Contacts of the helix formed by residues 83 - 88 (chain B) in PDB entry 1YCH
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 GLU 83 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TRP* 3.3 15.0 + - + +
701A FMN 2.7 31.8 - - - +
25B HIS* 3.0 18.9 + - - -
81B HIS* 3.2 18.5 + - + +
82B THR* 1.3 85.2 - - - +
84B SER* 1.4 70.7 + - - +
85B ASP* 3.1 15.7 - - - +
86B HIS* 3.5 1.9 + - - -
87B ALA* 3.0 23.4 + - - +
148B HIS* 2.8 12.5 + - - -
149B TRP* 3.3 22.6 - - + -
511B FEO 2.2 36.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TRP* 3.5 38.4 - - - +
54B TYR* 3.9 14.0 - - - -
55B GLU* 5.8 1.2 - - - +
83B GLU* 1.4 76.7 - - - +
85B ASP* 1.3 61.0 + - - +
86B HIS 3.1 2.7 - - - -
88B GLY* 3.1 31.7 + - - +
115B HIS* 6.5 0.7 - - - -
116B TYR* 5.0 5.6 + - - -
149B TRP* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A TRP* 3.9 7.2 - - + -
24B PHE* 3.7 23.3 - - + -
37B TYR* 3.8 21.4 - - + +
53B VAL* 3.4 2.3 - - - -
54B TYR* 3.1 31.7 + - + +
83B GLU* 3.1 18.5 - - - +
84B SER* 1.3 72.7 - - - +
86B HIS* 1.3 71.4 + - - +
228B HIS* 2.7 8.3 + - - -
511B FEO 2.0 46.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B TYR* 5.2 2.7 - + - -
38B ASN 4.8 5.3 + - - -
51B ASP* 4.6 11.1 + - + -
52B THR* 2.3 46.6 + - - -
53B VAL 4.1 1.3 - - - -
81B HIS* 3.5 37.5 - + - +
83B GLU* 3.5 3.4 + - + +
84B SER 3.1 0.2 - - - -
85B ASP* 1.3 107.1 + - - +
87B ALA* 1.3 52.8 + - - +
88B GLY 3.5 0.9 - - - -
166B ASN* 3.8 14.4 - - - +
167B ASP* 2.9 5.9 + - - -
227B SER* 3.0 30.2 + - - -
228B HIS* 3.1 15.3 - + - -
511B FEO 2.2 26.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B THR* 3.4 4.5 - - - -
79B VAL* 5.0 5.8 - - + -
81B HIS 4.2 3.6 - - - +
82B THR* 3.9 24.5 - - + +
83B GLU 3.0 18.5 + - - +
86B HIS* 1.3 75.7 - - - +
88B GLY* 1.3 65.0 + - - +
89B ALA 3.2 3.1 - - - -
90B PHE* 3.0 21.8 + - + +
112B LEU* 4.6 7.0 - - + -
116B TYR* 3.0 23.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL 3.5 6.0 + - - -
55B GLU* 3.5 30.0 - - - +
84B SER* 3.1 24.9 + - - -
87B ALA* 1.3 79.4 - - - +
89B ALA* 1.3 57.4 + - - +
90B PHE 3.2 2.3 + - - -
91B PRO* 3.6 11.1 - - - +
116B TYR* 3.8 10.8 + - - -
----------------------------------------------------------
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