Contacts of the helix formed by residues 463 - 471 (chain B) in PDB entry 5Y9F
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 463 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B HIS* 3.2 58.1 - + + +
455B ARG 5.4 2.7 - - - -
457B SER* 3.6 31.0 - - - -
459B ASP 3.4 22.2 - - - -
460B LEU 3.2 4.9 + - - +
461B ASP 3.3 0.6 - - - -
462B GLN* 1.3 92.2 - - + +
464B PRO* 1.3 76.5 - - + +
466B GLY 3.1 1.0 + - - -
467B ARG* 2.9 29.6 + - - +
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Residues in contact with PRO 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER* 3.7 36.6 - - - +
239A ALA* 4.4 12.6 - - + -
240A ASP 5.9 0.4 - - - +
317A GLN* 4.9 4.5 - - - +
36B HIS* 5.2 0.2 - - - +
106B GLU* 5.7 0.4 - - - +
374B GLN* 3.4 18.6 - - - +
462B GLN 4.8 0.7 - - - +
463B PHE* 1.3 88.3 - - + +
465B LEU* 1.3 64.2 + - - +
467B ARG* 3.0 25.7 + - - +
468B LYS* 2.9 45.0 + - - +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 4.1 7.0 - - + -
104B GLY 4.3 3.1 - - - +
105B VAL 4.5 1.1 - - - -
106B GLU* 3.6 32.1 - - + +
310B PRO* 3.9 10.5 - - + -
312B TRP* 3.5 25.8 - - + -
374B GLN* 3.5 28.4 + - + +
375B PHE* 3.4 43.1 - - - +
376B ILE* 3.7 12.3 - - + +
463B PHE* 3.5 0.6 - - - +
464B PRO* 1.3 80.4 - - - +
466B GLY* 1.3 57.5 + - - +
468B LYS* 4.3 4.4 - - - +
469B PHE* 2.9 27.7 + - - +
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Residues in contact with GLY 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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36B HIS* 4.0 7.6 - - - -
376B ILE* 4.1 12.6 - - - -
460B LEU* 3.1 32.6 - - - +
463B PHE 3.1 4.8 + - - -
464B PRO 3.1 1.2 - - - -
465B LEU* 1.3 79.5 - - - +
467B ARG* 1.3 56.2 + - - +
469B PHE* 3.3 4.4 + - - +
470B LEU* 2.9 31.2 + - - +
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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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238A SER 3.7 16.6 + - - -
240A ASP 4.8 8.9 + - - -
241A ALA 5.2 1.4 + - - -
316A ALA 5.8 0.7 - - - -
317A GLN* 2.9 31.0 + - - +
318A GLY* 3.9 11.5 - - - -
319A LEU* 3.3 28.0 - - - +
461B ASP* 3.3 32.5 + - + +
462B GLN 3.6 5.1 + - - -
463B PHE* 2.9 29.3 + - - +
464B PRO* 3.4 25.1 - - - +
466B GLY* 1.3 73.4 - - - +
468B LYS* 1.3 58.6 + - + +
470B LEU* 2.7 31.8 + - + +
471B LEU* 3.0 18.1 + - + +
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Residues in contact with LYS 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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238A SER* 6.0 1.2 + - - -
317A GLN* 6.2 3.8 - - - -
106B GLU* 2.8 36.4 + - - +
308B ASN 5.7 0.2 + - - -
310B PRO* 3.7 27.1 - - + +
312B TRP* 3.5 21.0 - - + -
464B PRO* 2.9 37.1 + - - +
465B LEU* 3.9 4.5 - - - +
467B ARG* 1.3 75.8 - - + +
469B PHE* 1.3 59.1 + - - +
471B LEU* 3.3 25.5 + - - +
472B GLN* 4.0 2.9 + - - +
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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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34B PHE* 3.7 50.7 - + - -
103B VAL* 3.8 20.0 - - + -
312B TRP* 3.4 29.8 - + + -
376B ILE* 4.0 15.3 - - + -
460B LEU* 3.6 25.4 - - + -
465B LEU 2.9 18.7 + - - +
466B GLY* 3.5 3.4 - - - +
467B ARG 3.1 0.2 - - - -
468B LYS* 1.3 72.1 - - - +
470B LEU* 1.3 67.8 + - + +
471B LEU 3.1 2.0 - - - -
472B GLN* 3.1 34.3 - - + +
473B LEU 4.6 0.3 + - - -
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Residues in contact with LEU 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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460B LEU* 4.2 21.1 - - + -
461B ASP* 3.7 35.0 - - + +
466B GLY 2.9 18.4 + - - +
467B ARG* 2.7 19.9 + - + +
469B PHE* 1.3 71.4 - - + +
471B LEU* 1.3 59.9 + - + +
472B GLN 3.0 10.7 + - - -
473B LEU* 3.9 12.4 + - - +
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Residues in contact with LEU 471 (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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315A LYS* 4.3 30.7 - - + +
467B ARG* 3.0 16.7 + - + +
468B LYS* 3.6 13.5 - - - +
469B PHE 3.1 1.2 - - - -
470B LEU* 1.3 78.6 - - + +
472B GLN* 1.3 77.8 + - - +
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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