Contacts of the helix formed by residues 523 - 538 (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 TRP 523 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ARG 4.1 12.6 - - - -
465A ASP 3.9 4.3 - - - -
466A MET* 3.1 62.9 - - + +
469A THR* 3.7 23.6 - - + -
505A HIS* 3.2 48.1 - + + -
522A GLU* 1.3 90.5 - - + +
524A GLU* 1.3 65.2 + - - +
525A SER* 3.1 4.2 + - - -
526A VAL* 3.1 26.5 + - + +
527A LEU* 3.1 19.1 + - - +
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Residues in contact with GLU 524 (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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521A ILE* 5.9 2.7 - - + -
522A GLU* 3.1 6.7 + - - -
523A TRP* 1.3 75.1 - - - +
525A SER* 1.3 53.4 + - - +
527A LEU* 3.5 10.4 + - - +
528A THR* 2.6 44.6 + - - +
565A GLU* 4.4 12.8 - - - +
573A SER* 4.0 23.0 + - - -
575A LEU* 4.2 17.0 + - + +
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Residues in contact with SER 525 (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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466A MET* 5.9 6.3 - - - -
470A GLU* 3.6 22.6 + - - +
523A TRP 4.9 0.9 - - - -
524A GLU* 1.3 79.7 - - - +
526A VAL* 1.3 60.5 + - - +
528A THR* 3.3 7.2 + - - -
529A ASN* 3.0 35.2 + - - +
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Residues in contact with VAL 526 (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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466A MET* 4.1 14.4 - - + +
469A THR* 3.7 20.4 - - + -
470A GLU* 3.7 36.1 - - + +
473A THR* 3.9 9.4 + - + +
501A VAL* 3.5 23.8 - - + -
505A HIS* 4.9 0.7 - - + -
523A TRP* 3.1 31.5 + - + +
525A SER* 1.3 73.4 - - - +
527A LEU* 1.3 58.2 + - - +
529A ASN* 3.2 4.4 + - - +
530A THR* 2.7 38.1 + - - +
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Residues in contact with LEU 527 (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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501A VAL* 3.8 25.6 - - + +
502A ILE* 4.0 25.7 - - + +
505A HIS* 3.8 20.4 - - + +
506A SER 4.3 0.2 - - - +
521A ILE* 3.9 23.8 - - + -
522A GLU 3.3 20.6 - - - +
523A TRP 3.1 11.7 + - - +
524A GLU* 3.6 8.1 - - - +
526A VAL* 1.3 76.9 - - + +
528A THR* 1.3 63.1 + - - +
530A THR* 3.7 3.9 - - - -
531A ALA* 2.9 28.1 + - - +
561A ILE* 4.3 11.4 - - + -
575A LEU* 3.7 18.7 - - + +
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Residues in contact with THR 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TRP* 4.3 9.2 - - + -
524A GLU* 2.6 30.0 + - - +
525A SER* 3.5 9.0 - - - -
526A VAL 3.2 0.4 - - - -
527A LEU* 1.3 78.3 - - - +
529A ASN* 1.3 63.2 + - - +
531A ALA 4.0 0.2 - - - -
532A GLY 3.0 6.4 + - - -
574A LYS* 3.7 26.0 - - + -
575A LEU* 3.4 27.6 + - - +
578A ASN* 2.8 39.4 + - - +
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Residues in contact with ASN 529 (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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470A GLU* 2.9 48.9 + - - +
473A THR* 3.3 27.7 + - - +
474A GLY* 3.6 8.6 - - - +
477A TRP* 3.3 33.4 - - + +
525A SER* 3.0 18.4 + - - +
526A VAL 3.6 2.2 - - - +
528A THR* 1.3 78.1 - - - +
530A THR* 1.3 58.7 + - - +
532A GLY* 3.4 0.5 + - - -
533A CYS* 2.9 29.3 + - - +
761B GLY 4.7 1.6 - - - +
762B GLY* 5.0 0.7 - - - -
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Residues in contact with THR 530 (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* 3.4 18.1 - - - +
497A LEU* 3.9 34.3 - - + -
501A VAL* 3.3 20.7 - - + +
502A ILE* 3.6 24.0 - - + -
526A VAL 2.7 20.7 + - - -
527A LEU 3.7 3.4 - - - -
528A THR 3.1 0.2 - - - -
529A ASN* 1.3 75.4 - - - +
531A ALA* 1.3 61.6 + - - +
533A CYS* 3.2 7.5 + - - +
534A LEU* 3.0 29.2 + - + +
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Residues in contact with ALA 531 (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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502A ILE* 4.5 4.8 - - + +
527A LEU 2.9 15.5 + - - +
