Contacts of the helix formed by residues 461 - 468 (chain B) in PDB entry 2JI8
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 GLU 461 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456A GLY 5.2 0.3 - - - +
53B PHE* 3.4 16.7 - - + -
54B ARG* 2.9 30.7 + - - +
55B HIS* 3.2 13.3 + - - +
58B HIS* 3.3 34.4 - - + -
432B MET* 3.4 20.6 - - + -
436B VAL* 5.6 0.4 - - + -
458B SER 3.0 17.2 + - - +
459B GLY 3.0 0.6 + - - -
460B MET* 1.3 74.1 - - + +
462B LEU* 1.3 64.5 + - - +
463B GLU 3.0 2.0 - - - -
464B THR* 2.6 42.8 + - - +
465B ILE* 3.0 15.9 + - + +
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Residues in contact with LEU 462 (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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432B MET* 3.9 25.0 - - - +
455B PHE* 3.5 30.5 - - + -
458B SER 4.4 0.6 + - - -
459B GLY 2.9 10.5 + - - +
460B MET 4.4 1.1 - - - +
461B GLU* 1.3 75.4 - - - +
463B GLU* 1.3 57.8 + - - +
465B ILE* 3.1 10.6 + - + +
466B CYS* 2.9 32.7 + - - -
474B VAL* 4.2 14.1 - - + -
508B MET* 4.1 24.2 - - + -
509B MET* 3.7 29.5 - - + +
512B PHE* 4.6 8.5 - - + -
540B LEU* 3.8 18.8 - - + -
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A LEU* 4.7 0.9 - - - -
501A THR* 2.6 45.0 + - - +
505A TYR* 5.2 0.2 - - - +
54B ARG* 3.0 32.3 + - - +
460B MET 3.3 13.0 + - - +
461B GLU 3.0 0.8 - - - -
462B LEU* 1.3 78.4 - - - +
464B THR* 1.3 58.4 + - - +
466B CYS* 3.8 1.5 - - - +
467B ARG* 2.9 55.8 + - - +
512B PHE* 3.5 43.0 - - + -
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Residues in contact with THR 464 (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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52B SER 3.3 23.3 - - - +
53B PHE* 3.8 18.2 - - + -
54B ARG* 3.7 8.3 - - - +
436B VAL* 4.4 11.9 - - + -
461B GLU* 2.6 33.9 + - - +
463B GLU* 1.3 77.9 + - - +
465B ILE* 1.3 61.7 + - - +
467B ARG* 3.3 17.0 + - - +
468B TYR* 3.2 45.1 + - + +
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Residues in contact with ILE 465 (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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432B MET* 3.8 32.5 - - + -
435B CYS* 4.1 19.3 - - + -
436B VAL* 3.8 18.8 - - + -
461B GLU 3.0 16.3 + - - +
462B LEU* 3.1 15.0 + - + +
464B THR* 1.3 77.3 - - - +
466B CYS* 1.3 59.1 + - - +
468B TYR 3.8 0.3 + - - -
469B ASN 3.3 2.4 + - - -
470B LEU* 3.1 34.5 + - + +
472B VAL* 3.8 32.3 - - + -
474B VAL* 4.6 1.8 - - + -
509B MET* 4.8 5.4 - - + -
538B PRO* 3.8 16.6 - - + +
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Residues in contact with CYS 466 (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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501A THR* 5.1 0.2 - - - +
462B LEU 2.9 19.2 + - - +
463B GLU 3.8 4.0 - - - +
465B ILE* 1.3 74.8 - - - +
467B ARG* 1.3 60.7 + - - +
468B TYR 3.2 0.2 - - - -
469B ASN* 2.9 24.1 + - - +
509B MET* 3.5 34.3 - - - -
512B PHE* 3.4 27.8 - - + +
513B GLY 4.8 1.1 - - - -
514B GLY* 3.5 24.5 - - - +
538B PRO* 3.9 11.3 - - + +
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Residues in contact with ARG 467 (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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495A ILE* 3.4 37.7 - - + +
496A SER 5.4 0.8 + - - -
499A ARG 3.4 27.4 + - - -
500A LEU* 3.9 16.7 - - - +
501A THR* 3.9 10.7 + - - +
52B SER* 3.2 30.3 + - - -
53B PHE 4.7 0.4 + - - -
54B ARG* 4.0 3.8 - - - +
463B GLU* 2.9 53.4 + - - +
464B THR* 3.3 15.2 + - - +
466B CYS* 1.3 72.3 - - - +
468B TYR* 1.3 92.8 + - + +
469B ASN* 3.3 1.6 + - - +
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Residues in contact with TYR 468 (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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495A ILE* 3.3 31.9 + - + +
496A SER 4.9 3.1 + - - -
497A CYS* 5.1 1.0 - - - -
50B PHE 3.5 11.1 + - - -
51B TYR* 3.8 35.0 - + + -
52B SER* 3.0 36.2 + - - -
464B THR* 3.2 32.7 + - + +
467B ARG* 1.3 104.1 + - + +
469B ASN* 1.3 70.7 + - - +
470B LEU* 3.3 30.8 + - + +
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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