Contacts of the strand formed by residues 423 - 431 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PRO* 3.9 11.3 - - - +
422B ASP* 1.3 94.7 - - + +
424B ILE* 1.3 72.4 + - - +
465B ASP* 4.3 2.8 - - - +
726B GLU* 4.2 30.7 - - + +
727B VAL 3.4 7.9 - - - +
728B GLY* 5.3 3.4 - - - -
729B VAL* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B PRO* 4.8 7.9 - - + -
423B MET* 1.3 85.1 - - - +
425B SER* 1.3 59.5 + - - +
426B VAL* 3.8 4.4 + - + -
465B ASP* 3.4 21.3 - - + +
466B ILE* 3.6 29.6 - - + -
518B HIS* 4.9 0.9 - - - +
550B PHE* 3.7 32.3 - - + -
555B PHE* 3.9 15.3 - - + -
725B PHE 3.8 0.3 - - - +
726B GLU* 3.6 4.4 - - - -
727B VAL* 2.8 48.4 + - + +
729B VAL* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ILE* 1.3 72.3 - - - +
426B VAL* 1.3 60.8 + - - +
462B ILE* 6.0 1.4 - - - +
463B PRO 4.3 2.9 + - - -
464B HIS* 3.5 24.1 + - - -
465B ASP* 2.9 48.4 + - - +
466B ILE 3.2 7.4 + - - -
724B THR* 6.4 0.4 - - - -
725B PHE 3.3 10.3 - - - -
726B GLU* 4.6 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ILE* 4.1 8.5 - - + +
425B SER* 1.3 78.3 - - - +
427B PHE* 1.3 64.2 + - - +
428B ILE* 3.3 25.8 - - + -
464B HIS* 4.8 2.7 - - - -
466B ILE* 3.6 26.7 - - + +
468B VAL* 4.2 9.0 - - + -
555B PHE* 4.6 7.0 - - + -
557B PHE* 4.1 15.7 - - + -
603B PHE* 5.1 2.9 - - + -
723B GLY 3.9 0.5 - - - +
724B THR* 3.3 5.9 - - - -
725B PHE* 3.0 34.6 + - + +
727B VAL* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B VAL* 1.3 71.5 - - - +
428B ILE* 1.3 59.3 + - - +
429B GLY* 3.5 26.2 - - - -
445B TRP* 3.1 37.2 - + - -
446B PHE* 3.4 20.4 - - - -
448B SER* 4.2 3.1 - - - -
464B HIS* 3.8 12.5 - + + +
466B ILE 3.0 9.2 + - - +
467B TYR* 3.7 28.0 - + + -
468B VAL* 2.7 36.2 + - - +
469B PHE* 3.4 26.9 - + - -
722B PHE* 3.8 16.8 - - + -
723B GLY 3.6 3.1 - - - -
724B THR* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B VAL* 3.3 28.5 - - + -
427B PHE* 1.3 73.1 - - - +
429B GLY* 1.3 59.3 + - - +
468B VAL* 3.4 5.4 - - + -
557B PHE* 3.8 13.5 - - + -
603B PHE* 3.8 28.9 - - + -
605B PHE* 3.4 51.4 - - + -
692B ILE* 3.1 26.5 - - + +
722B PHE* 3.6 0.2 - - - -
723B GLY 2.8 41.6 + - - +
725B PHE* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B PHE* 3.5 20.3 - - - -
428B ILE* 1.3 76.1 - - - +
430B THR* 1.3 55.0 + - - -
445B TRP* 3.4 13.1 - - - -
468B VAL 3.0 9.3 + - - +
469B PHE* 3.6 2.4 - - - -
470B GLY* 2.7 32.9 + - - +
605B PHE* 4.4 1.6 - - - -
721B VAL 3.4 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B GLY* 1.3 74.1 - - - -
431B TRP* 1.3 63.6 + - - +
445B TRP* 3.6 1.3 - - - -
470B GLY 3.1 4.5 - - - -
472B GLN* 3.5 9.2 + - - -
605B PHE* 4.2 7.6 - - - -
606B GLY* 3.2 32.0 - - - +
690B ASP* 4.7 5.6 - - + +
691B ARG 4.0 14.8 - - - +
692B ILE* 4.0 15.9 - - + -
719B SER 4.8 0.2 - - - +
721B VAL* 2.8 62.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B THR* 1.3 78.4 + - - +
432B ASN* 1.3 81.1 + - - +
433B MET* 3.6 30.4 + - + -
438B PRO* 3.9 21.5 - - + -
439B PRO* 3.9 9.4 - - + -
442B VAL* 4.7 7.0 - - + -
445B TRP* 3.7 29.4 - + + -
470B GLY 3.0 6.1 + - - -
471B THR* 3.0 23.9 - - + +
472B GLN* 2.9 14.0 + - - +
690B ASP* 5.5 1.6 - - - -
713B ILE* 3.7 23.6 - - + -
715B THR* 3.3 26.7 - - - -
716B SER* 3.6 10.7 - - - -
718B HIS* 3.5 17.1 + - + -
719B SER 4.0 4.3 - - - -
720B PRO* 3.5 37.0 - - + +
----------------------------------------------------------
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