Contacts of the strand formed by residues 523 - 531 (chain A) in PDB entry 3V4V
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 ASN 523 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A LEU 3.9 1.4 - - - +
469A PHE* 2.9 37.2 + - - +
515A ILE* 3.2 31.1 - - - +
516A GLN 3.1 23.4 + - - +
517A VAL* 4.1 19.0 - - + +
518A SER 5.1 1.1 - - - +
521A GLU* 3.9 9.0 + - - +
522A ALA* 1.3 73.3 - - - +
524A CYS* 1.3 71.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A THR* 3.8 9.9 - - + -
467A LEU 3.0 7.4 - - - +
468A CYS* 2.0 63.7 - - - -
469A PHE 4.2 0.4 - - - -
515A ILE* 5.4 0.2 - - - -
522A ALA* 4.2 6.2 + - - -
523A ASN* 1.3 87.8 + - - +
525A ARG* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU 4.1 0.7 - - - +
466A THR* 3.8 1.1 - - - -
467A LEU* 3.2 32.5 + - + +
469A PHE* 6.2 1.5 - - + -
484A TYR* 3.1 37.5 + - + +
513A GLY* 5.1 0.2 - - - -
514A SER 2.6 37.8 + - - +
515A ILE* 3.6 28.6 - - + +
524A CYS* 1.3 75.0 - - - +
526A THR* 1.3 63.4 + - - +
527A HIS* 4.3 11.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASP* 4.1 18.8 - - + +
465A LEU 3.3 22.0 - - - +
466A THR* 2.8 29.6 + - - +
524A CYS 5.4 0.2 - - - -
525A ARG* 1.3 72.2 - - - +
527A HIS* 1.3 79.3 + - - +
528A GLN* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 2.9 37.6 + - - +
484A TYR* 3.0 43.7 + + - -
486A MET* 4.7 11.5 - - - -
502A PHE* 4.3 17.3 - - + -
511A ILE* 3.4 41.1 - - + +
512A THR 4.6 2.7 - - - -
525A ARG* 4.2 11.8 + - + +
526A THR* 1.3 91.6 - - - +
528A GLN* 1.3 60.9 + - - +
529A ALA 4.0 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A CYS* 4.6 2.4 - - - +
462A CYS* 4.2 16.9 - - + -
463A ILE 3.4 10.5 - - - +
464A ASP* 4.2 14.1 - - - +
501A TYR 4.2 0.9 - - - +
502A PHE* 3.4 16.4 - - - +
503A SER* 5.0 6.1 + - - +
526A THR* 4.3 0.9 - - + -
527A HIS* 1.3 73.0 - - - +
529A ALA* 1.3 61.2 + - - +
530A PHE* 3.3 40.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A CYS* 3.5 3.1 - - - -
463A ILE* 2.9 48.0 + - + +
465A LEU* 4.5 5.4 - - + -
488A LEU* 3.7 36.8 - - + -
500A PHE* 3.8 8.4 - - + -
501A TYR 3.4 4.5 - - - -
502A PHE* 4.2 5.4 - - + -
527A HIS 4.0 0.4 + - - -
528A GLN* 1.3 72.0 - - - +
530A PHE* 1.3 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A CYS* 3.4 41.3 - - + -
455A GLU* 3.8 28.9 - - + +
460A SER* 4.7 2.0 - - - +
461A VAL 4.0 4.0 - - - +
462A CYS* 4.1 0.7 - - + -
500A PHE* 3.1 12.4 - - - -
501A TYR* 3.2 44.9 + + + -
502A PHE 4.3 13.0 - - - -
503A SER* 3.6 31.2 - - - -
528A GLN* 3.3 41.1 - - + -
529A ALA* 1.3 73.0 - - - +
531A MET* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 531 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A VAL* 6.4 1.3 - - - -
448A ARG* 4.1 21.1 - - + +
455A GLU* 4.8 0.2 - - - +
460A SER* 4.4 8.7 + - - -
461A VAL* 3.1 43.4 + - + +
499A ARG* 3.8 14.8 - - + +
500A PHE* 3.5 27.4 - - + -
501A TYR* 3.7 10.9 + - - -
529A ALA 3.8 0.2 + - - -
530A PHE* 1.3 73.8 - - - +
532A ARG* 1.3 71.5 + - - +
533A LYS* 3.4 7.1 + - - +
535A VAL* 3.7 38.6 - - + -
537A ASP 5.9 0.4 - - - +
585A PHE* 4.4 20.2 - - + -
----------------------------------------------------------
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