Contacts of the helix formed by residues 83 - 88 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TRP* 3.3 15.7 + - - +
721C FMN 3.1 26.9 - - - +
25D HIS* 3.3 12.3 + - - -
81D HIS* 3.1 22.0 + - + +
82D THR* 1.3 83.1 - - - +
84D SER* 1.3 64.1 + - - +
85D ASP* 3.1 11.2 - - - +
86D HIS* 3.6 1.9 + - + -
87D ALA* 3.2 17.3 + - - +
115D HIS* 6.2 0.2 - - - -
148D HIS* 2.5 14.8 + - - -
149D TRP* 3.4 29.5 - - + -
531D FEO 1.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TRP* 2.9 45.7 - - - +
54D TYR* 3.7 15.1 - - - -
82D THR 5.1 0.4 - - - -
83D GLU* 1.3 74.5 - - - +
85D ASP* 1.3 58.2 + - - +
86D HIS 3.0 6.1 - - - -
87D ALA 4.7 0.4 - - - -
88D GLY* 3.2 31.6 + - - +
115D HIS* 6.1 4.7 - - - -
116D TYR* 4.6 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C TRP* 3.7 8.5 - - + -
24D PHE* 3.4 29.1 - - + -
37D TYR* 3.6 20.2 - - + +
53D VAL* 3.7 2.9 - - - -
54D TYR* 3.2 28.2 + - + -
83D GLU* 3.1 19.9 - - - +
84D SER* 1.3 73.7 + - - +
86D HIS* 1.3 71.1 + - - +
228D HIS* 2.9 5.2 + - - -
531D FEO 2.1 46.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D TYR* 5.1 2.0 - + - -
38D ASN 4.9 4.4 + - - -
51D ASP* 4.5 10.3 - - + +
52D THR* 2.6 47.1 + - - -
53D VAL 4.0 1.6 - - - +
81D HIS* 3.5 33.9 - + - +
83D GLU* 3.6 2.8 + - + +
84D SER 3.0 0.2 - - - -
85D ASP* 1.3 101.9 + - - +
87D ALA* 1.3 53.6 + - - +
88D GLY 3.5 1.1 - - - -
166D ASN* 3.9 10.5 - - - +
167D ASP* 3.1 4.2 + - - -
227D SER* 2.9 35.7 + - - -
228D HIS* 3.3 12.3 - + - -
531D FEO 2.2 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D THR* 3.5 5.2 - - - -
79D VAL* 5.0 5.6 - - + -
81D HIS 4.2 3.4 - - - +
82D THR* 3.9 20.4 - - + +
83D GLU 3.2 16.2 + - - +
86D HIS* 1.3 75.3 - - - +
88D GLY* 1.3 65.8 + - - +
89D ALA 3.2 3.1 - - - -
90D PHE* 3.0 24.3 - - + +
112D LEU* 4.5 7.6 - - + -
116D TYR* 2.8 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D VAL 3.6 4.8 + - - -
55D GLU* 3.6 30.7 - - - +
84D SER* 3.2 25.1 + - - -
86D HIS 3.5 1.4 - - - -
87D ALA* 1.3 79.0 - - - +
89D ALA* 1.3 57.2 + - - +
90D PHE 3.2 2.3 + - - -
91D PRO* 3.5 12.0 - - - +
116D TYR* 3.6 10.1 + - - -
----------------------------------------------------------
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