Contacts of the helix formed by residues 493 - 501 (chain A) in PDB entry 3L6X
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 ALA 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A VAL* 4.4 7.0 - - + -
457A VAL* 3.5 24.0 - - + -
476A LEU* 4.7 6.7 - - + -
489A ILE* 2.8 24.4 + - + +
492A HIS* 1.3 74.1 - - - +
494A LEU* 1.3 68.5 + - - +
495A HIS 3.2 2.4 + - - -
496A ALA* 3.2 2.9 + - - +
497A LEU* 2.8 43.7 + - + +
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Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A ILE 3.2 5.6 + - - -
490A VAL* 3.0 25.7 + - - +
491A ASP 5.0 0.2 - - - -
492A HIS 3.7 1.0 - - - -
493A ALA* 1.3 77.0 - - - +
495A HIS* 1.3 72.1 + - + +
497A LEU* 3.4 4.0 + - - +
498A THR* 3.0 44.1 + - - +
534A LEU* 3.9 19.1 - - + -
547A LYS* 3.6 27.1 - - + +
548A LEU* 3.6 33.9 - - + -
551A CYS* 4.1 12.8 - - + -
554A LEU* 4.2 10.8 - - + -
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Residues in contact with HIS 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ARG* 4.3 12.6 - - - +
490A VAL 5.5 0.7 - - - -
491A ASP 5.6 6.1 - - - -
492A HIS 5.4 0.6 + - - -
493A ALA 3.3 0.4 - - - -
494A LEU* 1.3 87.6 - - + +
496A ALA* 1.3 60.6 + - - +
498A THR 3.9 0.4 - - - +
499A ASP* 2.9 46.1 + - - +
547A LYS 6.0 0.2 - - - -
551A CYS* 3.7 32.3 - - + -
552A ASP 5.7 0.9 - - - -
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Residues in contact with ALA 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A VAL* 3.9 19.7 - - + -
460A LEU* 4.1 14.8 - - + -
461A ARG* 3.7 33.0 - - + +
492A HIS 5.4 0.6 + - - -
493A ALA* 3.2 7.4 + - - +
495A HIS* 1.3 75.4 - - - +
497A LEU* 1.3 66.8 + - - +
499A ASP* 4.9 0.4 - - - -
500A GLU* 2.8 39.9 + - + +
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU* 3.8 21.3 - - + -
473A THR* 4.2 11.9 - - + -
476A LEU* 4.1 15.5 - - + -
489A ILE* 4.7 1.3 - - + -
493A ALA* 2.8 39.5 + - + +
494A LEU 3.7 3.6 - - - +
496A ALA* 1.3 71.3 - - - +
498A THR* 1.3 58.9 + - - +
501A VAL* 3.2 12.0 + - + +
502A ILE* 3.0 25.7 + - - +
530A THR* 3.9 25.8 - - + +
533A CYS* 3.9 27.6 - - - -
534A LEU* 4.1 22.2 - - + -
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Residues in contact with THR 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A LEU* 3.0 26.0 + - - +
495A HIS 4.0 2.5 - - - -
496A ALA 3.2 0.2 - - - -
497A LEU* 1.3 76.9 - - - +
499A ASP* 1.3 61.3 + - - +
502A ILE* 3.4 8.7 + - + -
503A ILE* 2.9 54.7 + - + +
534A LEU* 4.8 2.1 - - - +
551A CYS* 3.5 22.3 - - - -
552A ASP 3.8 12.6 - - - +
554A LEU* 3.9 27.1 - - + +
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Residues in contact with ASP 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A HIS* 2.9 35.5 + - - +
496A ALA* 4.9 0.7 - - - -
498A THR* 1.3 79.5 - - - +
500A GLU* 1.3 69.8 + - - +
503A ILE* 3.7 21.2 - - - +
504A PRO* 3.2 19.0 - - - +
551A CYS* 5.6 1.5 - - - -
552A ASP* 4.6 3.3 - - - +
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU* 4.4 13.4 - - + +
461A ARG* 3.6 48.3 + - + +
469A THR* 5.9 0.2 - - - +
496A ALA* 2.8 29.3 + - + +
499A ASP* 1.3 81.6 - - - +
501A VAL* 1.3 67.2 + - + +
504A PRO* 3.3 14.3 - - - +
505A HIS* 3.9 10.9 + - - -
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU* 4.2 17.7 - - + -
469A THR* 4.2 22.9 - - + -
473A THR* 4.4 4.0 - - + -
497A LEU* 3.2 14.0 + - - +
499A ASP 3.5 0.6 - - - -
500A GLU* 1.3 86.7 - - + +
502A ILE* 1.3 68.4 + - - +
503A ILE 3.4 1.1 - - - -
504A PRO* 3.5 1.3 - - - -
505A HIS* 3.1 33.2 + - + +
526A VAL* 3.5 19.5 - - + -
527A LEU* 3.8 10.4 - - + +
530A THR* 3.3 31.9 - - + +
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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