Contacts of the helix formed by residues 499 - 507 (chain D) in PDB entry 6X34
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 THR 499 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497D TYR* 3.5 8.0 - - - +
498D THR* 1.3 94.0 - - + +
500D ALA* 1.3 71.1 + - - +
501D ALA* 3.5 23.8 + - + +
502D HIS 3.7 2.7 + - - +
503D PHE* 3.5 17.7 + - - +
515D TRP* 4.5 19.8 - - - -
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Residues in contact with ALA 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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499D THR* 1.3 82.8 + - - +
501D ALA* 1.3 57.6 + - - +
503D PHE* 3.4 8.9 + - - +
504D ALA* 2.9 30.2 + - - +
512D ALA* 3.7 23.5 - - - +
515D TRP* 4.1 25.4 - - + -
516D LYS* 5.5 1.6 - - + +
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Residues in contact with ALA 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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499D THR* 3.3 14.3 + - + +
500D ALA* 1.3 79.5 - - - +
502D HIS* 1.3 57.6 + - - +
504D ALA* 3.3 6.5 + - - +
505D GLU* 2.9 29.7 + - - +
1261D ASP* 6.2 4.0 - - + -
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Residues in contact with HIS 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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497D TYR* 4.0 17.6 - - + -
498D THR* 3.7 28.5 - - + +
499D THR* 3.7 5.9 + - - +
500D ALA 3.4 0.2 - - - -
501D ALA* 1.3 79.0 - - - +
503D PHE* 1.3 58.1 + - - +
505D GLU* 3.3 6.7 + - - +
506D PHE* 2.9 32.2 + - - +
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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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418D LEU* 6.5 1.6 - - + -
421D PHE* 5.6 4.7 - - + -
436D LEU* 5.0 15.5 - - + -
494D LEU* 4.6 14.8 - - + -
497D TYR* 4.1 34.2 - + + -
499D THR 3.5 12.1 + - - +
500D ALA* 3.4 11.6 + - - +
501D ALA 3.2 0.4 - - - -
502D HIS* 1.3 78.8 - - - +
504D ALA* 1.3 59.0 + - - +
507D ALA* 2.9 46.5 + - + -
508D GLY 3.4 13.0 + - - -
510D GLU* 6.3 0.2 - - + -
511D ALA* 3.9 40.2 - - + -
512D ALA* 4.9 1.1 - - - -
515D TRP* 4.3 21.5 - + + +
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Residues in contact with ALA 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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500D ALA 2.9 18.0 + - - +
501D ALA* 3.8 6.1 - - - +
503D PHE* 1.3 78.2 - - - +
505D GLU* 1.3 60.9 + - - +
508D GLY* 3.3 32.0 - - - +
509D GLU* 3.9 5.9 + - + +
512D ALA* 3.8 24.5 - - + -
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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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426D ARG* 3.9 12.9 - - + +
427D GLY 4.1 12.5 + - - +
430D ALA 4.8 2.9 - - - +
431D PRO* 6.1 0.2 - - - +
501D ALA 2.9 17.3 + - - +
502D HIS* 3.8 7.2 - - - +
503D PHE 3.2 0.2 - - - -
504D ALA* 1.3 79.0 - - - +
506D PHE* 1.3 60.1 + - - +
508D GLY* 4.7 0.4 - - - -
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Residues in contact with PHE 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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421D PHE 5.1 3.3 - - - +
424D LYS* 5.0 5.8 - - - +
425D PRO 4.4 2.9 - - - +
426D ARG* 3.8 29.0 - - + +
430D ALA 4.5 2.1 - - - +
431D PRO 3.1 17.2 - - - +
497D TYR* 3.9 26.9 - - + +
502D HIS 2.9 16.9 + - - +
503D PHE 4.2 0.2 - - - +
505D GLU* 1.3 79.7 - - - +
507D ALA* 1.3 60.8 + - - +
508D GLY 3.5 0.2 - - - -
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Residues in contact with ALA 507 (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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421D PHE* 3.9 32.1 - - + +
431D PRO* 3.3 23.2 - - - +
433D GLY* 4.8 6.6 + - - +
434D THR 5.7 0.2 - - - +
497D TYR* 5.3 2.5 - - - +
503D PHE* 2.9 40.2 + - + +
506D PHE* 1.3 76.9 - - + +
508D GLY* 1.3 58.0 + - - +
510D GLU* 5.9 1.6 - - - +
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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