Contacts of the strand formed by residues 423 - 431 (chain A) in PDB entry 3NR8
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 423 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ASP* 1.3 91.8 + - + +
424A ILE* 1.3 70.9 + - - +
465A ASP* 4.4 2.1 - - - +
726A GLU* 3.4 37.5 - - + +
727A VAL 3.5 7.6 - - - +
728A GLY* 4.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 1.3 82.2 - - - +
425A SER* 1.3 60.0 + - - +
426A VAL* 3.7 12.3 + - + +
465A ASP* 3.2 22.2 - - + +
466A ILE* 4.0 21.8 - - + -
518A HIS* 4.8 2.9 - - + +
550A PHE* 4.0 31.4 - - + -
555A PHE* 3.7 20.9 - - + -
725A PHE 3.4 2.1 - - - +
726A GLU* 3.6 5.2 - - - -
727A VAL* 3.0 39.4 + - + +
729A VAL* 3.6 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 1.3 72.5 - - - +
426A VAL* 1.3 60.1 + - - +
427A PHE 4.2 0.2 - - - -
462A ILE* 5.5 1.6 + - - +
463A PRO 4.3 3.1 + - - -
464A HIS* 3.5 26.8 - - - +
465A ASP* 2.7 49.5 + - - +
466A ILE 3.2 8.5 + - - +
724A THR* 6.3 0.7 - - - -
725A PHE 3.3 8.3 - - - -
726A GLU* 4.8 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ILE* 3.9 27.1 - - + +
425A SER* 1.3 77.0 - - - +
427A PHE* 1.3 62.1 + - - +
428A ILE* 3.3 28.0 + - + -
464A HIS* 5.0 0.4 - - - -
466A ILE* 3.7 17.0 - - + +
468A VAL* 4.9 1.6 - - + -
555A PHE* 4.3 11.4 - - + -
557A PHE* 4.1 17.0 - - + -
603A PHE* 4.5 4.5 - - + -
723A GLY 3.7 1.6 - - - +
724A THR* 3.5 5.8 - - - -
725A PHE* 3.0 38.7 + - + +
727A VAL* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A SER 4.2 0.4 - - - -
426A VAL* 1.3 69.8 - - - +
428A ILE* 1.3 61.3 + - - +
429A GLY* 3.6 21.3 - - - -
445A TRP* 3.2 28.7 - + - -
446A PHE* 3.1 33.4 - - - -
448A SER* 4.3 3.6 - - - -
464A HIS* 3.7 20.8 - + + +
466A ILE 3.0 10.6 + - - +
467A TYR* 3.6 25.8 - + + -
468A VAL* 2.6 39.0 + - - +
469A PHE* 3.6 22.7 - + - -
722A PHE* 4.0 18.6 - - + -
723A GLY 3.7 3.4 - - - -
724A THR* 3.9 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A VAL* 3.3 29.6 - - + -
427A PHE* 1.3 78.4 - - - +
429A GLY* 1.3 60.2 + - - +
468A VAL* 3.6 5.2 - - + -
557A PHE* 3.9 12.3 - - + -
603A PHE* 3.5 42.8 - - + -
605A PHE* 3.6 31.9 - - + -
692A ILE* 3.3 30.3 - - + -
722A PHE* 3.7 0.7 - - - -
723A GLY 2.9 36.2 + - - +
725A PHE* 4.1 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PHE* 3.6 18.4 - - - -
428A ILE* 1.3 77.2 - - - +
430A THR* 1.3 62.1 + - - -
445A TRP* 3.6 10.3 - - - -
468A VAL 2.8 11.1 + - - +
469A PHE* 3.6 0.9 - - - -
470A GLY* 2.9 26.3 + - - +
605A PHE* 4.3 2.9 - - - -
692A ILE* 4.8 0.4 - - - -
721A VAL 3.4 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLY* 1.3 75.3 - - - -
431A TRP* 1.3 60.0 + - - +
445A TRP* 3.6 1.6 - - - -
470A GLY 3.3 4.7 - - - -
472A GLN* 3.4 7.4 + - - -
559A ASN* 4.1 0.9 + - - -
605A PHE* 4.2 8.7 - - - -
606A GLY* 3.1 32.9 - - - +
690A ASP* 4.4 12.2 - - + +
691A ARG 3.9 17.9 - - - +
692A ILE* 4.1 6.3 - - + -
719A SER 4.8 0.5 - - - +
720A PRO* 3.7 0.2 - - - +
721A VAL* 2.7 65.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR* 1.3 78.2 + - - +
432A ASN* 1.3 81.3 + - - +
433A MET* 3.6 24.8 + - + -
438A PRO* 3.9 23.1 - - + -
439A PRO* 3.9 7.9 - - + -
442A VAL* 4.5 9.6 - - + -
445A TRP* 3.9 30.0 - + + -
470A GLY 3.0 7.1 + - - -
471A THR* 3.0 29.3 - - + -
472A GLN* 3.0 5.5 + - - -
690A ASP* 5.5 1.3 - - - -
713A ILE* 3.5 24.0 - - + -
715A THR* 3.4 27.4 - - - -
716A SER* 3.6 11.4 - - - -
718A HIS* 3.1 20.5 + - + -
719A SER 4.0 2.7 - - - -
720A PRO* 3.5 35.1 - - + +
----------------------------------------------------------
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