Contacts of the strand formed by residues 614 - 618 (chain B) in PDB entry 1XR2
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 GLN 614 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ASP* 5.4 0.6 + - - -
395B GLN* 3.2 36.6 + - + +
396B ARG* 5.4 3.6 - - - +
399B LEU* 4.9 11.4 - - + +
401B LEU* 5.4 1.8 - - - +
572B LYS 3.0 8.4 + - - +
573B ILE* 3.4 24.3 - - + +
574B VAL 2.9 27.2 + - - +
612B GLU 3.7 2.8 + - - -
613B THR* 1.3 71.2 - - - +
615B ILE* 1.3 60.8 + - - +
616B HIS* 2.7 28.7 + - + +
637B ASP* 3.4 11.9 - - + -
638B VAL* 4.0 5.2 - - + -
663B GLN* 3.8 23.2 + - - +
699B TRP* 3.3 18.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 615 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ARG* 3.2 33.9 - - - +
563B VAL* 5.0 3.1 - - + -
574B VAL* 3.5 24.0 - - + +
576B ILE* 4.5 15.0 - - + -
603B PHE* 4.6 3.4 - - + -
607B ALA* 4.0 25.6 - - + +
609B ALA* 3.7 21.1 - - + -
613B THR* 3.9 4.3 - - + +
614B GLN* 1.3 74.6 - - - +
616B HIS* 1.3 67.8 + - - +
636B PHE* 3.7 19.9 - - + -
637B ASP* 2.6 36.8 + - - +
638B VAL 3.0 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 616 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B THR* 5.7 0.6 - - + +
527B LYS* 4.1 16.6 + - - -
573B ILE* 3.5 26.2 - - + +
574B VAL 3.0 6.7 + - - -
575B GLN* 3.2 22.9 - - + +
576B ILE* 2.8 29.5 + - - +
614B GLN* 2.7 31.3 + - + -
615B ILE* 1.3 82.3 - - - +
617B ALA* 1.3 62.3 + - - +
638B VAL* 3.1 24.8 - - + +
640B SER* 6.1 3.1 - - - +
699B TRP* 3.4 36.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 617 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ILE 3.6 6.1 - - - +
578B GLU* 6.5 0.2 - - + -
603B PHE* 4.0 17.3 - - + -
616B HIS* 1.3 75.4 - - - +
618B HIS* 1.3 60.7 + - - +
619B MET* 4.9 11.4 - - + -
636B PHE* 3.8 32.7 - - + +
638B VAL 2.7 8.7 + - - +
639B ILE* 3.1 11.3 - - + +
640B SER* 2.9 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 618 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 3.4 34.6 + - + +
575B GLN* 3.8 12.3 - - - +
576B ILE 3.6 7.1 + - - -
577B ASP* 3.3 30.1 - - + +
578B GLU 3.6 18.4 + - - -
579B PRO* 4.6 1.7 - - - +
617B ALA* 1.3 73.3 - - - +
619B MET* 1.3 73.4 + - - +
620B CYS* 2.9 36.5 - - - -
640B SER* 2.5 33.8 + - - +
641B ILE* 5.2 0.4 - - - -
703B ASP 3.5 8.7 - - - -
704B CYS* 3.3 9.2 - - - -
----------------------------------------------------------
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