Contacts of the helix formed by residues 678 - 685 (chain B) in PDB entry 5B2S
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 THR 678 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668B ASN* 2.6 49.0 + - - +
669B GLY 3.8 2.7 - - - +
670B ILE 3.4 19.5 - - - +
671B ARG* 3.5 32.8 - - + +
677B LYS* 1.3 76.5 - - - +
679B ILE* 1.3 65.8 + - - +
680B LEU 3.8 0.3 + - - -
681B ASP* 2.9 24.7 + - - +
682B PHE* 3.1 20.4 + - - -
704B PHE* 3.9 2.9 - - - -
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Residues in contact with ILE 679 (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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518B PHE* 4.4 2.5 - - + -
666B LEU* 3.3 33.2 + - + +
667B ILE* 3.4 16.7 + - - +
670B ILE 4.2 1.2 + - - -
678B THR* 1.3 74.6 - - - +
680B LEU* 1.3 65.5 + - - +
682B PHE* 3.2 5.7 + - - +
683B LEU* 3.0 32.7 + - + +
693B PHE* 3.9 19.7 - - + -
696B LEU* 3.8 18.3 - - + +
697B ILE* 3.8 29.2 - - + -
704B PHE* 3.8 31.1 - - + -
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Residues in contact with LEU 680 (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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514B LEU* 4.9 13.9 - - + +
517B TYR* 4.1 23.6 - - + +
518B PHE* 4.1 25.6 - - + +
521B TYR* 4.2 18.6 - - + -
667B ILE* 2.7 24.6 + - + +
668B ASN* 3.7 28.7 - - + +
678B THR 3.3 0.4 - - - -
679B ILE* 1.3 72.9 - - - +
681B ASP* 1.3 63.7 + - - +
683B LEU* 3.3 8.8 + - + -
684B LYS* 2.9 44.0 + - - +
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Residues in contact with ASP 681 (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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668B ASN* 4.3 4.6 - - - +
671B ARG* 3.8 11.8 + - - -
677B LYS* 3.5 24.9 - - + +
678B THR* 2.9 39.4 + - - +
680B LEU* 1.3 77.8 - - - +
682B PHE* 1.3 57.9 + - - +
684B LYS* 3.2 16.1 + - - +
685B SER* 3.0 28.2 + - - +
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Residues in contact with PHE 682 (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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525B THR* 4.9 0.9 + - - -
545B LYS* 4.5 1.0 + - - -
672B ASP* 3.9 4.7 - - + -
675B SER* 3.4 28.0 - - - -
677B LYS* 3.5 30.7 - - + -
678B THR 3.1 20.6 + - - -
679B ILE 3.2 1.3 + - - +
681B ASP* 1.3 78.6 - - - +
683B LEU* 1.3 65.1 + - - +
685B SER 3.2 19.8 + - - -
686B ASP* 3.3 29.1 + - + +
691B ARG* 3.5 23.6 - - - +
696B LEU* 3.6 25.1 - - + -
702B LEU* 4.1 17.7 - - + -
704B PHE* 3.7 28.7 - + - -
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Residues in contact with LEU 683 (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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518B PHE* 3.5 48.9 - - + +
521B TYR* 3.8 21.6 - - + +
522B ASN* 3.5 26.7 - - - +
525B THR* 3.7 12.0 + - + -
545B LYS* 2.9 21.0 + - - -
679B ILE* 3.0 21.9 + - + +
680B LEU* 3.3 14.8 + - + +
682B PHE* 1.3 76.1 - - - +
684B LYS* 1.3 57.6 + - - +
691B ARG 3.6 21.5 - - - +
692B ASN* 3.7 10.3 - - - -
693B PHE* 4.0 0.7 - - - +
696B LEU* 4.0 5.4 - - + -
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Residues in contact with LYS 684 (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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517B TYR* 5.7 4.4 - - - -
521B TYR* 3.8 46.3 - - + +
542B GLY* 3.3 11.6 - - - +
545B LYS* 3.1 20.5 + - - +
680B LEU* 2.9 42.6 + - + +
681B ASP* 3.2 14.8 + - - +
683B LEU* 1.3 78.4 - - - +
685B SER* 1.3 62.3 + - - +
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Residues in contact with SER 685 (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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542B GLY* 4.0 19.1 + - - +
543B GLU* 5.8 0.3 + - - -
545B LYS* 4.1 3.6 - - - +
677B LYS* 2.5 34.0 + - - -
681B ASP 3.0 10.2 + - - +
682B PHE 3.2 5.8 + - - +
684B LYS* 1.3 82.1 - - - +
686B ASP* 1.3 52.3 + - - +
687B GLY 3.8 5.4 + - - -
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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