Contacts of the strand formed by residues 459 - 464 (chain A) in PDB entry 7ACN
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 THR 459 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PHE* 3.3 18.7 - - - -
430A ARG* 3.9 5.8 - - - +
439A ASN* 2.8 22.8 + - - +
441A ILE* 3.8 31.6 - - + -
448A ASN 5.8 0.2 - - - +
451A GLY* 5.5 2.5 + - - -
453A ASN* 5.6 2.0 - - + +
454A ASP* 2.9 30.5 + - - +
456A ASN* 3.1 22.6 + - - +
457A PRO 3.3 0.4 - - - +
458A GLU* 1.3 77.8 - - - +
460A HIS* 1.3 63.5 + - - +
461A ALA* 3.6 5.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PRO* 4.0 13.2 - - + -
326A PHE* 3.8 23.0 - + - -
346A TRP* 3.6 32.7 - + - -
347A PRO* 3.7 14.9 - - + +
438A LYS* 3.8 20.6 + - + +
439A ASN 2.7 14.9 + - - +
440A THR* 3.4 14.1 - - - +
441A ILE 3.0 24.3 + - - +
458A GLU* 2.9 50.5 + - - -
459A THR* 1.3 73.0 - - - +
461A ALA* 1.3 58.4 + - - +
462A PHE* 3.9 8.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PRO* 3.4 14.0 + - - +
441A ILE* 3.4 22.9 - - + -
443A THR* 5.0 6.1 - - + +
448A ASN* 3.0 41.4 + - + +
453A ASN* 3.8 18.8 - - - +
459A THR* 3.6 7.8 + - + +
460A HIS* 1.3 72.8 - - - +
462A PHE* 1.3 60.4 + - - +
463A VAL* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.6 32.3 - - + -
323A ASN 3.2 8.3 - - - -
324A GLY 3.5 29.6 - - - -
325A PRO* 3.8 14.6 - - + -
332A HIS* 4.9 0.7 - + - -
337A VAL* 4.3 13.9 - - + -
346A TRP* 3.9 30.1 - + + -
440A THR* 3.8 31.9 - - + -
441A ILE 3.1 9.9 + - - -
442A VAL* 3.3 8.9 - - + +
443A THR* 2.8 27.3 + - - +
460A HIS* 3.9 16.2 - - + -
461A ALA* 1.3 73.1 - - - +
463A VAL* 1.3 60.6 + - - +
478A LEU* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 5.0 0.2 - - - -
222A LEU* 3.9 15.6 - - + +
259A MET* 4.4 6.1 - - + -
322A ILE* 3.4 1.0 - - - -
323A ASN* 2.9 52.7 + - + +
328A PRO* 5.0 1.6 - - + -
443A THR* 3.3 20.9 - - - +
445A TYR 3.8 20.2 - - - +
446A ASN 3.8 24.9 - - - +
447A ARG 4.0 10.5 - - - +
448A ASN* 4.2 14.1 - - + +
461A ALA* 5.9 0.4 - - + -
462A PHE* 1.3 72.1 - - - +
464A THR* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 2.7 33.6 + - - -
222A LEU* 4.0 9.2 - - - -
321A HIS 2.8 20.4 + - - -
322A ILE* 4.0 18.7 - - + +
442A VAL* 4.7 7.2 - - + -
443A THR 2.9 9.1 + - - +
444A SER* 3.2 8.7 - - - -
463A VAL* 1.3 75.9 - - - +
465A SER* 1.3 64.4 + - - +
468A ILE* 3.5 27.1 - - + +
469A VAL* 3.6 27.1 - - + +
472A LEU* 5.0 0.2 - - + -
----------------------------------------------------------
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