Contacts of the helix formed by residues 506 - 511 (chain A) in PDB entry 3BKK
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 PHE 506 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG 5.5 1.0 + - - -
190A GLY* 3.3 25.7 - - - +
191A ARG 4.5 4.9 - - - +
193A ILE* 3.9 9.9 - - + -
194A LEU* 3.7 33.2 - - + -
197A TYR* 3.5 40.2 - + + -
467A TRP* 3.9 17.9 - + - -
481A TYR* 3.4 42.4 - + + -
482A ASN* 3.5 2.5 - - - -
504A GLY 3.6 1.6 + - - +
505A ASP* 1.3 76.7 - - - +
507A ASP* 1.3 60.6 + - - +
508A PRO* 3.2 12.3 - - + -
509A GLY* 2.9 37.5 + - - -
514A ILE* 4.3 2.2 - - + -
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Residues in contact with ASP 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 3.2 28.2 + - - +
279A TRP* 5.7 1.2 - - - -
482A ASN* 2.8 22.0 + - - +
485A TRP* 4.1 5.5 - - - +
486A TRP* 2.7 27.8 + - - +
501A ARG* 2.8 37.4 + - - -
505A ASP* 4.5 2.3 - - - +
506A PHE* 1.3 72.5 + - - +
508A PRO* 1.3 66.3 - - + +
510A ALA* 2.8 20.7 + - - +
511A LYS* 4.1 2.3 + - - +
702A CL 3.8 18.6 - - + -
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Residues in contact with PRO 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A TRP* 3.8 33.9 - - + -
481A TYR 4.8 0.9 - - - +
482A ASN* 3.3 12.6 - - - +
485A TRP* 3.5 49.3 - - + -
506A PHE* 3.2 15.3 - - + -
507A ASP* 1.3 91.0 - - + +
509A GLY* 1.3 60.0 + - - +
510A ALA 3.1 1.4 + - - -
511A LYS* 3.1 9.3 + - + +
514A ILE* 3.0 29.2 - - + +
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Residues in contact with GLY 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 3.7 7.8 - - - -
189A ALA 4.4 1.0 - - - +
190A GLY* 4.0 7.2 - - - -
193A ILE* 3.7 19.9 - - - +
506A PHE* 2.9 34.4 + - - -
508A PRO* 1.3 80.3 - - - +
510A ALA* 1.3 55.2 + - - +
511A LYS 3.2 4.3 + - - -
514A ILE* 4.1 6.5 - - - -
515A PRO* 3.6 13.7 - - - +
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Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 3.4 10.4 - - - -
185A TRP* 3.0 35.4 + - + +
186A ARG* 3.8 22.4 - - + -
189A ALA* 4.5 0.9 - - - -
190A GLY* 3.8 16.8 - - - +
279A TRP* 2.7 28.0 + - + +
507A ASP 2.8 14.8 + - - +
509A GLY* 1.3 75.1 - - - +
511A LYS* 1.3 52.6 + - - +
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Residues in contact with LYS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A TYR* 3.9 1.6 - - - -
279A TRP* 3.7 38.8 - - + +
281A GLN* 2.6 29.0 + - - +
353A HIS* 4.8 4.4 - - - -
460A PHE* 4.1 14.4 - - + -
464A VAL* 5.7 3.6 - - + -
485A TRP* 5.3 8.5 - - + -
507A ASP 4.1 1.3 + - - +
508A PRO* 3.1 13.2 + - + +
509A GLY 3.2 0.2 - - - -
510A ALA* 1.3 79.7 - - - +
512A PHE* 1.3 69.2 + - - +
513A HIS* 3.7 23.3 + - + +
514A ILE* 2.8 24.3 + - + +
515A PRO* 3.0 7.8 - - - +
520A TYR* 3.8 11.9 - - + -
704A KAF 2.8 26.2 + - - -
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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