Contacts of the helix formed by residues 467 - 475 (chain B) in PDB entry 5I94
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 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B MET* 2.8 15.6 + - + +
466B ASP* 1.3 78.5 - - - +
468B SER* 1.3 54.1 + - - +
469B GLY 3.3 3.3 + - - -
470B GLN* 3.3 33.3 + - + +
471B PHE* 2.8 55.4 + + + +
474B HIS* 6.1 0.7 - + - -
505B ASP* 6.0 2.0 - - - -
507B MET* 3.8 31.4 - - + +
509B ASN* 3.4 14.6 - - - +
514B ILE* 4.2 22.2 - - + -
518B HIS* 4.0 29.4 - + - -
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Residues in contact with SER 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PRO* 5.8 0.2 - - - -
460B HIS 4.2 4.5 - - - +
461B SER* 3.0 28.4 - - - -
462B CYS* 3.2 10.7 - - - -
463B GLY 4.2 0.4 - - - -
464B MET* 2.9 28.2 + - - +
465B TYR 2.8 20.2 + - - -
466B ASP 3.4 1.4 - - - -
467B PHE* 1.3 77.9 - - - +
469B GLY* 1.3 57.0 + - - +
471B PHE* 3.9 2.0 - - - +
472B ALA* 2.9 31.4 + - - +
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Residues in contact with GLY 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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310A LYS 4.5 3.8 - - - +
311A GLU* 3.7 36.1 + - - +
312A PRO* 5.4 5.2 - - - -
461B SER 5.6 0.4 - - - -
466B ASP 5.1 1.0 + - - -
467B PHE 3.3 0.6 - - - -
468B SER* 1.3 75.3 - - - +
470B GLN* 1.3 64.5 + - - +
472B ALA* 3.9 3.9 - - - +
473B PHE* 3.2 22.5 + - - +
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Residues in contact with GLN 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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310A LYS* 3.6 34.8 - - - +
311A GLU* 3.9 18.8 + - - +
466B ASP 5.6 1.1 - - - +
467B PHE* 3.3 39.9 + - + +
469B GLY* 1.3 74.3 - - - +
471B PHE* 1.3 64.6 + - - +
473B PHE* 3.2 6.3 + - - +
474B HIS* 3.0 38.9 + - + +
507B MET* 6.0 1.6 - - + -
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Residues in contact with PHE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B MET 6.1 0.7 - - - -
460B HIS 5.8 2.0 - - - -
464B MET* 3.7 35.2 - - + -
467B PHE* 2.8 33.7 + + + +
468B SER 3.9 3.4 - - - +
470B GLN* 1.3 71.5 - - - +
472B ALA* 1.3 58.6 + - - +
474B HIS* 5.3 0.9 - - - -
475B VAL* 2.8 63.2 + - + +
476B GLY 3.0 5.7 + - - -
477B LEU* 3.3 27.1 - - + -
479B ALA* 3.6 21.8 - - + -
489B LEU* 4.3 1.6 - - + -
514B ILE* 3.9 22.4 - - + -
517B CYS* 4.0 26.7 - - + -
518B HIS* 4.9 0.7 - + - -
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Residues in contact with ALA 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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457A SER* 4.6 3.1 + - - -
460B HIS* 3.6 38.4 + - + +
461B SER* 5.4 1.1 - - - -
468B SER 2.9 19.6 + - - +
469B GLY* 3.9 5.6 - - - +
470B GLN 3.2 0.2 - - - -
471B PHE* 1.3 76.5 - - - +
473B PHE* 1.3 67.6 + - - +
476B GLY* 3.0 26.0 + - - +
477B LEU 5.3 1.1 - - - +
527B HIS* 3.6 4.0 + - - -
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Residues in contact with PHE 473 (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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292A TYR* 3.6 10.1 - - - -
301A THR* 4.3 7.2 - - + -
305A HIS* 3.7 7.4 - - - -
310A LYS* 3.7 33.2 - - + +
453A ARG* 5.4 1.9 + - - -
454A ASN* 3.5 42.7 - - - +
457A SER* 4.1 14.8 + - - -
458A LEU* 3.6 37.7 - - + -
469B GLY 3.2 11.2 + - - +
470B GLN* 3.2 9.9 + - - +
472B ALA* 1.3 78.0 - - - +
474B HIS* 1.3 85.4 + + + +
527B HIS* 2.9 24.8 + - - -
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Residues in contact with HIS 474 (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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301A THR* 5.1 7.2 - - + -
310A LYS* 3.1 34.9 + - - -
453A ARG* 5.8 0.3 + - - -
467B PHE* 6.1 0.7 - + - -
470B GLN* 3.0 38.9 + - + +
473B PHE* 1.3 97.5 - + + +
475B VAL* 1.3 61.3 + - - +
518B HIS* 3.7 29.7 - + + +
521B VAL* 4.4 8.1 - - - +
527B HIS* 3.8 7.4 - - - -
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B PHE* 2.8 53.8 + - + +
474B HIS* 1.3 77.2 - - - +
476B GLY* 1.3 63.1 + - - +
477B LEU* 3.9 15.0 - - + +
517B CYS* 4.1 13.9 - - + +
518B HIS* 3.8 37.5 - - + +
521B VAL* 3.6 30.6 - - + +
527B HIS* 3.0 18.4 - - - -
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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