Contacts of the helix formed by residues 499 - 507 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497F TYR* 3.5 8.0 - - - +
498F THR* 1.3 93.8 - - + +
500F ALA* 1.3 72.4 + - - +
501F ALA* 3.5 23.6 + - + +
502F HIS 3.7 2.4 + - - +
503F PHE* 3.5 17.8 + - - +
515F TRP* 4.5 19.4 - - - -
554F LEU* 6.6 0.2 - - - -
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Residues in contact with ALA 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499F THR* 1.3 81.5 + - - +
501F ALA* 1.3 58.0 + - - +
503F PHE* 3.4 8.6 + - - +
504F ALA* 2.9 30.0 + - - +
512F ALA* 3.7 24.7 - - + +
515F TRP* 4.1 24.7 - - + -
516F LYS* 5.5 1.3 - - + +
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Residues in contact with ALA 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499F THR* 3.3 14.9 + - + +
500F ALA* 1.3 78.6 - - - +
502F HIS* 1.3 57.5 + - - +
504F ALA* 3.3 5.8 + - - +
505F GLU* 2.9 29.9 + - - +
1261F ASP* 6.2 4.0 - - + -
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Residues in contact with HIS 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497F TYR* 4.0 17.0 - - + -
498F THR* 3.7 28.5 - - + -
499F THR* 3.7 7.0 + - - +
500F ALA 3.4 0.2 - - - -
501F ALA* 1.3 78.6 - - - +
503F PHE* 1.3 57.2 + - - +
505F GLU* 3.3 5.9 + - - +
506F PHE* 2.9 32.6 + - - +
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Residues in contact with PHE 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F LEU* 6.5 1.1 - - + -
421F PHE* 5.6 4.0 - - + -
436F LEU* 5.0 15.5 - - + -
494F LEU* 4.6 15.3 - - + -
497F TYR* 4.1 34.2 - + + -
499F THR 3.5 11.3 + - - +
500F ALA* 3.4 11.6 + - - +
501F ALA 3.2 0.4 - - - -
502F HIS* 1.3 78.2 - - - +
504F ALA* 1.3 58.7 + - - +
507F ALA* 2.9 48.2 + - + -
508F GLY 3.4 13.9 + - - -
511F ALA* 3.9 39.5 - - + -
512F ALA* 4.9 1.3 - - - -
515F TRP* 4.3 21.8 - + + +
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Residues in contact with ALA 504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500F ALA 2.9 18.3 + - - +
501F ALA* 3.3 6.7 + - - +
503F PHE* 1.3 77.6 - - - +
505F GLU* 1.3 60.9 + - - +
508F GLY* 3.3 31.4 - - - +
509F GLU* 3.9 5.4 + - + +
512F ALA* 3.8 24.0 - - + -
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Residues in contact with GLU 505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426F ARG* 3.9 13.2 - - + +
427F GLY 4.1 12.6 + - - +
430F ALA 4.8 2.6 - - - +
501F ALA 2.9 17.5 + - - +
502F HIS* 3.8 6.7 - - - +
504F ALA* 1.3 79.8 - - - +
506F PHE* 1.3 60.3 + - - +
508F GLY 4.7 0.2 - - - -
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Residues in contact with PHE 506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F PHE 5.1 3.2 - - - +
424F LYS* 5.0 5.5 - - - +
425F PRO 4.4 2.9 - - - +
426F ARG* 3.8 28.5 - - + +
430F ALA 4.5 1.9 - - - +
431F PRO 3.1 17.2 - - - +
497F TYR* 3.9 26.7 - - + +
502F HIS 2.9 16.6 + - - +
503F PHE 4.2 0.4 - - - +
505F GLU* 1.3 79.4 - - - +
507F ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F PHE* 3.9 32.9 - - + +
431F PRO* 3.3 24.3 - - - +
433F GLY* 4.8 6.9 + - - +
434F THR 5.7 0.3 - - - +
497F TYR* 5.3 2.7 - - - +
503F PHE* 2.9 39.7 + - + +
506F PHE* 1.3 76.1 - - + +
508F GLY* 1.3 58.3 + - - +
510F GLU* 5.9 1.8 - - - +
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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