Contacts of the helix formed by residues 465 - 480 (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 ASP 465 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A LYS* 2.6 28.1 + - - +
463A ALA* 3.6 1.0 - - - +
464A ARG* 1.3 92.7 + - - +
466A MET* 1.3 65.1 + - - +
467A ASP* 3.4 18.4 - - - +
468A LEU* 3.5 5.2 + - + +
469A THR* 2.8 28.4 + - - -
523A TRP* 3.9 2.9 - - - -
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Residues in contact with MET 466 (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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465A ASP* 1.3 73.2 - - - +
467A ASP* 1.3 55.6 + - - +
469A THR* 3.1 0.7 + - - -
470A GLU* 2.7 42.0 + - + +
523A TRP* 3.1 72.0 - - + +
525A SER* 5.9 6.1 - - - -
526A VAL* 4.1 16.3 - - + +
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Residues in contact with ASP 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 3.0 34.4 + - - -
426A LEU* 4.1 14.6 - - + +
465A ASP* 3.4 6.4 - - - +
466A MET* 1.3 80.5 - - - +
468A LEU* 1.3 77.5 + - - +
470A GLU* 3.3 6.7 + - - +
471A VAL* 3.2 29.1 + - + +
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Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS* 4.4 13.9 - - + -
425A HIS* 3.8 25.1 - - + +
426A LEU* 3.8 35.2 - - + -
429A CYS* 4.7 4.9 - - + -
459A LEU* 4.0 27.4 - - + -
463A ALA* 3.8 24.5 - - + -
464A ARG 5.3 0.7 - - - +
465A ASP* 3.5 7.5 + - + +
466A MET 3.3 0.4 - - - -
467A ASP* 1.3 85.2 + - - +
469A THR* 1.3 65.7 + - - +
471A VAL* 3.2 1.2 + - - -
472A ILE* 3.0 33.6 + - + +
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Residues in contact with THR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.7 23.1 - - + -
463A ALA* 3.7 14.7 + - - +
464A ARG 5.1 0.2 - - - -
465A ASP 2.8 21.7 + - - -
466A MET 3.8 3.1 - - - -
468A LEU* 1.3 76.9 - - - +
470A GLU* 1.3 63.2 + - - +
472A ILE* 3.8 7.8 - - - +
473A THR* 2.9 27.7 + - + +
500A GLU 5.9 0.2 - - - +
501A VAL* 4.2 8.3 - - + -
505A HIS* 5.7 0.2 - - - +
523A TRP* 3.7 20.1 - - + -
526A VAL* 3.7 24.7 - - + -
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Residues in contact with GLU 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LYS* 4.1 16.0 + - - -
466A MET* 2.7 21.8 + - + +
467A ASP* 3.4 9.2 - - - +
469A THR* 1.3 77.0 - - - +
471A VAL* 1.3 65.8 + - - +
473A THR* 3.8 1.8 - - - -
474A GLY* 3.0 23.6 + - - -
525A SER* 3.6 22.9 + - - +
526A VAL* 3.7 15.9 - - + +
529A ASN* 2.9 29.1 + - - +
762B GLY 5.8 0.2 - - - +
765B GLU* 4.5 6.7 - - - +
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A LEU* 4.0 18.6 - - + -
429A CYS* 3.7 36.1 - - + +
430A GLY* 3.8 11.2 - - - +
433A LYS* 4.1 19.7 - - + +
467A ASP* 3.2 17.8 + - + +
468A LEU 3.2 4.2 + - - +
470A GLU* 1.3 84.4 - - - +
472A ILE* 1.3 59.7 + - - +
474A GLY* 3.4 0.7 + - - -
475A THR* 2.7 34.0 + - - -
765B GLU* 5.6 5.2 - - - +
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Residues in contact with ILE 472 (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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429A CYS* 4.0 22.0 - - - -
456A LEU* 3.8 25.1 - - + +
459A LEU* 3.9 14.1 - - + +
460A LEU* 3.7 43.1 - - + +
463A ALA* 4.4 3.6 - - + -
468A LEU* 3.0 39.2 + - + +
469A THR* 3.8 3.8 - - - +
471A VAL* 1.3 76.4 - - - +
473A THR* 1.3 64.5 + - + +
475A THR* 3.1 5.9 + - - -
476A LEU* 2.9 37.8 + - + +
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Residues in contact with THR 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 4.5 6.3 - - + -
469A THR* 2.9 36.0 + - + +
470A GLU* 3.3 2.4 + - - -
472A ILE* 1.3 77.0 - - + +
474A GLY* 1.3 58.3 + - - +
476A LEU* 3.3 9.2 + - - +
477A TRP* 2.9 27.7 + - - +
497A LEU* 4.2 17.7 - - + -
501A VAL* 4.4 3.8 - - + -
526A VAL* 3.9 7.5 + - + -
529A ASN* 3.3 26.4 + - - +
530A THR* 3.4 27.8 - - - +
533A CYS* 4.9 0.5 - - - +
