Contacts of the strand formed by residues 467 - 473 (chain A) in PDB entry 3SV1
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 ILE 467 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LEU* 5.1 5.6 - - + -
402A VAL* 4.6 10.8 - - + -
406A LYS* 6.4 2.5 - - + -
462A ALA 3.7 4.7 - - - +
463A ASP* 3.7 0.7 - - - -
464A ILE* 3.0 44.8 + - + +
465A GLY* 2.6 14.5 + - - +
466A ASN* 1.3 99.9 - - - +
468A VAL* 1.3 61.3 + - - +
469A VAL* 4.3 8.1 - - + -
504A VAL* 4.0 19.3 - - + -
505A PHE 3.3 14.6 - - - +
506A GLU* 5.4 3.4 - - + -
510A ALA* 3.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 5.5 1.6 - - + -
461A ILE* 5.4 1.1 - - + -
462A ALA 3.3 17.5 - - - +
463A ASP* 4.5 1.1 - - + -
467A ILE* 1.3 72.7 - - - +
469A VAL* 1.3 64.5 + - - +
470A LEU* 5.4 1.6 - - + -
503A HIS 3.7 1.6 - - - +
505A PHE* 2.9 49.3 + - + +
507A SER* 4.5 8.1 - - - -
510A ALA* 3.6 33.9 - - + +
513A ILE* 4.0 32.8 - - + -
514A ALA* 4.4 9.0 - - + +
517A ILE* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ALA* 4.6 15.0 - - + +
401A ALA* 4.8 0.7 - - + -
402A VAL* 3.4 30.3 - - + -
461A ILE* 3.1 4.3 - - - +
462A ALA* 2.9 36.3 + - + +
464A ILE* 5.3 3.6 - - + -
467A ILE* 4.0 6.0 + - + +
468A VAL* 1.3 83.6 - - - +
470A LEU* 1.3 62.5 + - - +
471A MET* 4.6 12.2 - - + +
502A CYS* 4.1 22.2 - - + -
503A HIS 3.2 13.2 - - - +
504A VAL* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 6.3 0.4 - - + -
439A ILE* 3.9 29.4 - - + +
453A HIS* 6.1 3.1 - - + +
458A ILE* 4.2 20.0 - - + -
460A TYR 3.3 5.4 - - - -
461A ILE* 3.4 25.1 - - + -
468A VAL* 5.0 2.2 - - + +
469A VAL* 1.3 75.9 - - - +
471A MET* 1.3 61.9 + - - +
472A ALA* 5.9 1.8 - - + +
501A ILE 3.8 0.7 - - - +
502A CYS* 3.5 1.2 - - - -
503A HIS* 2.9 46.7 + - + +
505A PHE* 3.4 36.3 - - + -
517A ILE* 4.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 5.8 0.4 - - - -
394A ARG* 4.0 22.4 - - - +
397A GLN* 4.1 10.3 - - + +
398A ALA* 3.7 37.0 - - + +
458A ILE* 3.8 2.8 - - - -
459A SER* 3.0 35.6 + - - +
460A TYR* 3.0 30.7 + - + +
469A VAL* 4.6 10.5 - - + +
470A LEU* 1.3 76.1 - - - +
472A ALA* 1.3 59.4 + - - +
500A MET* 4.8 12.3 - - + +
501A ILE 3.2 12.8 - - - +
502A CYS* 3.6 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A HIS* 3.3 34.8 - - + +
457A THR* 2.8 26.5 - - - +
458A ILE* 3.7 8.3 - - + -
459A SER 4.4 0.4 - - - +
470A LEU* 5.6 2.6 - - + +
471A MET* 1.3 75.8 - - - +
473A ARG* 1.3 60.8 + - - +
474A ARG 3.3 0.2 + - - -
500A MET* 3.7 9.5 - - - -
501A ILE* 3.2 32.0 + - + +
503A HIS* 5.9 2.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A HIS* 4.9 4.7 - - - -
457A THR* 2.7 28.0 + - + +
472A ALA* 1.3 70.5 - - - +
474A ARG* 1.3 61.5 + - - +
475A ARG* 3.1 13.2 + - + +
499A LYS 4.6 0.7 - - - -
500A MET* 3.5 20.7 - - + +
501A ILE* 4.9 0.4 - - - -
762D TYR* 4.0 12.1 - - + +
766D GLU* 4.5 13.9 - - - +
----------------------------------------------------------
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