Contacts of the helix formed by residues 499 - 507 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497H TYR* 3.5 8.2 - - - +
498H THR* 1.3 93.2 - - + +
500H ALA* 1.3 71.6 + - - +
501H ALA* 3.6 23.9 + - + +
502H HIS 3.7 2.6 + - - +
503H PHE* 3.5 17.2 + - - +
515H TRP* 4.5 19.8 - - - -
554H LEU* 6.6 0.2 - - - -
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Residues in contact with ALA 500 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499H THR* 1.3 80.9 + - - +
501H ALA* 1.3 57.5 + - - +
502H HIS 3.4 0.2 - - - -
503H PHE* 3.4 8.8 + - - +
504H ALA* 2.9 30.8 + - - +
512H ALA* 3.7 24.7 - - + +
515H TRP* 4.1 24.5 - - + -
516H LYS* 5.5 1.6 - - + +
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Residues in contact with ALA 501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499H THR* 3.3 14.2 + - + +
500H ALA* 1.3 78.3 - - - +
502H HIS* 1.3 57.9 + - - +
504H ALA* 3.3 6.4 + - - +
505H GLU* 2.9 29.9 + - - +
1261H ASP* 6.2 4.0 - - + -
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Residues in contact with HIS 502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497H TYR* 4.0 17.2 - - + -
498H THR* 3.7 28.5 - - + -
499H THR* 3.7 6.3 + - - +
500H ALA 3.4 0.4 - - - -
501H ALA* 1.3 78.3 - - - +
503H PHE* 1.3 58.0 + - - +
505H GLU* 3.3 6.1 + - - +
506H PHE* 2.9 32.4 + - - +
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Residues in contact with PHE 503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418H LEU* 6.5 1.1 - - + -
421H PHE* 5.6 4.0 - - + -
436H LEU* 5.0 16.2 - - + -
494H LEU* 4.6 15.5 - - + -
497H TYR* 4.1 34.8 - + + -
499H THR 3.5 11.1 + - - +
500H ALA* 3.4 11.4 + - - +
501H ALA 3.2 0.4 - - - -
502H HIS* 1.3 78.3 - - - +
504H ALA* 1.3 56.5 + - - +
507H ALA* 2.9 47.9 + - + +
508H GLY 3.4 13.5 + - - -
510H GLU* 6.3 0.2 - - + -
511H ALA* 3.9 39.7 - - + -
512H ALA* 4.9 1.1 - - - -
515H TRP* 4.3 20.9 - + + +
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Residues in contact with ALA 504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500H ALA 2.9 18.4 + - - +
501H ALA* 3.3 5.8 + - - +
503H PHE* 1.3 76.9 - - - +
505H GLU* 1.3 60.8 + - - +
508H GLY* 3.3 32.6 - - - +
509H GLU* 3.9 5.5 + - + +
512H ALA* 3.8 24.9 - - + -
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Residues in contact with GLU 505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426H ARG* 3.9 12.4 - - + +
427H GLY 4.1 12.6 + - - +
430H ALA 4.8 3.3 - - - +
501H ALA 2.9 17.9 + - - +
502H HIS* 3.8 7.0 - - - +
504H ALA* 1.3 79.0 - - - +
506H PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421H PHE 5.1 4.0 - - - +
424H LYS* 5.0 5.4 - - - +
425H PRO 4.4 3.3 - - - +
426H ARG* 3.8 28.6 - - + +
430H ALA 4.5 2.1 - - - +
431H PRO* 3.1 17.4 - - - +
497H TYR* 3.9 26.0 - - + +
502H HIS 2.9 17.7 + - - +
503H PHE 4.2 0.2 - - - +
505H GLU* 1.3 79.9 - - + +
507H ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H PHE* 3.9 32.8 - - + +
431H PRO* 3.3 23.5 - - - +
433H GLY* 4.8 6.5 + - - +
434H THR 5.7 0.3 - - - +
497H TYR* 5.3 2.9 - - - +
503H PHE* 2.9 39.5 + - + +
506H PHE* 1.3 77.0 - - + +
508H GLY* 1.3 58.3 + - - +
510H 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