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Residues in contact with GLY 474 (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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433A LYS* 4.7 9.0 - - - -
470A GLU* 3.0 18.0 + - - -
471A VAL 3.9 1.6 - - - -
472A ILE 3.2 0.2 - - - -
473A THR* 1.3 74.3 + - - +
475A THR* 1.3 65.0 + - - +
477A TRP* 3.3 1.3 + - - -
478A ASN* 2.9 22.0 + - - -
529A ASN* 3.7 12.6 - - - -
762B GLY* 3.2 26.5 - - - -
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Residues in contact with THR 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A CYS* 3.9 6.2 + - - -
432A LEU* 4.2 11.0 - - + +
433A LYS* 3.2 26.3 + - - +
436A SER* 3.6 25.4 - - - +
447A ILE* 5.3 2.2 - - + -
456A LEU* 4.0 24.7 - - + -
471A VAL 2.7 19.0 + - - -
472A ILE* 3.1 8.7 + - - -
474A GLY* 1.3 78.1 - - - +
476A LEU* 1.3 56.6 + - - +
478A ASN* 3.0 4.5 + - - +
479A LEU* 2.9 31.4 + - + +
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Residues in contact with LEU 476 (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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453A VAL* 4.4 22.2 - - + +
456A LEU* 3.9 28.0 - - + -
457A VAL* 5.0 3.4 - - + -
460A LEU* 4.9 3.6 - - + -
472A ILE* 2.9 33.5 + - + +
473A THR* 3.7 8.1 - - - +
475A THR* 1.3 76.7 - - - +
477A TRP* 1.3 56.1 + - - +
479A LEU* 3.2 8.2 + - + +
480A SER* 2.8 32.4 + - - -
489A ILE* 3.9 14.9 - - + +
493A ALA* 4.7 8.3 - - + -
497A LEU* 4.1 29.4 - - + -
533A CYS* 3.8 16.3 - - + -
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Residues in contact with TRP 477 (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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473A THR 2.9 14.2 + - - +
474A GLY 3.5 7.4 - - - +
476A LEU* 1.3 77.6 - - - +
478A ASN* 1.3 61.9 + - - +
480A SER* 2.7 20.1 + - - -
528A THR* 4.3 9.6 - - + -
529A ASN* 3.3 44.6 - - - +
532A GLY* 3.4 28.9 + - - -
533A CYS* 3.9 5.5 - - - +
536A ASN* 3.7 14.5 + - - +
574A LYS* 4.2 20.6 - - + -
578A ASN* 3.6 28.0 - - - -
759B GLU* 3.7 21.3 + - - +
761B GLY* 3.1 44.4 - - - -
762B GLY 3.4 3.4 - - - +
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Residues in contact with ASN 478 (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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433A LYS* 3.2 22.8 + - - +
436A SER* 3.2 26.9 + - - +
437A PHE* 3.6 8.8 - - - +
444A LYS* 3.3 10.2 - - - -
474A GLY 2.9 17.0 + - - -
475A THR 3.0 1.8 + - - +
477A TRP* 1.3 76.3 - - - +
479A LEU* 1.3 62.4 + - - +
481A SER* 3.0 21.3 + - - -
760B GLU* 3.3 15.6 - - + +
762B GLY 2.8 27.9 + - - -
763B GLY 2.9 30.8 + - - +
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Residues in contact with LEU 479 (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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436A SER* 3.7 21.5 - - - -
444A LYS* 3.9 35.7 - - + +
447A ILE* 4.0 19.7 - - + -
448A LYS 5.4 0.7 - - - +
453A VAL* 4.2 16.6 - - + -
456A LEU* 3.8 28.5 - - + -
475A THR* 2.9 20.5 + - + +
476A LEU* 3.2 8.3 + - + +
478A ASN* 1.3 75.6 - - - +
480A SER* 1.3 59.9 + - - +
481A SER 2.9 6.4 + - - -
482A HIS* 3.0 19.9 + - - +
485A ILE* 3.8 17.2 - - + +
489A ILE* 4.2 9.2 - - + -
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Residues in contact with SER 480 (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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476A LEU 2.8 13.5 + - - -
477A TRP* 2.7 24.1 + - - -
478A ASN 3.3 0.2 - - - -
479A LEU* 1.3 75.0 - - - +
481A SER* 1.3 56.6 + - - +
482A HIS 3.2 2.2 - - - -
485A ILE* 5.3 0.4 - - - -
486A LYS* 3.2 28.6 - - - +
489A ILE* 3.5 13.0 - - - -
533A CYS* 3.7 13.5 - - - -
536A ASN* 3.0 20.1 + - - +
537A VAL* 3.7 23.1 - - - -
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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
------------------------------------------------------------
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