Contacts of the strand formed by residues 414 - 421 (chain B) in PDB entry 3P08
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 GLY 414 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LYS* 4.3 3.3 + - - +
431A MET* 3.8 21.8 - - - +
409B GLY* 3.5 6.2 - - - -
410B THR* 3.0 41.7 + - - +
411B GLY 4.9 0.7 - - - +
412B GLN 4.5 0.2 - - - +
413B PHE* 1.3 81.7 - - - +
415B VAL* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLU* 3.8 13.5 - - + -
415A VAL* 2.5 43.0 - - + +
416A VAL* 4.0 0.9 - - - +
417A LYS* 3.7 43.5 - - + +
408B LEU 3.2 13.9 - - - +
410B THR* 3.9 2.4 - - - +
413B PHE 3.7 0.7 - - - +
414B GLY* 1.3 80.7 - - - +
416B VAL* 1.3 71.4 + - - +
548B ASP* 3.6 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 4.0 5.2 - - - +
407B GLU* 3.5 4.5 - - - -
408B LEU* 2.8 39.7 + - + +
409B GLY 5.3 0.9 - - - +
410B THR* 3.7 26.9 - - + -
415B VAL* 1.3 77.9 - - - +
417B LYS* 1.3 76.5 + - - +
418B TYR* 3.7 2.3 + - + +
428B ALA* 4.0 19.5 - - + -
476B TYR* 4.2 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLY* 5.1 3.0 - - - -
411A GLY 5.4 1.2 + - - -
412A GLN 3.5 23.2 + - - -
413A PHE* 3.4 33.6 - - - +
414A GLY 4.3 3.2 + - - +
415A VAL* 3.8 15.6 - - + +
405B LEU* 4.1 24.5 - - - +
406B LYS 3.5 11.7 - - - +
407B GLU* 2.7 28.0 + - + +
416B VAL* 1.3 74.4 - - - +
418B TYR* 1.3 60.7 + - - +
428B ALA* 3.3 5.4 - - - -
429B ILE* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PHE* 3.3 28.3 - - + +
405B LEU* 3.3 8.3 - - - +
406B LYS* 2.8 53.4 + - + +
408B LEU* 3.4 29.8 - - + -
416B VAL* 3.7 1.9 + - + +
417B LYS* 1.3 74.3 - - - +
419B GLY* 1.3 75.9 + - - +
420B LYS* 3.9 14.7 + - - +
426B ASP* 2.8 36.5 + - + -
427B VAL 3.5 10.5 - - - -
428B ALA* 4.8 0.4 - - - +
429B ILE* 4.3 3.9 - - - +
476B TYR* 4.1 25.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 5.3 1.1 - - - -
403B THR 3.7 8.3 - - - -
404B PHE 3.8 0.9 - - - -
405B LEU* 4.0 11.9 - - - -
418B TYR* 1.3 92.1 - - - +
420B LYS* 1.3 62.0 + - - -
425B TYR 3.8 0.2 - - - +
427B VAL* 2.9 40.7 + - - +
429B ILE* 4.3 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ASP 3.4 0.7 - - - +
402B LEU* 3.3 6.5 - - - -
403B THR* 2.7 56.1 + - - +
404B PHE* 4.3 18.6 - - + -
418B TYR* 3.9 13.4 + - - +
419B GLY* 1.3 74.4 - - - -
421B TRP* 1.3 59.4 + - - +
423B GLY 3.6 20.4 - - - +
424B GLN* 3.6 27.5 + - - +
425B TYR 3.2 13.7 - - - +
426B ASP* 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B ILE* 3.5 34.7 - - + +
401B ASP* 3.6 20.7 + - + +
402B LEU* 4.0 13.7 - - + -
419B GLY 4.1 0.2 - - - -
420B LYS* 1.3 71.0 - - - +
422B ARG* 1.3 123.0 + - + +
423B GLY 3.1 2.0 - - - -
424B GLN 3.3 0.2 + - - -
425B TYR* 2.7 55.3 + + + +
427B VAL* 3.9 17.3 - - + -
461B TYR* 3.6 45.1 - + + -
473B ILE* 3.5 11.4 - - + -
----------------------------------------------------------
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