Contacts of the strand formed by residues 446 - 451 (chain B) in PDB entry 4A8W
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 446 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 3.8 29.2 - - + -
414B GLN* 3.8 22.9 - - + +
415B LEU* 4.1 8.7 - - + -
418B THR* 3.9 5.6 - - - +
419B ALA* 4.4 3.8 - - + -
422B LEU* 3.8 27.8 - - + -
435B PHE* 4.5 2.0 - - + -
439B TYR* 3.3 24.4 - - + +
444B GLU* 3.5 10.7 + - + +
445B GLU* 1.3 76.1 - - + +
447B ARG* 1.3 67.8 + - - +
458B GLY 3.6 2.9 - - - -
459B TRP* 3.3 35.0 - - + +
464B ALA* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.4 24.2 + - + +
316B GLU* 3.8 27.9 + - - +
317B TRP* 3.5 25.9 - - + +
414B GLN* 3.0 12.3 + - - -
439B TYR* 3.9 9.6 - - - -
442B GLY* 3.2 31.8 + - - -
443B HIS* 4.8 4.2 + - - +
444B GLU 2.9 20.4 + - - +
445B GLU 4.7 1.1 - - - +
446B ILE* 1.3 80.2 - - - +
448B GLN* 1.3 59.7 + - - +
457B LEU 3.7 0.2 - - - -
458B GLY* 2.7 32.6 + - - +
460B THR* 3.6 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.9 5.4 - - - -
301B THR* 3.4 31.9 + - + +
317B TRP* 4.4 2.9 - - - -
407B SER* 2.9 46.8 + - - +
410B TYR* 3.6 13.5 - - - +
439B TYR* 2.9 31.6 + - + +
447B ARG* 1.3 78.8 - - - +
449B ILE* 1.3 66.6 - - - +
450B SER* 2.8 31.1 + - - -
456B MET 3.4 7.2 - - - -
457B LEU* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 3.5 24.5 - - + +
301B THR 3.5 4.0 - - - -
304B HIS* 3.6 11.0 - - + +
310B LYS* 4.7 12.6 - - + +
313B LYS* 3.8 17.5 - - + -
314B VAL* 3.7 27.4 - - + -
317B TRP* 4.0 13.7 - - + -
448B GLN* 1.3 75.1 - - - +
450B SER* 1.3 61.4 + - - +
455B ALA* 3.2 3.5 - - - +
456B MET* 3.0 51.9 + - + +
496B PHE* 3.5 28.7 - - + -
514B PHE* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B THR* 2.9 12.1 + - - +
302B PHE* 3.7 25.1 - - - +
304B HIS* 3.1 18.7 + - - -
403B THR* 5.0 2.4 + - - +
407B SER* 4.3 3.9 + - - -
410B TYR* 4.2 7.2 - - - -
448B GLN* 2.8 29.5 + - - -
449B ILE* 1.3 76.8 - - - +
451B LYS* 1.3 62.8 + - - +
452B SER 4.9 1.5 + - - -
454B ASP 3.4 11.0 - - - -
455B ALA* 3.7 10.1 - - - -
496B PHE* 3.7 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B TYR* 3.9 24.3 + - + +
302B PHE 5.5 3.1 - - - +
304B HIS* 4.6 3.6 - - + -
399B ASP* 5.3 12.3 - - + -
403B THR* 4.2 8.5 - - - +
450B SER* 1.3 75.9 - - - +
452B SER* 1.4 75.5 + - - +
453B ASP* 3.2 1.2 + - - +
454B ASP* 2.9 25.0 + - - +
496B PHE* 4.1 0.2 - - - -
497B LEU* 3.9 39.0 - - + +
----------------------------------------------------------
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