Contacts of the strand formed by residues 469 - 478 (chain A) in PDB entry 1LB6
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 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A HIS* 3.3 11.6 + - - -
457A LEU* 3.7 33.0 - - + +
458A ALA* 3.9 10.9 - - - +
467A ASN* 2.9 26.5 + - - +
468A PRO* 1.3 79.1 - - + +
470A GLY* 1.3 58.9 + - - +
606B GLU* 3.5 38.4 - - + +
607B ILE 3.4 4.3 - - - +
608B ASP* 2.4 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PHE* 3.9 7.0 - - - -
411A VAL 3.3 12.8 - - - -
412A HIS* 3.5 17.6 - - - -
458A ALA* 4.2 3.4 - - - -
469A LYS* 1.3 75.3 - - - +
471A PHE* 1.3 62.0 + - - -
605B GLN 3.9 0.3 - - - +
606B GLU* 3.3 5.0 - - - +
607B ILE* 2.9 33.6 + - - -
609B PHE* 4.1 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PHE* 3.3 4.6 - - - -
411A VAL* 2.9 29.8 + - + +
450A MET* 3.5 27.5 - - + +
451A ASP 3.8 16.8 - - - -
453A LYS* 4.0 22.2 - - + -
456A LEU* 3.5 28.0 - - + -
458A ALA* 4.3 6.5 - - + +
459A PHE* 3.4 32.5 - + + -
470A GLY* 1.3 72.4 - - - -
472A GLY* 1.3 58.6 + - - +
604B PRO* 3.4 35.0 - - + -
605B GLN* 3.5 30.5 - - - -
606B GLU* 3.6 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU 3.4 7.9 - - - -
410A PHE* 3.0 18.5 - - - -
450A MET* 4.1 9.6 - - - -
471A PHE* 1.3 78.0 - - - +
473A TYR* 1.3 69.9 + - - -
604B PRO* 3.2 4.7 - - - +
605B GLN* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A SER* 3.3 1.6 - - - -
409A LEU 2.9 37.6 + - - +
410A PHE* 3.7 3.5 - - - -
432A LEU* 4.1 9.4 - - + -
448A GLU* 3.5 26.0 + - + +
449A ILE 3.5 11.6 + - - -
450A MET* 3.3 41.1 - - + +
472A GLY* 1.3 74.8 - - - -
474A VAL* 1.3 65.0 + - - +
475A THR 3.4 1.3 + - - +
476A PHE* 3.6 36.7 + + + +
602B GLN* 3.4 40.4 + - + +
603B GLU 4.3 0.9 - - - -
604B PRO* 3.6 33.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
396A GLN* 4.2 4.4 - - - +
402A ARG* 6.1 1.3 - - + -
403A CYS* 3.6 35.0 - - + -
406A TYR* 3.9 5.9 - - - +
407A ILE 3.5 3.1 - - - +
408A SER* 2.6 35.2 + - - +
410A PHE* 3.7 5.3 - - + -
472A GLY 4.3 0.4 + - - -
473A TYR* 1.3 71.4 - - - +
475A THR* 1.3 61.8 + - + +
602B GLN* 5.4 0.2 + - - -
605B GLN* 3.2 27.7 + - - +
607B ILE* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG 4.8 4.0 - - - +
403A CYS* 3.9 15.9 - - + -
406A TYR* 3.6 46.6 - - + -
473A TYR* 4.3 0.4 - - - -
474A VAL* 1.3 83.0 - - + +
476A PHE* 1.3 61.9 + - - +
477A MET 3.4 2.0 - - - -
602B GLN* 2.5 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 3.0 16.8 + - + +
409A LEU* 3.9 26.7 - - + +
432A LEU* 3.4 38.6 - - + -
434A ILE* 3.6 38.4 - - + -
446A HIS* 2.8 43.4 - - - -
447A GLU* 4.1 2.7 - - - -
448A GLU* 3.6 25.7 - - + +
473A TYR* 3.6 33.1 + + - +
474A VAL 3.5 1.2 - - - -
475A THR* 1.3 77.2 - - - +
477A MET* 1.3 61.9 + - + +
602B GLN* 4.1 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A TYR* 3.6 5.4 - - - -
407A ILE* 2.8 39.3 + - + +
434A ILE* 3.8 28.3 - - + -
446A HIS* 3.5 37.5 - - + +
475A THR 3.4 0.6 - - - -
476A PHE* 1.3 89.8 - - + +
478A HIS* 1.3 73.9 + - - +
481A ALA* 3.3 21.1 - - + -
482A LEU* 4.7 4.9 - - + +
485A ARG* 4.6 0.9 - - - +
487A PHE* 3.3 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA 3.7 7.4 - - - -
405A ASN* 3.6 31.4 + - + +
406A TYR* 3.5 37.9 + + + +
407A ILE* 5.1 0.4 - - - +
446A HIS* 5.4 0.2 + - - -
477A MET* 1.3 76.4 - - - +
479A LEU* 1.3 70.9 + - - +
480A GLU* 2.9 45.3 + - + +
481A ALA* 3.0 26.1 + - + +
482A LEU* 4.2 1.6 + - - +
----------------------------------------------------------
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