Contacts of the helix formed by residues 489 - 499 (chain A) in PDB entry 1NHX
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 ASN 489 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 2.8 30.7 + - - +
101A ASP 3.1 7.8 + - - +
102A THR 3.1 9.5 + - - -
103A VAL* 3.8 2.4 + - - +
104A PRO* 3.5 16.1 - - - +
488A TYR* 1.3 75.9 - - - +
490A PHE* 1.3 59.5 + - - +
491A GLY* 2.7 31.5 + - - -
492A LYS* 3.0 34.3 + - + +
493A TYR 2.9 22.7 + - - -
603A ASP* 2.7 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 4.0 5.7 - - - +
113A LEU* 3.8 30.2 + - + -
458A ALA* 4.3 5.8 - - + -
479A PRO* 3.5 28.5 - - + -
480A PHE* 4.1 1.8 - + - -
486A PHE* 3.2 45.1 - + + -
488A TYR 3.2 5.6 + - - -
489A ASN* 1.3 72.6 + - - +
491A GLY* 1.3 56.3 + - - +
493A TYR* 3.1 23.7 + + - -
494A LEU* 2.9 59.9 + - + +
595A TYR* 5.5 0.7 - + - -
596A LEU* 4.1 11.0 - - + -
600A VAL* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 4.2 1.0 - - - +
489A ASN* 2.7 16.9 + - - -
490A PHE* 1.3 73.0 - - - +
492A LYS* 1.3 55.6 + - - -
494A LEU* 3.4 5.7 + - - +
495A ALA* 3.1 22.9 + - - +
600A VAL* 3.5 19.2 - - - +
603A ASP* 3.2 23.8 - - - -
605A PRO* 3.5 11.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 4.6 15.8 - - - +
101A ASP* 4.0 20.1 + - - +
256A LYS* 4.7 19.7 + - - +
488A TYR* 3.7 17.0 - - + -
489A ASN* 3.0 31.4 + - + +
491A GLY* 1.3 73.1 - - - +
493A TYR* 1.3 59.1 + - - +
495A ALA* 3.5 9.4 - - - +
496A HIS* 2.9 28.4 + - - +
603A ASP* 5.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 5.3 3.1 - - - -
261A LEU* 5.8 0.4 - - + -
262A ALA 5.1 0.9 - - - -
263A GLU* 2.5 40.1 + - - -
480A PHE* 3.3 39.5 - + - +
482A MET* 3.8 13.2 - - + +
486A PHE* 3.7 25.6 - + + -
488A TYR* 3.2 37.4 - + + +
489A ASN 2.9 10.8 + - - +
490A PHE* 3.1 26.6 + + - +
492A LYS* 1.3 77.8 - - - +
494A LEU* 1.3 60.4 + - - +
496A HIS* 3.2 4.7 + + - +
497A TRP* 3.0 54.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A VAL* 3.9 12.5 - - + +
458A ALA* 3.8 15.0 - - + -
480A PHE* 3.6 31.4 - - + -
490A PHE* 2.9 45.7 + - + +
491A GLY* 3.5 9.0 - - - +
493A TYR* 1.3 74.5 - - - +
495A ALA* 1.3 59.7 + - - +
497A TRP* 3.3 5.1 + - - +
498A LEU* 2.9 32.9 + - - +
596A LEU* 5.1 0.4 - - + -
600A VAL* 4.6 0.4 - - + -
604A LEU* 4.0 26.0 - - + -
605A PRO* 3.9 15.9 - - + -
608A ILE* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS* 6.3 0.2 - - - +
491A GLY 3.1 14.4 + - - +
492A LYS* 3.5 13.0 - - - +
493A TYR 3.4 0.2 - - - -
494A LEU* 1.3 76.0 - - - +
496A HIS* 1.3 57.1 + - - +
498A LEU* 3.4 7.5 + - - +
499A SER* 3.0 28.8 + - - -
605A PRO* 3.7 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER 5.6 0.4 - - - -
255A ALA* 3.9 2.7 - - + -
256A LYS* 3.6 45.4 + - + +
259A GLY* 4.0 16.4 - - - -
260A TRP 2.7 29.7 + - - -
261A LEU* 3.7 20.8 - - + +
488A TYR* 3.9 12.1 - - - +
492A LYS 2.9 14.5 + - - +
493A TYR* 3.4 9.9 - + - +
494A LEU 3.2 0.2 - - - -
495A ALA* 1.3 75.8 - - - +
497A TRP* 1.3 64.6 + + - +
499A SER* 2.7 28.7 + - - -
500A MET* 3.6 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.7 21.0 - - + +
263A GLU* 2.9 43.3 + - + -
265A MET* 3.9 18.6 - - + -
431A ILE* 4.0 15.7 - - + -
433A PHE* 4.4 8.1 - + - -
450A TRP* 2.9 58.5 + + - -
454A VAL* 3.8 20.4 - - + -
480A PHE* 3.6 26.9 - + - -
493A TYR* 3.0 44.3 + + - +
494A LEU* 3.6 7.9 - - - +
496A HIS* 1.3 76.9 - + - +
498A LEU* 1.3 61.8 + - - +
500A MET* 3.3 21.0 + - - +
511A ILE* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A TRP* 4.1 4.1 + - + +
451A GLN* 4.0 19.6 + - + -
454A VAL* 4.0 26.5 - - + -
494A LEU 2.9 21.7 + - - +
495A ALA* 3.7 5.8 - - - +
496A HIS 3.3 0.2 - - - -
497A TRP* 1.3 77.3 - - - +
499A SER* 1.3 60.9 + - - +
500A MET 3.1 1.8 + - - -
501A ALA* 3.2 20.1 + - - +
502A GLN* 3.7 8.1 + - - +
605A PRO* 3.6 30.5 - - + -
607A GLU* 3.5 50.2 - - + +
608A ILE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ALA 3.0 14.3 + - - -
496A HIS* 2.7 30.6 + - - -
498A LEU* 1.3 72.3 - - - +
500A MET* 1.3 64.3 + - - +
501A ALA 3.1 0.7 - - - -
502A GLN* 3.1 26.6 + - - +
503A HIS* 3.6 7.8 + - - +
----------------------------------------------------------
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