3.0 29.2 + - + +
499B HIS* 2.7 48.6 + + + +
500B SER 3.0 9.0 + - - -
517B HIS* 4.6 11.7 + + - -
632B TYR* 3.4 27.3 - - + +
1397F ALA* 3.7 11.6 - - + +
1398F GLN* 3.2 27.6 + - + +
1399F SER* 4.4 12.1 - - - -
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Residues in contact with PRO 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B VAL 3.7 1.1 - - - +
496B HIS* 1.3 100.2 - - + +
498B HIS* 1.3 61.7 + - - +
500B SER* 2.7 26.5 + - - +
501B MET* 4.2 3.1 + - - +
510B ARG 5.8 0.4 - - - +
513B ILE* 4.0 15.9 - - + -
514B ALA* 4.3 12.1 - - + +
517B HIS* 3.4 35.2 - - + +
632B TYR* 3.7 24.9 - - + -
655B TYR* 3.5 18.7 + - - +
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Residues in contact with HIS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B HIS* 2.9 24.1 + - + +
497B PRO* 1.3 79.0 - - - +
499B HIS* 1.3 68.2 + + - +
501B MET* 3.3 25.2 - - + +
502B LEU* 5.4 0.2 - - - +
632B TYR 4.1 4.0 - - - +
633B THR* 4.0 21.8 - - + +
655B TYR* 3.5 24.0 + - + -
656B PRO* 4.2 16.1 - - + +
841B TYR* 5.0 6.8 + + - -
1200B 12V 3.3 29.3 + - - +
1395F DNP 4.6 7.0 + - - -
1396F SER* 4.8 6.0 - - - -
1397F ALA* 4.2 18.6 - - + -
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Residues in contact with HIS 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B LYS* 5.0 3.8 - - - -
458B ASN* 6.0 2.5 - - - -
461B HIS* 3.2 56.3 - + + +
495B VAL* 4.6 1.8 - - + -
496B HIS* 2.7 26.5 + + + +
498B HIS* 1.3 89.0 - + - +
500B SER* 1.3 55.9 + - - +
501B MET 3.0 3.6 - - - -
502B LEU* 2.8 43.3 + - + +
503B TYR* 3.9 18.3 + - + +
841B TYR* 6.4 0.9 - + - -
1397F ALA* 3.4 29.5 + - + +
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Residues in contact with SER 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B VAL* 3.9 10.1 - - - +
496B HIS 3.0 10.0 + - - -
497B PRO* 2.7 25.0 + - - +
499B HIS* 1.3 76.7 - - - +
501B MET* 1.3 62.2 + - - +
502B LEU 3.1 0.9 + - - -
503B TYR* 3.3 10.6 + - - -
505B LEU* 3.4 16.0 - - - +
510B ARG* 3.0 42.0 + - - +
513B ILE* 4.2 13.5 - - - -
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Residues in contact with MET 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B PRO 4.2 2.2 + - - +
498B HIS* 3.3 34.8 - - + +
499B HIS 2.9 1.4 + - - -
500B SER* 1.3 83.0 + - - +
502B LEU* 1.3 79.3 + - + +
503B TYR 3.4 3.0 + - - +
510B ARG* 3.7 13.0 + - - +
655B TYR* 5.8 2.5 - - + +
656B PRO* 3.8 34.5 - - + +
841B TYR* 5.8 2.0 - - - -
916B LEU* 4.1 14.4 - - - +
917B CYS* 4.4 15.9 - - + -
940B THR* 4.5 24.0 + - + +
942B ALA* 4.1 20.4 - - + -
1200B 12V 5.0 6.1 - - + -
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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
------------------------------------------------------------
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