Contacts of the helix formed by residues 85 - 93 (chain B) in PDB entry 4A9H
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 VAL 85 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 2.9 57.7 + - + +
84B LYS* 1.3 85.3 - - + +
86B VAL* 1.3 66.6 + - - +
88B LYS* 4.2 0.6 - - - +
89B ALA* 3.4 22.0 + - - +
176B LYS* 4.5 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.1 39.6 + - + +
82B LEU* 3.5 25.4 - - + +
85B VAL* 1.3 76.4 - - - +
87B MET* 1.3 67.4 + - - +
89B ALA* 3.6 1.9 - - - +
90B LEU* 3.1 33.5 + - + +
145B PHE* 4.6 3.4 - - + -
173B PHE* 3.8 32.1 - - + +
176B LYS* 3.7 29.3 - - + +
177B VAL 4.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU 2.8 22.1 + - - +
83B HIS* 3.5 14.8 + - + +
86B VAL* 1.3 73.4 - - - +
88B LYS* 1.3 53.1 + - - +
90B LEU* 4.5 1.6 - - - +
91B TRP* 2.7 52.0 + - + +
123B MET* 3.4 50.9 - - + +
126B ILE* 3.3 35.2 - - + -
127B LYS* 3.8 17.7 - - + +
130B LEU* 4.6 3.1 - - + -
145B PHE* 3.3 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B HIS 3.6 6.4 + - - +
84B LYS* 3.3 37.5 + - + +
85B VAL 4.3 1.1 - - - +
86B VAL 3.3 0.8 - - - -
87B MET* 1.3 77.3 - - - +
89B ALA* 1.3 63.9 + - - +
91B TRP* 3.8 5.0 - - - +
92B LYS* 3.3 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL 3.4 17.3 + - - +
86B VAL 3.3 4.1 + - - +
88B LYS* 1.3 80.5 - - - +
90B LEU* 1.3 63.4 + - - +
92B LYS* 3.7 13.5 + - - +
93B HIS* 3.6 18.2 + - - +
172B ILE* 4.7 9.1 - - + +
176B LYS* 3.9 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.1 23.7 + - + +
87B MET* 3.9 1.8 - - - +
89B ALA* 1.3 76.4 - - - +
91B TRP* 1.3 64.0 + - - +
93B HIS* 3.1 13.7 + - - +
96B ALA* 3.1 19.2 - - - +
123B MET* 3.8 17.3 - - - -
145B PHE* 3.5 32.5 - - + -
149B PHE* 5.0 4.3 - - + -
169B LEU* 3.3 37.0 - - + +
172B ILE* 3.4 27.8 - - + -
173B PHE* 3.7 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B MET* 2.7 32.2 + - + +
88B LYS* 3.8 6.7 - - - +
89B ALA 3.4 0.2 - - - -
90B LEU* 1.3 75.1 - - - +
92B LYS* 1.3 60.4 + - + +
93B HIS 3.5 0.2 + - - -
96B ALA* 3.5 1.7 - - - +
100B ARG* 2.8 80.5 + - + +
123B MET* 3.5 52.0 - - + +
124B GLY* 3.7 7.2 - - - -
127B LYS* 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LYS* 3.3 16.7 + - + +
89B ALA* 3.7 13.7 - - - +
91B TRP* 1.3 80.0 - - + +
93B HIS* 1.3 68.5 + - - +
94B GLN* 3.6 1.6 + - - -
100B ARG* 4.1 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA 3.6 10.8 + - - +
90B LEU* 3.1 16.4 + - - +
92B LYS* 1.3 81.2 - - - +
94B GLN* 1.3 75.7 + - + +
95B PHE* 2.9 51.6 + + + +
96B ALA* 3.1 20.8 + - - +
97B TRP 4.5 0.2 + - - -
100B ARG* 3.5 8.0 + - - -
168B THR* 4.0 12.0 - - + +
169B LEU* 3.6 14.1 - - + +
172B ILE* 3.4 33.1 - - + +
----------------------------------------------------------
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