Contacts of the helix formed by residues 496 - 503 (chain D) in PDB entry 4PE5
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 496 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481D VAL* 4.3 0.9 - - - -
483D ASN 3.6 14.3 + - - -
485D LYS 4.1 1.1 - - - -
486D HIS 3.3 16.4 - - - -
487D GLY* 4.2 3.4 - - - -
488D LYS 4.6 0.8 + - - +
494D TRP 4.0 0.8 - - - -
495D ASN* 1.3 77.7 - - - +
497D MET* 1.3 55.6 + - - -
498D ILE 3.3 2.0 - - - -
499D GLY* 3.3 3.9 - - - +
500D GLU* 2.7 39.9 + - - +
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Residues in contact with MET 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D VAL* 3.7 20.3 - - + +
410D THR* 3.8 6.5 - - - -
411D LEU* 3.6 25.8 - - - -
481D VAL* 4.0 13.9 - - + -
485D LYS 3.3 17.9 + - - +
486D HIS* 4.1 8.1 + - - -
487D GLY 5.1 0.9 - - - +
496D GLY* 1.3 71.0 - - - -
498D ILE* 1.3 64.4 + - + +
500D GLU* 2.9 12.4 + - - +
501D VAL* 2.9 33.4 + - - +
509D ALA* 3.8 16.4 - - + +
510D VAL 3.3 27.8 - - - +
511D GLY* 5.2 1.8 - - - -
512D SER 5.4 2.5 - - - +
513D LEU* 4.7 21.8 - - + -
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D GLY* 4.1 13.0 - - - -
494D TRP* 4.6 14.6 - - + -
496D GLY* 3.3 0.4 - - - -
497D MET* 1.3 75.0 - - - +
499D GLY* 1.3 57.4 + - - +
501D VAL* 3.3 5.6 + - - +
502D VAL* 2.9 29.0 + - - +
513D LEU* 3.7 34.8 - - + -
519D ARG* 3.9 26.0 - - + +
522D VAL* 3.8 21.1 - - + -
523D VAL* 3.8 20.6 - - + +
525D PHE* 3.9 13.7 - - + -
765D ALA* 3.7 14.6 - - + -
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Residues in contact with GLY 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D TRP* 3.7 28.9 - - - +
495D ASN* 5.1 0.2 - - - -
496D GLY 3.0 14.7 + - - +
498D ILE* 1.3 78.8 - - - +
500D GLU* 1.3 61.0 + - - +
502D VAL* 3.6 5.4 - - - +
503D MET* 3.2 29.3 + - - +
505D ARG* 4.8 1.0 - - - -
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Residues in contact with GLU 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D VAL* 4.3 9.4 - - + -
479D TYR* 3.3 28.9 + - - +
481D VAL* 3.9 24.8 - - + +
482D THR* 4.5 9.2 + - - -
483D ASN* 4.9 6.8 + - - +
496D GLY 2.7 20.5 + - - +
497D MET* 2.9 11.6 + - - +
499D GLY* 1.3 74.4 - - - +
501D VAL* 1.3 53.1 + - - +
503D MET 4.3 0.2 - - - -
505D ARG* 3.0 62.3 + - - +
506D ALA 2.7 30.0 + - - -
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Residues in contact with VAL 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D VAL* 4.7 0.4 - - + -
497D MET 2.9 18.1 + - - +
498D ILE* 3.6 6.5 - - - +
499D GLY 3.1 0.2 - - - -
500D GLU* 1.3 77.7 - - - +
502D VAL* 1.3 65.1 + - - +
503D MET 3.2 2.0 - - - -
504D LYS* 3.1 12.6 + - - -
506D ALA* 3.2 24.5 - - + +
507D TYR 4.0 1.1 - - - +
508D MET 4.3 4.7 - - - +
509D ALA* 3.7 26.0 - - + -
523D VAL* 3.8 12.6 - - + -
765D ALA* 3.7 10.5 - - + +
766D ILE 3.5 34.3 - - - +
767D GLN* 3.8 10.4 - - - +
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Residues in contact with VAL 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D TRP* 4.3 16.4 - - + +
498D ILE 2.9 20.6 + - - +
499D GLY* 3.6 14.4 - - - +
501D VAL* 1.3 76.4 - - - +
503D MET* 1.3 61.6 + - + +
504D LYS* 3.1 4.1 + - - +
522D VAL* 4.0 32.8 - - + +
523D VAL* 4.2 9.9 - - + -
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Residues in contact with MET 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D GLY 3.2 19.8 + - - +
501D VAL 3.2 1.2 - - - -
502D VAL* 1.3 78.6 - - + +
504D LYS* 1.3 69.3 + - - +
505D ARG* 3.1 25.1 + - + +
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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