Contacts of the strand formed by residues 499 - 506 (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 LYS 499 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLN* 3.3 35.7 - - + +
383A LEU 3.7 4.7 - - - +
384A LEU* 4.1 7.4 - - + -
473A ARG* 4.6 0.7 - - - -
474A ARG* 3.2 69.0 + - - +
498A TYR* 1.3 78.1 - - - +
500A MET* 1.3 58.3 + - - +
445B ASP* 3.4 26.3 + - - +
446B THR* 5.0 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLN* 3.0 22.6 - - - +
383A LEU* 3.0 31.5 + - + -
385A SER* 3.7 30.3 - - - +
394A ARG* 4.7 12.1 - - - +
459A SER* 3.9 17.3 - - - -
471A MET* 4.8 12.6 - - + -
472A ALA 3.7 10.1 - - - +
473A ARG* 3.5 32.5 - - + +
474A ARG* 4.5 0.2 - - - -
498A TYR* 3.8 4.9 + - - +
499A LYS* 1.3 75.9 - - - +
501A ILE* 1.3 62.8 + - - +
502A CYS* 4.3 0.4 - - - -
762D TYR* 2.8 30.7 - - + +
767D GLN* 5.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER* 4.1 5.4 - - - -
381A THR* 3.6 32.3 - - - +
382A GLN* 3.7 20.6 - - + +
453A HIS* 4.2 20.4 - - - +
470A LEU 3.8 1.0 - - - +
471A MET* 3.2 19.1 - - - -
472A ALA 3.2 16.6 + - - +
474A ARG* 3.9 22.9 - - + +
500A MET* 1.3 76.3 - - - +
502A CYS* 1.3 62.7 + - - +
503A HIS* 3.9 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER* 3.3 5.2 - - - -
381A THR* 2.9 43.1 + - - +
383A LEU* 4.1 23.3 - - - -
401A ALA* 3.8 27.8 - - + -
469A VAL* 4.1 11.0 - - + -
470A LEU 3.5 4.3 - - - +
471A MET* 3.6 32.8 - - - -
500A MET* 5.0 0.2 - - - -
501A ILE* 1.3 74.9 - - - +
503A HIS* 1.3 65.2 + - - +
504A VAL* 3.9 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 4.4 1.6 - - + -
380A SER* 2.6 28.4 + - - +
441A VAL* 5.7 0.4 - - + -
451A MET* 3.8 27.5 - - + -
453A HIS* 3.2 37.3 + + - -
468A VAL 3.7 0.7 - - - +
469A VAL* 3.2 9.7 - - - +
470A LEU* 2.9 48.7 + - + +
472A ALA* 5.9 1.8 - - + -
501A ILE* 3.9 24.4 - - + +
502A CYS* 1.3 74.3 - - - +
504A VAL* 1.3 60.7 + - - +
505A PHE* 3.6 24.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.5 6.1 - - - -
378A LEU* 2.8 52.1 + - + -
379A GLY 3.1 15.8 + - - +
381A THR* 4.8 0.9 - - + -
401A ALA 3.8 11.2 - - - +
402A VAL* 4.3 6.1 - - + +
405A VAL* 3.3 30.7 - - + -
406A LYS* 6.1 1.1 - - + -
467A ILE* 4.0 12.3 - - + -
468A VAL 3.8 1.8 - - - -
469A VAL* 3.8 24.7 - - + -
502A CYS 4.2 7.2 - - - +
503A HIS* 1.3 76.9 - - - +
505A PHE* 1.3 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA* 4.2 13.5 - - + -
376A ASN 2.9 10.1 - - - +
377A TYR* 3.3 42.6 - + + -
378A LEU* 4.3 3.1 - - - -
430A VAL* 3.9 9.0 - - + -
432A LEU* 4.3 15.7 - - + -
441A VAL* 3.3 40.6 - - + -
451A MET* 4.7 0.7 - - - -
467A ILE* 3.3 12.3 - - - +
468A VAL* 2.9 45.5 + - + +
470A LEU* 3.4 30.3 - - + -
503A HIS* 3.6 20.0 - + + -
504A VAL* 1.3 72.7 - - - +
506A GLU* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA 3.6 0.9 - - - -
376A ASN* 2.6 57.7 + - + +
378A LEU* 4.1 20.1 - - + +
427A LEU* 5.3 1.0 - - - +
466A ASN* 3.2 25.5 + - - +
467A ILE* 5.1 3.1 - - + -
505A PHE* 1.3 75.3 - - - +
507A SER* 1.3 61.2 + - - +
508A GLU* 4.4 15.5 - - - +
----------------------------------------------------------
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