Contacts of the helix formed by residues 117 - 128 (chain B) in PDB entry 5BXD
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 LEU 117 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.6 27.4 - - + -
54B SER* 3.8 8.1 - - - -
56B ILE* 3.9 9.0 - - + -
87B ILE* 3.7 24.7 - - + -
90B PHE* 4.2 13.5 - - + -
91B LEU* 3.6 24.9 - - + -
112B ALA* 2.9 14.0 + - - +
113B LYS* 5.1 0.4 - - - +
115B PHE* 3.7 19.3 - - + +
116B GLN* 1.3 75.9 - - - +
118B GLN* 1.3 64.6 + - - +
119B PRO* 3.5 4.7 - - - -
120B MET* 3.3 21.3 + - + +
121B LEU* 3.2 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLN 3.6 5.0 + - - +
117B LEU* 1.3 70.7 - - - +
119B PRO* 1.4 76.2 - - + +
121B LEU* 3.0 35.5 + - - +
122B LEU* 3.2 38.1 + - + +
125B GLU* 5.4 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.5 33.4 - - + +
90B PHE* 3.5 16.2 - - + -
117B LEU* 3.6 3.6 - - - -
118B GLN* 1.4 95.2 - - + +
120B MET* 1.3 59.0 + - - +
122B LEU* 3.6 13.3 + - + +
123B GLU* 3.2 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TYR 3.5 23.8 - - - +
87B ILE* 3.7 20.0 - - + -
90B PHE* 3.3 47.3 - - + -
96B LEU* 4.1 16.2 - - + -
108B LEU* 3.8 38.1 - - + -
112B ALA* 4.0 10.1 - - + -
117B LEU* 3.3 15.2 + - + +
118B GLN 3.1 0.8 - - - -
119B PRO* 1.3 76.6 - - - +
121B LEU* 1.3 66.1 + - - +
123B GLU* 3.4 3.9 + - - +
124B MET* 3.1 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.6 48.0 - - + +
112B ALA* 3.7 24.2 - - + -
113B LYS* 3.9 25.6 - - + +
116B GLN* 6.4 0.4 - - - -
117B LEU 3.4 13.9 - - - +
118B GLN* 3.0 34.0 + - - +
120B MET* 1.3 78.6 - - - +
122B LEU* 1.3 60.0 + - - +
124B MET* 3.6 4.4 + - - +
125B GLU* 3.1 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLN* 3.2 34.3 + - + +
119B PRO* 3.8 13.7 - - + +
120B MET 3.3 0.2 - - - -
121B LEU* 1.3 76.6 - - - +
123B GLU* 1.3 59.8 + - + +
125B GLU* 3.4 21.4 + - - +
126B ARG* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.9 11.1 - - - -
94B SER 3.7 13.4 - - - +
95B LYS* 3.7 3.3 - - - -
96B LEU* 3.1 40.8 + - + +
119B PRO* 3.2 18.5 - - - +
120B MET 3.4 6.8 + - - +
121B LEU 3.3 0.4 - - - -
122B LEU* 1.3 75.9 - - + +
124B MET* 1.3 61.0 + - - +
126B ARG* 3.2 36.1 + - - +
127B TRP* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.8 26.5 - - + -
98B ILE* 6.4 1.3 - - + -
102B PHE* 5.5 0.7 - - + -
105B TYR* 3.2 66.7 - - + +
108B LEU* 3.8 30.3 - - + +
109B TYR* 3.5 28.0 - - + +
112B ALA* 4.7 3.8 - - - -
120B MET* 3.1 25.5 + - - +
121B LEU 3.9 4.5 - - - +
122B LEU 3.4 0.2 - - - -
123B GLU* 1.3 72.8 - - - +
125B GLU* 1.3 59.9 + - - +
127B TRP* 3.2 2.1 + - - +
128B LYS 2.8 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.7 8.1 - - - +
109B TYR* 3.1 30.1 + - + +
118B GLN* 5.4 2.3 + - - -
121B LEU* 3.1 21.3 + - - +
122B LEU* 3.5 23.7 - - - +
123B GLU 3.3 0.2 - - - -
124B MET* 1.3 76.7 - - - +
126B ARG* 1.3 59.1 + - - +
128B LYS* 3.3 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU 3.0 13.9 + - - +
123B GLU* 3.2 46.9 + - - +
124B MET 3.2 0.2 - - - -
125B GLU* 1.3 75.4 - - - +
127B TRP* 1.3 67.3 + - - +
128B LYS 3.3 3.6 + - - +
129B GLN* 3.7 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASP* 4.9 6.7 - - - -
96B LEU* 4.0 11.0 - - + -
98B ILE* 3.5 37.8 - - + +
99B PRO 5.6 1.3 - - - -
102B PHE* 4.1 27.4 - + + -
105B TYR* 3.8 34.8 - + + -
123B GLU 2.9 17.7 + - - +
124B MET 3.2 4.5 + - - +
126B ARG* 1.3 78.6 - - - +
128B LYS* 1.3 66.5 + - + +
129B GLN* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TYR* 3.8 35.6 - - + +
124B MET 2.8 16.8 + - - +
125B GLU* 3.3 16.9 - - - +
126B ARG 3.2 2.0 - - - +
127B TRP* 1.3 82.7 - - + +
129B GLN* 1.3 64.3 + - - +
130B ASP 4.6 7.2 - - - +
----------------------------------------------------------
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