528A THR 4.1 0.2 - - - +
530A THR* 1.3 73.1 - - - +
532A GLY* 1.3 60.9 + - - +
534A LEU* 3.9 7.9 - - - +
535A ARG* 2.8 32.6 + - - +
558A LEU* 4.7 8.3 - - + -
575A LEU* 4.6 1.6 - - + -
578A ASN* 3.7 21.4 - - + +
579A CYS* 4.0 26.5 - - - +
582A LEU* 4.4 4.6 - - + +
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Residues in contact with GLY 532 (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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477A TRP* 3.4 19.4 + - - -
528A THR 3.0 12.7 + - - -
530A THR 3.2 0.2 - - - -
531A ALA* 1.3 76.8 - - - +
533A CYS* 1.3 62.1 + - - +
535A ARG* 3.5 5.6 + - - +
536A ASN* 3.1 29.1 + - - +
578A ASN* 3.3 25.9 - - - +
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Residues in contact with CYS 533 (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 4.9 0.4 - - - +
476A LEU* 3.8 26.2 - - + -
477A TRP* 3.6 12.9 - - - +
480A SER* 3.7 11.7 - - - -
489A ILE* 3.9 20.2 - - - -
497A LEU* 3.9 23.8 - - + -
529A ASN 2.9 14.4 + - - +
530A THR* 3.4 11.2 - - - +
532A GLY* 1.3 77.8 - - - +
534A LEU* 1.3 63.3 + - - +
536A ASN* 3.3 3.6 + - - +
537A VAL* 3.2 27.9 + - - +
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Residues in contact with LEU 534 (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* 5.5 2.2 - - + -
490A VAL* 6.3 0.7 - - - -
494A LEU* 3.9 26.5 - - + -
497A LEU* 4.1 23.6 - - + -
498A THR* 4.8 4.7 - - - +
502A ILE* 4.5 7.4 - - + -
530A THR* 3.0 30.8 + - + +
531A ALA* 4.0 0.9 - - - +
533A CYS* 1.3 73.1 - - - +
535A ARG* 1.3 65.2 + - - +
537A VAL* 3.4 12.1 - - + +
538A SER* 2.9 28.9 + - - -
548A LEU* 3.9 10.6 - - + +
554A LEU* 4.1 31.0 - - + -
582A LEU* 3.6 20.1 - - + +
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Residues in contact with ARG 535 (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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477A TRP* 6.2 0.2 - - - +
531A ALA 2.8 18.2 + - - +
532A GLY* 3.6 4.7 - - - +
534A LEU* 1.3 77.5 - - - +
536A ASN* 1.3 73.5 + - - +
538A SER* 3.0 9.4 + - - -
539A SER* 3.4 4.2 + - - -
577A GLU* 4.4 12.7 + - - -
578A ASN* 4.0 25.7 + - - +
581A CYS* 3.3 45.9 - - + +
582A LEU* 3.9 10.2 - - + +
584A ARG* 3.7 15.6 - - - +
585A ASN* 2.9 30.8 + - - +
673A ALA* 6.0 0.6 - - - +
759B GLU* 5.0 9.3 + - - +
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Residues in contact with ASN 536 (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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477A TRP* 3.7 9.5 + - - -
480A SER* 3.0 35.7 + - - +
481A SER* 3.8 11.3 - - - +
486A LYS* 2.9 25.1 + - - -
532A GLY 3.1 14.4 + - - +
533A CYS 3.6 2.0 - - - +
535A ARG* 1.3 88.7 + - - +
537A VAL* 1.3 62.0 + - - +
538A SER 3.1 0.4 + - - -
539A SER* 3.1 11.2 + - - -
758B ASP* 3.7 20.6 - - - +
759B GLU* 3.1 29.1 + - - +
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Residues in contact with VAL 537 (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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480A SER* 3.7 20.0 - - - -
486A LYS* 3.8 39.7 - - + +
489A ILE* 3.8 16.2 - - + -
490A VAL* 3.5 27.3 - - + +
533A CYS 3.2 14.1 + - - +
534A LEU* 3.4 24.0 - - + +
536A ASN* 1.3 76.5 - - - +
538A SER* 1.3 60.3 + - - +
539A SER 3.3 1.7 + - - -
540A GLU 4.0 4.0 + - - +
541A ARG* 5.5 1.2 + - - -
544A ALA* 3.3 18.5 - - - +
548A LEU* 4.6 7.4 - - + -
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Residues in contact with SER 538 (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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534A LEU 2.9 20.4 + - - -
535A ARG 3.0 0.2 + - - -
536A ASN 3.1 0.4 - - - -
537A VAL* 1.3 77.7 - - - +
539A SER* 1.3 62.9 + - - +
540A GLU* 3.2 6.6 + - - +
544A ALA* 4.2 10.5 - - - -
545A ARG* 4.4 13.7 + - - +
548A LEU* 4.1 19.3 - - - -
582A LEU* 3.3 12.2 - - - +
585A ASN* 2.8 40.5 + - - +
586A LEU* 4.4 8.7 - - - -
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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