Contacts of the strand formed by residues 463 - 471 (chain H) in PDB entry 1P8J
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 463 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461H ILE* 3.2 0.6 + - - -
462H GLY* 1.3 72.7 - - - -
464H ARG* 1.3 65.8 + - + +
552H GLU* 3.6 2.2 - - - +
553H ASN* 2.9 53.6 + - - +
554H THR 4.8 0.8 - - - -
555H SER 2.8 29.3 + - - -
556H GLU* 4.6 10.9 + - - +
557H ALA 5.0 1.3 + - - +
559H ASN 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 464 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460H ASP 4.8 1.2 - - - +
461H ILE 3.1 13.1 + - - +
463H LYS* 1.3 89.9 + - + +
465H LEU* 1.3 65.4 + - - +
466H GLU* 3.7 27.2 + - - +
550H GLU* 4.0 28.0 + - - +
551H ILE 3.4 8.5 + - - +
552H GLU* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 465 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459H LYS* 3.9 28.9 - - + +
460H ASP 4.1 13.5 - - - +
461H ILE* 4.0 19.1 - - + +
464H ARG* 1.3 82.3 + - - +
466H GLU* 1.3 77.7 + - - +
467H VAL* 4.1 10.5 - - + -
549H LEU 3.8 0.5 - - - +
550H GLU* 3.6 3.5 - - - +
551H ILE* 2.7 47.2 + - + +
563H LEU* 3.8 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459H LYS* 5.3 2.1 - - - +
464H ARG* 3.7 25.5 + - - +
465H LEU* 1.3 84.3 - - - +
467H VAL* 1.3 66.3 + - - +
468H ARG* 2.7 43.9 + - + +
548H VAL* 3.6 18.4 - - + +
549H LEU 3.3 3.1 - - - +
550H GLU* 3.8 14.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 467 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454H ILE* 3.8 29.4 - - + +
455H LEU* 4.1 12.1 - - + -
459H LYS* 4.1 21.1 - - + +
465H LEU* 4.1 21.1 - - + -
466H GLU* 1.3 79.0 - - - +
468H ARG* 1.3 66.7 + - - +
469H LYS* 5.6 0.2 - - - +
547H TRP 3.7 1.0 - - - +
548H VAL* 3.3 3.5 - - - -
549H LEU* 2.8 51.0 + - + +
563H LEU* 4.2 14.4 - - + -
566H PHE* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 468 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466H GLU* 2.7 50.0 + - + +
467H VAL* 1.3 79.7 - - - +
469H LYS* 1.3 70.4 + - - +
546H GLU* 2.9 41.5 + - - +
547H TRP 3.3 5.2 - - - +
548H VAL* 3.8 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 469 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H VAL* 5.3 2.2 - - + -
453H GLU 5.0 3.1 - - - +
454H ILE* 3.6 60.6 + - + +
456H VAL* 5.1 10.3 - - - +
468H ARG* 1.3 79.9 + - - +
470H ALA* 1.3 80.1 + - - +
471H VAL* 3.5 6.5 + - + +
546H GLU* 4.2 5.5 - - - +
547H TRP* 2.8 39.1 + - + +
566H PHE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H LYS* 1.3 89.8 - - - +
471H VAL* 1.3 61.0 + - - +
472H THR* 4.3 3.7 + - + +
545H GLY 3.6 6.7 - - - +
546H GLU* 4.2 9.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 471 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452H VAL* 4.4 16.8 - - + -
454H ILE* 4.4 6.3 - - + -
469H LYS* 3.8 17.7 - - + +
470H ALA* 1.3 78.6 - - - +
472H THR* 1.3 60.2 + - - +
473H ALA* 3.3 23.8 - - + +
543H PRO 4.5 1.6 - - - +
544H ALA* 3.4 4.3 - - - +
545H GLY* 2.7 42.3 + - - +
547H TRP* 3.5 26.5 - - + +
568H LEU* 4.2 11.0 - - + -
570H LEU* 4.3 16.6 - - + -
----------------------------------------------------------
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