Contacts of the helix formed by residues 496 - 506 (chain D) in PDB entry 6PUO
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 LYS 496 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460D VAL* 4.0 27.3 + - + +
461D ALA* 5.0 5.0 + - - +
463D ASN* 3.3 33.2 - - - +
490D ALA 4.9 1.8 + - - -
491D ALA* 3.5 14.4 + - - +
494D SER* 2.5 38.0 + - - +
495D ASN* 1.3 78.9 - - - +
497D PRO* 1.3 66.3 - - - +
498D GLU* 3.2 3.7 + - + +
499D PHE* 3.5 30.9 + - + +
500D VAL* 3.3 16.0 + - - +
637D LEU* 5.4 1.4 - - - +
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Residues in contact with PRO 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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495D ASN* 3.7 14.3 - - - +
496D LYS* 1.3 85.0 - - - +
498D GLU* 1.3 76.1 + - + +
500D VAL* 3.1 13.6 + - + +
501D LYS* 3.0 32.8 + - + +
636D GLU* 4.2 27.1 - - + -
637D LEU* 4.3 14.8 - - + -
640D ILE* 4.4 9.4 - - + +
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Residues in contact with GLU 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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465D VAL* 4.3 27.7 - - + +
469D ARG* 4.9 5.6 + - - +
496D LYS* 3.2 2.1 - - + -
497D PRO* 1.3 93.8 - - + +
499D PHE* 1.3 61.5 + - + +
501D LYS* 3.3 24.3 + - - +
502D LEU* 2.9 27.9 + - - +
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Residues in contact with PHE 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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456D LEU* 5.5 2.9 - - + -
459D ALA 3.5 16.8 - - - -
460D VAL* 3.6 28.5 - - + -
462D TRP 4.6 0.2 - - - -
463D ASN* 3.3 22.7 - - - -
464D ARG 3.3 23.1 - - - -
465D VAL* 3.6 25.1 - - + -
468D ALA* 4.6 11.9 - - + -
491D ALA* 3.9 20.0 - - + -
496D LYS* 3.5 21.9 + - + +
497D PRO 3.3 0.4 - - - -
498D GLU* 1.3 78.7 - - + +
500D VAL* 1.3 60.1 + - - +
502D LEU* 4.2 7.0 - - + -
503D PHE* 2.9 53.2 + + + -
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Residues in contact with VAL 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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488D MET* 3.8 28.7 - - + -
491D ALA* 4.2 12.1 - - + +
492D LEU* 4.1 15.9 - - + -
496D LYS 3.3 18.2 - - - +
497D PRO* 3.1 13.0 + - + +
499D PHE* 1.3 78.5 - - - +
501D LYS* 1.3 57.3 + - - +
503D PHE* 3.3 1.9 + - - +
504D LEU* 2.9 41.6 + - + +
510D LEU* 6.2 0.9 - - + -
637D LEU* 4.0 21.5 - - + -
640D ILE* 5.1 9.2 - - + -
641D ILE* 6.4 2.2 - - + -
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Residues in contact with LYS 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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469D ARG* 5.6 2.5 - - - +
497D PRO* 3.0 21.4 + - + +
498D GLU* 3.7 28.9 - - - +
500D VAL* 1.3 76.1 - - - +
502D LEU* 1.3 57.8 + - - +
504D LEU* 3.3 8.0 + - - +
505D GLU* 2.9 44.2 + - - +
640D ILE* 3.7 27.6 - - + +
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Residues in contact with LEU 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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465D VAL* 4.0 20.0 - - + -
468D ALA* 4.2 13.5 - - + -
469D ARG* 3.5 48.6 - - + +
473D PHE* 3.9 33.9 - - + -
498D GLU 2.9 17.4 + - - +
499D PHE* 3.8 7.9 - - + +
501D LYS* 1.3 78.9 - - - +
503D PHE* 1.3 67.6 + - + +
505D GLU* 3.3 11.5 + - + +
506D ASN* 3.2 27.8 + - - +
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Residues in contact with PHE 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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456D LEU* 4.4 14.4 - - + -
460D VAL* 5.2 2.9 - - + -
473D PHE* 4.3 20.0 - + - -
484D LEU* 3.7 29.2 - - + +
487D THR* 3.5 28.7 - - - -
488D MET* 3.5 44.4 - - + -
491D ALA* 4.2 10.3 - - + -
499D PHE* 2.9 41.4 + + + +
500D VAL 3.9 3.4 - - - +
502D LEU* 1.3 80.6 - - + +
504D LEU* 1.3 62.4 + - - +
506D ASN* 3.4 5.5 + - - +
507D GLY 3.2 14.4 + - - -
508D VAL* 3.3 18.7 + - + +
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Residues in contact with LEU 504 (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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488D MET* 5.0 0.7 - - + -
500D VAL* 2.9 30.6 + - + +
501D LYS* 3.8 6.7 - - - +
502D LEU 3.3 0.2 - - - -
503D PHE* 1.3 75.1 - - - +
505D GLU* 1.3 60.4 + - + +
507D GLY* 3.0 17.4 + - - +
508D VAL* 3.4 32.8 - - + +
510D LEU* 4.2 26.5 - - + -
640D ILE* 4.0 26.5 - - + -
644D GLN* 4.2 20.9 - - - +
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Residues in contact with GLU 505 (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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223C ARG* 4.2 12.8 + - - -
227C LEU* 5.9 11.0 - - + +
469D ARG* 3.9 23.9 + - - -
501D LYS* 2.9 32.5 + - - +
502D LEU* 3.3 10.3 + - + +
503D PHE 3.3 0.2 - - - -
504D LEU* 1.3 78.4 - - + +
506D ASN* 1.3 67.4 + - - +
507D GLY* 3.2 0.9 + - - -
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Residues in contact with ASN 506 (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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223C ARG* 5.0 10.5 - - - +
473D PHE* 3.3 43.0 - - - +
479D TRP* 4.3 31.1 + - + +
481D PRO* 4.3 9.7 - - - +
484D LEU* 5.1 7.9 - - + +
502D LEU* 3.2 18.5 + - - +
503D PHE* 3.4 7.2 + - - +
504D LEU 3.2 0.4 - - - -
505D GLU* 1.3 82.3 + - - +
507D GLY* 1.3 63.4 + - - +
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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