Contacts of the strand formed by residues 466 - 471 (chain X) in PDB entry 3Q0F
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 VAL 466 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407X ALA* 3.9 22.4 - - + +
408X THR 3.8 3.4 - - - +
409X SER* 3.7 20.2 - - - +
410X ILE* 4.1 12.3 - - + +
456X LEU* 5.0 0.7 - - + -
459X SER* 4.4 1.8 - - - +
464X ASN* 3.8 11.7 - - - +
465X PRO* 1.3 79.8 - - - +
467X ARG* 1.3 77.2 + - - +
468X VAL* 3.7 0.7 + - + -
491X LEU* 3.4 4.8 - - - -
492X TYR* 2.8 40.0 + - - +
494X VAL* 4.2 20.4 - - + -
513X LEU* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 467 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362X GLN* 4.3 5.1 + - - -
363X ILE 3.1 29.9 + - - -
365X GLY* 2.6 47.4 + - - +
367X VAL* 3.6 25.4 - - - +
386X GLY 3.8 8.5 + - - -
387X ILE* 3.0 41.1 + - - +
396X ASP* 5.2 0.8 + - - -
408X THR* 2.9 32.9 + - - +
409X SER* 3.1 9.7 + - - -
410X ILE 2.9 26.1 + - - -
465X PRO 4.3 0.2 - - - -
466X VAL* 1.3 78.2 - - - +
468X VAL* 1.3 59.2 + - - +
469X ILE* 4.3 4.5 - - + -
488X TYR* 3.9 16.4 - - + +
490X GLY 3.7 4.9 - - - -
491X LEU* 3.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 468 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410X ILE* 3.6 27.1 - - + -
412X SER* 5.7 1.3 - - - -
426X LEU* 4.1 18.6 - - + -
466X VAL* 4.1 3.6 - - + +
467X ARG* 1.3 79.6 - - - +
469X ILE* 1.3 71.5 + - - +
470X ARG* 4.3 5.6 - - + -
488X TYR* 3.7 4.5 - - - -
489X ASP* 2.8 44.0 + - + +
490X GLY 3.2 7.0 + - - +
492X TYR* 3.5 42.8 - - + -
513X LEU* 4.6 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 469 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382X LEU* 4.1 18.8 - - + -
387X ILE* 3.7 31.0 - - + -
388X HIS* 4.7 4.0 - - + -
409X SER* 4.6 6.1 - - - -
410X ILE 3.0 18.2 + - - +
411X VAL* 3.4 13.6 - - + -
412X SER* 2.7 29.3 + - - -
467X ARG* 4.5 5.2 - - + -
468X VAL* 1.3 87.8 - - - +
470X ARG* 1.3 64.7 + - - +
486X TYR* 3.7 36.1 - - + -
487X VAL 3.2 13.7 - - - +
488X TYR* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 470 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412X SER 3.3 6.5 - - - +
420X LEU* 3.5 41.1 - - + +
421X ASP 3.4 22.6 + - - +
423X SER 4.4 12.1 + - - -
425X VAL 5.1 1.8 + - - -
426X LEU* 4.4 11.9 - - - +
468X VAL* 4.3 7.4 - - + +
469X ILE* 1.3 82.0 - - - +
471X GLY* 1.3 68.9 + - - +
472X ILE* 4.9 1.3 - - + -
486X TYR* 3.2 3.5 - - - -
487X VAL* 2.8 40.0 + - + +
489X ASP* 2.8 29.6 + - + -
492X TYR* 3.1 24.4 + - - -
522X LEU* 4.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 471 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412X SER 2.7 18.2 + - - +
413X SER* 4.1 13.2 - - - +
470X ARG* 1.3 75.1 - - - +
472X ILE* 1.3 71.6 + - - +
485X ASN 3.0 10.8 - - - -
486X TYR* 3.9 11.2 - - - -
----------------------------------------------------------
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