Contacts of the helix formed by residues 104 - 128 (chain H) in PDB entry 5KHR
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 ASP 104 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H HIS* 3.8 28.7 - - - +
105H ASP* 3.8 24.2 - - - +
107H VAL* 4.7 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ASP* 3.8 25.1 - - - +
106H ILE* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ASP* 3.8 29.2 - - - +
107H VAL* 3.9 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H ASP* 4.7 15.5 - - - +
106H ILE* 3.9 28.0 - - - +
108H THR* 3.9 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H VAL* 3.9 26.0 - - - +
109H GLU* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H THR* 3.8 26.7 - - - +
110H PHE* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 110 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H GLU* 3.8 29.2 - - - +
111H GLY* 3.8 26.9 - - - +
114H ALA* 4.7 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H PHE* 3.8 28.9 - - - +
112H ASP* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H GLY* 3.8 28.9 - - - +
113H SER* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 113 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H ASP* 3.8 28.7 - - - +
114H ALA* 3.9 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H PHE* 4.7 17.0 - - - +
113H SER* 3.9 25.4 - - - +
115H CYS* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 115 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H ALA* 3.8 26.0 - - - +
116H PHE* 3.8 28.7 - - - +
141H SER* 4.5 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H CYS* 3.8 28.9 - - - +
117H THR* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H PHE* 3.8 26.0 - - - +
118H LEU* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR* 3.8 25.4 - - - +
119H SER* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H LEU* 3.8 28.9 - - - +
120H LEU* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119H SER* 3.8 25.6 - - - +
121H LEU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H LEU* 3.8 28.5 - - - +
122H GLY* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H LEU* 3.8 26.9 - - - +
123H HIS* 3.8 29.4 - - - +
134H GLY* 4.7 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H GLY* 3.8 29.2 - - - +
124H VAL* 3.9 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H HIS* 3.9 26.0 - - - +
125H TYR* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H VAL* 3.8 26.5 - - - +
126H CYS* 3.7 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H TYR* 3.7 29.4 - - - +
127H LYS* 3.8 25.8 - - - +
131H LEU* 4.6 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H CYS* 3.8 28.9 - - - +
128H THR* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H LYS* 3.8 28.7 - - - +
129H ASP* 3.9 25.4 - - - +
----------------------------------------------------------
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