Contacts of the helix formed by residues 487 - 494 (chain A) in PDB entry 5YDJ
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 GLY 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A GLU* 1.3 79.2 - - - +
488A TYR* 1.3 64.7 + - - +
490A PHE* 2.8 21.0 + - - +
491A ILE* 3.1 17.3 + - - +
552A ASP* 3.2 22.9 + - - -
555A VAL* 3.9 12.6 - - - -
556A GLY* 3.7 10.7 - - - -
560A PHE* 5.8 0.2 - - - -
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Residues in contact with TYR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A GLU* 3.6 20.0 - - + +
486A GLU 3.5 1.0 - - - -
487A GLY* 1.3 70.6 - - - +
489A TYR* 1.3 52.8 + - - +
491A ILE* 3.2 5.7 + - + +
492A ILE* 2.8 44.9 + - + +
499A LEU* 4.2 11.7 - - + -
548A ARG* 2.7 43.7 + - + +
549A ASP* 3.4 21.7 + - - +
552A ASP* 2.8 41.3 + - + +
595A TRP* 3.5 38.6 - + - -
596A THR* 3.1 21.3 - - - +
599A MET* 4.1 16.4 - - + -
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Residues in contact with TYR 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASP* 4.4 3.6 + - - -
245A TRP* 3.9 29.0 - + - +
282A TYR* 5.5 3.6 - - - -
360A SEB 4.0 29.3 - + - -
486A GLU 4.1 4.6 + - - +
487A GLY 3.0 1.0 + - - -
488A TYR* 1.3 78.1 - - - +
490A PHE* 1.3 87.5 + + + +
492A ILE* 3.5 3.9 + - - +
493A TYR* 3.3 58.4 + + - -
592A TRP* 3.9 28.0 - + - -
599A MET* 3.6 31.8 - - + +
600A HIS* 4.6 16.6 - + + -
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Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A TYR* 5.6 2.7 - - - -
360A SEB 3.9 15.9 - + + -
446A ILE* 3.7 8.2 - - + +
447A CYS* 3.5 29.4 - - - +
449A PHE* 4.4 21.3 - + - -
486A GLU 3.6 18.2 - - - -
487A GLY* 2.8 9.1 + - - +
489A TYR* 1.3 93.3 - + + +
491A ILE* 1.3 56.8 + - - +
492A ILE 3.3 2.5 - - - -
493A TYR* 3.8 3.9 + - - +
494A TYR* 3.0 30.7 + - - +
555A VAL* 4.7 0.4 - - + -
560A PHE* 3.3 41.3 - + - -
600A HIS* 3.5 27.8 - + + -
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Residues in contact with ILE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ILE* 3.6 19.7 - - + -
487A GLY 3.1 14.9 + - - +
488A TYR* 3.5 7.9 - - + +
490A PHE* 1.3 73.5 - - - +
492A ILE* 1.3 54.3 + - - +
494A TYR 2.4 23.9 - - - +
495A LEU* 3.2 36.0 - - + +
499A LEU* 3.6 25.9 - - + +
519A LEU* 4.5 7.2 - - + -
551A LEU* 3.1 41.7 - - + +
552A ASP* 3.7 11.2 - - - +
555A VAL* 3.6 12.1 - - + -
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A PHE* 3.4 36.0 - - + -
488A TYR 2.8 23.3 + - - +
489A TYR* 3.5 5.6 - - - +
490A PHE 3.3 0.2 - - - -
491A ILE* 1.3 77.3 - - - +
493A TYR* 1.3 69.5 + - + +
494A TYR 3.2 4.6 - - - +
495A LEU 3.7 6.6 - - - +
496A THR* 3.8 8.8 + - - -
499A LEU* 4.1 16.0 - - + +
501A LYS* 5.0 8.5 - - + -
592A TRP* 4.0 24.7 - - + -
593A PRO* 5.7 0.9 - - + -
595A TRP* 4.2 18.2 - - + -
596A THR* 4.0 26.2 - - + -
599A MET* 4.1 8.1 - - - -
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Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 2.4 33.3 + - - -
235A VAL* 3.2 32.4 - - + +
236A PHE* 3.6 17.9 - + - -
242A ALA* 3.3 21.8 - - - +
489A TYR* 3.3 46.3 + + - +
490A PHE* 4.3 3.6 - - - +
492A ILE* 1.3 82.9 - - + +
494A TYR* 1.3 59.4 + - - +
496A THR* 3.6 13.1 + - - -
592A TRP* 3.9 12.5 - + - -
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Residues in contact with TYR 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU 3.5 11.6 + - - -
445A GLY* 3.5 32.5 - - - -
446A ILE* 3.8 32.8 - - + -
490A PHE 3.0 20.3 + - - +
491A ILE 2.4 30.0 - - - +
492A ILE 3.2 1.9 - - - +
493A TYR* 1.3 75.7 - - - +
495A LEU* 1.3 93.8 + - + +
496A THR 3.6 0.2 - - - -
518A GLU* 4.3 19.9 + - + +
519A LEU* 4.4 5.2 - - + -
814A SO4 4.0 13.5 - - - -
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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