Contacts of the helix formed by residues 105 - 116 (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 THR 105 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL 4.8 0.4 + - - -
104B CYS* 1.3 83.6 - - - +
106B GLN* 1.3 60.3 + - - +
107B ARG* 4.3 4.7 - - - -
108B ALA* 2.9 19.6 + - - +
109B PHE* 3.0 23.7 + - - +
125B ILE* 4.1 3.0 - - - +
126B VAL 3.9 9.9 - - - +
143B GLU* 4.2 23.8 - - + +
150B PRO 5.6 0.7 - - - +
151B ASP* 2.8 31.8 + - - +
152B SER 4.1 4.3 - - - +
153B MET* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 1.3 71.3 - - - +
107B ARG* 1.3 79.7 + - + +
109B PHE* 2.9 20.7 + - - +
110B ASP* 3.0 47.4 + - - +
125B ILE* 3.4 36.2 - - + +
126B VAL 4.7 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TRP* 4.9 11.9 - - - +
376A TRP* 6.4 0.6 - - - -
105B THR* 4.1 3.3 + - - +
106B GLN* 1.3 85.4 - - + +
108B ALA* 1.3 62.5 + - - +
110B ASP* 3.3 18.9 + - - +
111B SER* 3.0 23.6 + - - -
150B PRO* 3.7 37.1 - - + +
151B ASP* 3.7 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL 4.5 4.7 - - - +
82B THR* 3.7 12.3 - - + +
104B CYS* 3.8 12.1 - - + -
105B THR* 2.9 35.3 + - - +
107B ARG* 1.3 79.4 - - - +
109B PHE* 1.3 52.6 + - - +
111B SER* 3.1 4.0 + - - -
112B LEU* 2.8 37.6 + - - +
151B ASP* 3.3 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B CYS* 3.9 13.4 - - - -
105B THR 3.0 13.1 + - - +
106B GLN* 2.9 16.1 + - - +
108B ALA* 1.3 76.9 - - - +
110B ASP* 1.3 71.2 + - - +
112B LEU* 3.5 5.3 + - - +
113B LYS* 3.1 45.7 + - + +
121B PHE* 3.7 22.0 - + - -
123B TYR* 3.0 67.8 - + - -
125B ILE* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A TRP* 5.6 1.1 - - - +
106B GLN* 3.0 43.3 + - - +
107B ARG* 3.4 24.8 + - - +
109B PHE* 1.3 79.2 - - - +
111B SER* 1.3 66.3 + - - +
113B LYS* 3.3 7.4 + - - +
114B ALA* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A TRP* 3.9 22.4 - - - +
82B THR* 2.7 27.3 + - - -
107B ARG 3.0 13.1 + - - -
108B ALA 3.1 6.9 + - - -
110B ASP* 1.3 75.4 - - - +
112B LEU* 1.3 52.1 - - - +
114B ALA* 2.9 7.5 + - - +
115B HIS* 2.8 61.0 + - - -
149B TRP* 4.6 0.3 - - - -
151B ASP* 4.1 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 4.5 14.4 - - + -
82B THR* 3.9 18.4 - - + +
87B ALA* 4.6 5.6 - - + -
90B PHE* 3.8 42.6 - - + -
102B VAL* 4.4 13.2 - - + -
104B CYS* 4.8 6.7 - - - -
108B ALA 2.8 19.5 + - - +
109B PHE* 3.7 6.5 - - - +
111B SER* 1.3 73.3 - - - +
113B LYS* 1.3 56.4 + - - +
115B HIS* 5.0 0.2 - - - -
116B TYR* 3.0 61.5 + - + +
117B SER 3.8 0.3 + - - -
121B PHE* 4.2 21.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.1 40.9 + - + +
110B ASP* 3.6 8.5 - - - +
112B LEU* 1.3 76.6 - - - +
114B ALA* 1.3 58.3 + - - +
117B SER* 2.9 46.1 + - - +
118B HIS 5.2 0.2 - - - +
119B ILE 3.5 23.0 + - - +
120B ASP* 4.7 9.7 + - - +
121B PHE* 4.1 21.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLN 5.7 0.4 - - - +
376A TRP* 3.7 33.2 - - + -
377A VAL* 3.9 19.1 - - + +
110B ASP 3.0 12.5 + - - +
111B SER 2.9 9.1 + - - +
113B LYS* 1.3 79.3 - - - +
115B HIS* 1.3 62.3 + - - +
116B TYR* 3.4 1.4 + - - -
117B SER* 4.6 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A TRP* 3.2 49.6 - + - +
377A VAL* 3.7 25.6 - - + +
701A FMN 5.2 2.0 + - - -
82B THR* 4.7 14.2 + - - +
84B SER* 6.5 0.7 - - - -
111B SER* 2.8 46.1 + - - +
114B ALA* 1.3 72.9 - - - +
116B TYR* 1.3 96.7 + - + +
149B TRP* 4.9 4.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 5.0 3.9 + - - -
84B SER* 5.0 7.1 + - - -
87B ALA* 3.0 37.6 + - + +
88B GLY* 3.8 8.1 - - - -
90B PHE* 3.8 19.7 - + + -
91B PRO* 3.9 24.5 - - + -
112B LEU* 3.0 36.5 + - + +
114B ALA 3.2 1.0 - - - -
115B HIS* 1.3 111.5 - - + +
117B SER* 1.4 84.7 + - - +
118B HIS* 3.8 7.1 + - - +
119B ILE* 4.2 16.0 - - + +
----------------------------------------------------------
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