Contacts of the helix formed by residues 470 - 480 (chain A) in PDB entry 4NGM
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 MET 470 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A ALA* 3.9 18.2 - - + -
450A ILE* 4.0 9.2 - - + -
466A CYS* 4.0 8.3 - - - -
467A THR* 2.9 15.3 + - + +
469A LEU* 1.3 80.0 - - - +
471A TYR* 1.3 64.3 + - - +
472A SER 3.3 2.9 + - - -
473A LEU* 3.3 17.3 + - + +
474A VAL* 3.0 25.0 + - - +
531A ALA* 3.4 39.0 - - + +
532A SER* 3.6 22.0 - - - +
533A GLY* 3.9 5.2 - - - +
583A MET* 3.8 27.8 - - + -
587A LEU* 4.5 3.4 - - + -
595A PHE* 4.2 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A CYS* 3.7 20.1 + - - -
467A THR 3.7 3.1 - - - -
468A PRO* 3.1 40.9 + - + +
469A LEU 3.5 0.2 - - - -
470A MET* 1.3 77.8 - - - +
472A SER* 1.3 58.1 + - - +
474A VAL* 3.3 1.4 + - - +
475A HIS* 2.9 48.3 + + + -
512A ILE* 3.6 44.1 + - + -
513A SER 5.2 3.0 + - - -
514A LYS* 5.6 1.6 + - - -
599A ASP* 4.0 18.6 - - + +
603A VAL* 3.7 31.7 - - + +
606A LYS* 5.4 2.3 + - - -
607A TYR* 4.4 6.1 + - - -
692A TYR* 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU 5.1 0.6 + - - -
470A MET 3.3 0.2 - - - -
471A TYR* 1.3 74.9 - - - +
473A LEU* 1.3 66.3 + - - +
475A HIS* 3.3 8.0 + - - +
476A ASN* 2.9 27.1 + - - +
594A PRO 5.6 0.2 - - - -
596A ASP* 4.2 16.3 + - - -
599A ASP* 3.9 15.7 + - - -
1F NAG 2.8 44.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU 5.4 0.2 + - - -
470A MET* 3.3 15.3 + - + +
472A SER* 1.3 78.7 - - - +
474A VAL* 1.3 57.8 + - - +
476A ASN* 3.9 4.2 - - + +
477A LEU* 2.9 35.8 + - + +
583A MET* 4.2 34.1 - - + -
586A GLU* 3.6 34.8 - - + -
587A LEU* 4.2 30.1 - - + -
594A PRO* 3.7 25.3 + - + +
1F NAG 3.9 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A VAL* 4.2 20.9 - - + -
466A CYS* 4.6 2.9 - - - -
470A MET 3.0 21.5 + - - +
471A TYR 3.6 3.4 - - - +
473A LEU* 1.3 73.8 - - - +
475A HIS* 1.3 67.9 + - - +
477A LEU* 3.4 4.1 + - - +
478A THR* 3.0 31.8 + - + +
497A TRP* 3.5 31.9 - - + -
512A ILE* 4.0 11.7 - - + -
579A VAL* 5.9 2.0 - - + -
583A MET* 3.5 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A TYR* 2.9 34.0 + + + +
472A SER* 3.3 7.9 + - - +
474A VAL* 1.3 77.9 - - + +
476A ASN* 1.3 67.1 + - - +
478A THR* 3.2 7.1 + - - -
479A LYS* 3.2 34.7 + - - +
494A TYR* 3.7 24.2 + + + -
497A TRP* 4.7 0.4 - + - -
509A MET* 4.1 30.6 - - + +
510A PRO* 4.0 20.9 + - + +
512A ILE* 3.8 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A SER* 2.9 17.8 + - - +
473A LEU* 4.0 4.5 - - + +
475A HIS* 1.3 77.2 - - - +
477A LEU* 1.3 67.7 + - - +
479A LYS* 3.5 22.3 + - - +
480A GLU* 3.6 18.9 + - - +
1F NAG 1.5 65.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 4.0 31.9 - - + -
62A LEU* 5.0 1.3 - - + -
473A LEU* 2.9 25.0 + - + +
474A VAL* 4.0 3.6 - - - +
476A ASN* 1.3 77.8 - - - +
478A THR* 1.3 60.0 + - + +
480A GLU* 3.1 22.2 + - + +
481A LEU* 3.4 28.5 + - + +
578A GLN 4.0 4.0 - - - +
579A VAL* 3.5 33.9 - - + +
582A GLY* 3.7 6.3 - - - -
583A MET* 3.6 25.1 - - + +
586A GLU* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A LEU* 4.0 9.6 - - + -
474A VAL* 3.0 28.3 + - + +
475A HIS 3.2 7.3 + - - -
477A LEU* 1.3 75.6 - - + +
479A LYS* 1.3 62.8 + - - +
480A GLU 3.1 0.2 - - - -
481A LEU* 3.3 21.3 + - - +
493A LEU* 3.4 23.0 + - + +
494A TYR* 3.1 43.9 + - - +
497A TRP* 3.8 21.0 - - + -
579A VAL* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A HIS* 3.2 23.6 + - - +
476A ASN* 3.7 16.0 + - - +
478A THR* 1.3 76.6 - - - +
480A GLU* 1.3 69.0 + - - +
481A LEU 3.4 0.2 - - - -
492A SER* 3.5 19.3 - - - +
494A TYR* 3.6 53.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 5.8 2.2 - - + +
476A ASN 3.6 11.7 - - - +
477A LEU* 3.1 15.7 + - + +
479A LYS* 1.3 89.0 - - - +
481A LEU* 1.3 65.5 + - + +
482A LYS* 4.3 1.2 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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