Contacts of the helix formed by residues 415 - 419 (chain B) in PDB entry 2XLR
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 THR 415 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B HIS 5.4 0.3 + - - -
412B ASN* 3.1 42.2 + - - +
414B MET* 1.3 84.8 - - + +
416B PHE* 1.3 59.5 + - - +
417B ARG* 3.0 4.0 - - - -
418B ASP* 2.8 41.2 + - - +
419B HIS* 3.6 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP* 3.7 10.5 - - - -
102B TYR* 3.3 26.2 + + - -
216B ASP* 5.1 2.7 - - - -
219B SER* 6.1 0.9 - - - -
405B TRP* 3.7 28.0 - - - -
408B HIS* 3.8 32.1 - - + +
409B LYS* 3.6 24.9 - - + +
412B ASN 3.2 5.1 + - - +
413B ILE* 3.0 37.0 - - + -
414B MET 5.0 0.9 - - - -
415B THR* 1.3 76.3 - - - +
417B ARG* 1.3 105.6 + - + +
418B ASP 3.2 1.3 + - - -
419B HIS* 3.6 20.2 + - - +
421B TYR* 4.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.4 34.5 + - + +
77B SER 2.9 25.6 + - - -
78B ASP* 3.4 20.0 - - - +
102B TYR* 3.2 32.5 - - + +
216B ASP* 2.9 36.5 + - - -
219B SER* 5.6 1.2 - - - -
220B GLN* 4.4 4.9 - - - +
414B MET 5.2 0.6 + - - +
415B THR 3.0 2.0 + - - -
416B PHE* 1.3 108.0 - - + +
418B ASP* 1.3 63.0 + - - +
419B HIS 3.4 1.4 - - - +
433B HIS* 6.2 0.2 - - - +
437B TRP* 3.7 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 5.7 0.9 - - - -
414B MET 4.9 0.5 - - - +
415B THR* 2.8 28.9 + - - +
417B ARG* 1.3 79.8 - - - +
419B HIS* 1.3 64.8 + - + +
420B SER* 4.8 1.0 + - - -
432B LYS* 3.7 36.5 + - - +
433B HIS* 5.5 1.7 + - - +
435B THR 4.4 1.7 - - - +
436B PRO* 3.5 15.9 - - - +
437B TRP* 2.7 40.2 + - - +
438B ILE* 5.0 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ALA* 5.8 0.5 - - - +
101B SER* 3.8 9.2 + - - -
102B TYR* 3.8 15.6 - - - -
408B HIS* 3.4 53.5 + + + +
411B GLU* 4.7 9.8 + - - -
415B THR* 3.6 20.0 + - - -
416B PHE* 3.6 19.6 - - - +
417B ARG 3.4 2.3 - - - +
418B ASP* 1.3 82.4 - - + +
420B SER* 1.3 63.6 + - - +
421B TYR* 3.9 10.5 - - + +
----------------------------------------------------------
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