Contacts of the strand formed by residues 452 - 457 (chain W) in PDB entry 5IY8
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 452 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W LYS 5.1 0.7 - - - +
71W ILE* 4.6 5.9 - - - +
212W LEU* 4.4 16.8 - - - +
222W SER* 5.1 5.7 + - - -
225W LEU* 5.8 2.3 - - - +
228W LYS* 5.5 0.2 - - - -
229W ALA* 3.1 30.3 - - + +
230W VAL 4.6 0.4 - - - -
231W VAL* 3.4 30.9 - - + +
446W PRO 4.8 2.5 + - - +
447W VAL* 2.9 34.9 + - - +
448W PHE 3.9 6.9 - - - +
449W GLU 2.9 14.7 + - - +
450W ARG* 4.2 4.8 - - - +
451W PHE* 1.4 80.8 - - + +
453W SER* 1.3 74.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 453 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32W LEU* 6.2 2.9 - - - -
35W LYS* 3.3 12.4 + - - +
36W GLY* 3.3 34.3 + - - -
229W ALA 3.0 7.6 + - - -
230W VAL* 3.2 14.9 - - - -
231W VAL* 2.9 28.8 + - - +
447W VAL 4.7 3.8 - - - -
448W PHE* 5.3 0.9 - - - +
452W GLN* 1.3 79.9 + - - +
454W VAL* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 454 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32W LEU* 5.8 1.0 - - - +
36W GLY 3.2 5.8 + - - +
37W HIS* 2.8 74.2 + - + +
230W VAL* 4.8 2.0 - - - +
231W VAL* 3.3 22.4 - - + +
233W PHE* 3.6 35.7 - - + -
447W VAL* 3.8 13.9 - - + -
448W PHE* 5.1 5.2 - - + -
453W SER* 1.3 74.6 - - - +
455W ILE* 1.3 77.9 + - - +
456W ILE* 4.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 455 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W LEU* 6.4 0.2 - - + -
31W THR* 6.1 2.7 - - + +
32W LEU* 4.8 18.4 - - + -
37W HIS 5.3 0.2 - - - -
38W GLY* 3.4 20.9 - - - +
40W LEU* 4.4 29.8 - - + -
52W LEU* 4.6 12.1 - - + -
56W ILE* 5.1 11.7 - - + -
70W LEU* 5.1 2.9 - - + -
230W VAL* 3.9 17.9 - - + -
231W VAL 2.9 12.1 + - - +
232W VAL* 3.3 28.4 - - + +
233W PHE 3.1 23.7 + - - -
454W VAL* 1.3 79.1 - - - +
456W ILE* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 456 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W HIS* 3.9 15.3 - - + -
38W GLY 3.1 12.8 + - - +
39W VAL* 3.4 15.7 - - + +
40W LEU* 2.8 32.8 + - - +
233W PHE* 3.4 37.0 - - + -
236W ALA* 3.7 10.5 - - + -
239W ILE* 5.2 5.2 - - + -
454W VAL* 4.0 0.4 - - + -
455W ILE* 1.3 77.7 - - - +
457W THR* 1.4 59.1 + - - +
467W TYR* 3.7 31.6 - - + -
471W LEU* 3.9 27.6 - - + -
475W PRO* 4.9 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 457 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40W LEU* 2.8 31.9 + - + -
42W MET* 3.6 22.8 - - + +
48W LYS* 4.2 6.7 - - + +
52W LEU* 6.2 0.9 - - + -
232W VAL* 4.4 14.8 - - + -
233W PHE 3.3 13.1 + - - +
234W ASP* 4.0 18.8 - - - +
235W GLU 3.0 20.5 + - - -
236W ALA* 3.1 13.0 + - - +
456W ILE* 1.4 76.0 - - - +
458W SER* 1.3 65.0 + - - +
459W GLY 4.1 0.9 + - - -
461W LEU* 3.9 6.0 - - - +
467W TYR* 4.7 0.4 - - - -
----------------------------------------------------------
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