Contacts of the helix formed by residues 462 - 472 (chain B) in PDB entry 5IJ7
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 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B ALA* 3.5 9.2 - - - -
459B GLY 5.5 2.0 - - - +
460B THR 5.3 2.5 - - - +
461B LYS* 1.3 73.7 - - - +
463B CYS* 1.3 56.2 + - - +
464B ARG* 4.2 19.4 + - - +
465B GLN* 2.7 38.7 + - - +
466B VAL* 2.8 35.3 + - - +
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Residues in contact with CYS 463 (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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451B PHE* 4.0 10.3 - - - +
452B CYS* 2.7 49.8 - - - -
455B ALA* 3.5 12.5 - - + +
462B THR* 1.3 72.9 - - - +
464B ARG* 1.4 63.3 + - + +
466B VAL* 3.6 2.9 + - - +
467B TYR* 3.1 27.8 + - - +
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Residues in contact with ARG 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B THR* 3.4 17.9 + - - +
463B CYS* 1.4 82.2 - - + +
465B GLN* 1.3 60.2 + - + +
467B TYR* 3.4 8.1 + - - +
468B GLU* 2.9 45.7 + - - +
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Residues in contact with GLN 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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430B VAL* 3.4 31.5 - - + +
432B TRP* 3.3 15.7 + - + +
460B THR 4.5 3.1 + - - +
461B LYS* 3.5 28.4 - - + +
462B THR* 2.7 44.0 + - - +
464B ARG* 1.3 76.0 - - + +
466B VAL* 1.4 56.7 + - - +
468B GLU* 3.6 12.6 + - - +
469B PHE* 3.1 22.0 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TRP* 3.9 21.1 - - + -
440B PHE* 3.5 21.0 - - + -
451B PHE* 3.6 31.4 - - + +
454B ILE* 3.8 15.9 - - + -
455B ALA* 3.9 22.0 - - - +
458B ILE* 4.4 7.9 - - + -
461B LYS* 4.2 8.1 - - + -
462B THR 2.8 23.3 + - - +
463B CYS 3.9 3.8 - - - +
465B GLN* 1.4 68.1 - - - +
467B TYR* 1.4 64.0 + - - +
469B PHE* 3.2 2.1 + - - +
470B ARG* 3.1 18.5 + - - +
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Residues in contact with TYR 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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451B PHE* 3.7 37.9 - + + -
463B CYS 3.1 18.6 + - - +
464B ARG* 3.5 9.6 - - - +
466B VAL* 1.4 74.7 - - - +
468B GLU* 1.3 66.8 + - + +
470B ARG* 3.4 13.0 - - + +
471B VAL* 3.4 37.2 - - + +
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Residues in contact with GLU 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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430B VAL 5.8 2.3 + - - -
464B ARG* 2.9 34.0 + - + +
465B GLN* 3.6 12.1 + - - +
467B TYR* 1.3 81.1 - - + +
469B PHE* 1.4 63.7 + - - +
471B VAL* 3.3 9.8 + - - +
472B LYS* 3.2 20.8 + - - +
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Residues in contact with PHE 469 (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 TRP* 3.4 70.2 - + + -
437B ALA* 4.4 6.1 - - + -
440B PHE* 3.7 32.7 - + + -
441B ARG* 3.9 26.2 - - - -
465B GLN 3.1 7.0 + - - +
466B VAL 3.2 7.2 + - - +
468B GLU* 1.4 73.8 - - - +
470B ARG* 1.4 62.2 + - - +
472B LYS* 3.4 47.5 + - + +
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Residues in contact with ARG 470 (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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440B PHE* 3.7 18.0 - - + -
444B ILE* 5.7 4.7 - - - -
448B TYR 6.0 0.4 - - - -
451B PHE* 3.6 39.8 - - + -
466B VAL 3.1 5.9 + - - +
467B TYR* 3.4 11.7 - - + +
468B GLU 3.2 0.2 - - - -
469B PHE* 1.4 76.7 - - - +
471B VAL* 1.4 62.2 + - + +
472B LYS 3.1 14.0 - - - +
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B TYR* 3.4 37.7 - - + +
468B GLU* 3.3 9.3 + - - +
470B ARG* 1.4 76.0 - - + +
472B LYS* 1.4 64.9 + - - +
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Residues in contact with LYS 472 (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 VAL 4.9 10.5 + - - -
432B TRP* 5.3 1.0 - - - -
468B GLU 3.2 12.1 + - - +
469B PHE* 3.6 45.0 - - + +
470B ARG 3.1 12.2 - - - +
471B VAL* 1.4 79.9 - - - +
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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