Contacts of the strand formed by residues 277 - 283 (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 LYS 277 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY* 4.1 10.3 - - - -
270A ILE 3.2 7.0 - - - +
271A THR* 3.5 20.2 - - + +
275A GLY 3.6 5.0 + - - +
276A GLU* 1.3 76.6 - - - +
278A LYS* 1.3 72.6 + - - +
279A TYR* 3.3 27.8 + - + +
306A GLU* 2.9 23.6 + - - +
417A ASP* 2.6 31.8 + - - -
418A ALA* 5.1 3.8 - - - +
429A GLU* 4.2 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY* 3.4 2.1 - - - -
270A ILE* 2.8 38.4 + - + +
276A GLU* 2.9 24.4 + - - +
277A LYS* 1.3 77.6 + - - +
279A TYR* 1.3 68.4 + - - +
280A LEU* 4.8 4.0 - - + -
429A GLU* 2.7 40.6 + - + +
541A PHE* 3.6 40.4 - - + +
544A ILE* 3.5 25.1 - - + +
545A ASP* 3.1 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A VAL* 4.5 0.9 - - + -
268A LEU 3.3 14.6 - - - -
269A GLY* 3.7 7.4 - - - -
277A LYS* 3.3 25.7 + - + +
278A LYS* 1.3 76.8 - - - +
280A LEU* 1.3 65.0 + - - +
308A VAL* 3.6 16.2 - - + -
417A ASP* 2.6 39.8 + - - -
419A ALA* 3.8 9.4 - - + +
426A VAL* 3.7 30.7 - - + -
427A PRO* 3.4 33.3 + - + +
428A ILE* 3.7 15.1 - - + -
429A GLU* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.4 0.9 - - - +
267A VAL* 3.4 4.3 - - - +
268A LEU* 2.9 46.3 + - + +
270A ILE* 3.8 27.4 - - + -
278A LYS* 4.8 6.7 - - + -
279A TYR* 1.3 82.9 - - - +
281A ALA* 1.3 60.7 + - - +
428A ILE* 4.4 4.0 - - - -
430A GLY* 3.5 16.8 - - - +
432A ILE* 4.2 15.3 - - + -
512A PHE* 5.9 0.7 - - + -
537A LEU* 3.8 33.0 - - + +
540A MET* 4.9 7.2 - - + -
541A PHE* 6.0 1.8 - - + +
544A ILE* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A MET* 3.8 26.0 - - + -
266A LEU* 3.2 10.8 - - - +
267A VAL* 4.6 4.9 - - + -
280A LEU* 1.3 74.6 - - - +
282A ALA* 1.3 61.2 + - - +
313A ALA* 5.3 0.2 - - + -
315A MET* 4.7 4.5 - - - -
428A ILE* 4.1 25.9 - - + +
430A GLY 2.9 7.6 + - - +
431A ILE* 3.3 4.9 - - + -
432A ILE* 2.8 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS 4.0 0.2 - - - +
265A MET* 3.2 6.0 - - - +
266A LEU* 2.9 57.9 + - + +
281A ALA* 1.3 74.9 - - - +
283A ALA* 1.3 60.3 - - - +
284A PHE* 3.8 21.1 + - + -
290A LYS* 4.2 2.8 - - - -
293A LEU* 4.6 2.0 - - + -
432A ILE* 3.1 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS 3.4 19.7 - - - +
265A MET* 3.7 13.3 - - + +
282A ALA* 1.3 71.4 - - - +
284A PHE* 1.3 69.7 + - - +
432A ILE 2.8 9.1 + - - -
433A PHE* 3.6 21.7 - - + -
434A GLY 3.3 13.7 + - - -
460A MET* 3.7 5.5 - - - +
480A PHE 3.5 22.0 - - - +
481A ALA* 4.0 2.5 - - + -
----------------------------------------------------------
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