Contacts of the helix formed by residues 81 - 94 (chain B) in PDB entry 1AVZ
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 TYR 81 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 1.3 70.5 - - - +
82B LYS* 1.3 70.8 + - + +
84B ALA* 3.0 3.2 + - - +
85B VAL* 2.8 43.2 + - + +
138B THR* 5.6 0.2 - - - +
139B PHE* 3.5 59.1 + + + +
140B GLY* 3.7 11.2 - - - -
190B ALA* 2.4 35.3 + - - +
191B PHE* 4.9 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.9 13.2 - - - +
81B TYR* 1.3 86.2 - - + +
83B ALA* 1.3 63.5 + - - +
85B VAL* 3.3 4.2 + - - +
86B ASP* 3.1 36.8 + - - +
99C ASP* 3.2 29.7 + - - +
132C TYR* 6.1 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 3.9 3.6 - - - -
80B THR* 2.9 31.4 + - - +
82B LYS* 1.3 77.8 - - + +
84B ALA* 1.3 62.7 + - - +
86B ASP 3.8 0.2 + - - -
87B LEU* 3.1 27.2 + - - +
120B TYR* 3.3 34.5 - - + +
97C THR* 3.9 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 3.6 17.2 - - + -
80B THR 2.6 21.8 + - - +
81B TYR 3.3 4.5 - - - +
83B ALA* 1.3 70.7 - - - +
85B VAL* 1.3 59.5 - - - +
87B LEU* 3.4 6.0 + - - +
88B SER* 3.0 31.5 + - - -
124B TRP* 6.1 0.2 - - + -
138B THR* 4.2 11.9 - - + -
140B GLY* 3.0 24.5 - - - +
141B TRP* 3.8 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 2.8 55.4 + - + +
82B LYS* 3.8 5.6 - - - +
84B ALA* 1.3 69.0 - - - +
86B ASP* 1.3 71.4 + - - +
88B SER* 2.9 15.3 + - - -
89B HIS* 3.0 39.0 + - + +
140B GLY* 3.0 16.4 + - - +
142B CYS* 5.0 5.6 - - - -
190B ALA* 4.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 3.1 21.6 + - - +
83B ALA 4.1 2.7 - - - +
85B VAL* 1.3 80.1 - - - +
87B LEU* 1.3 56.9 + - - +
89B HIS* 3.5 10.5 + - - +
90B PHE* 3.0 26.2 + - - +
93B GLU* 5.1 0.2 - - - +
96C ARG 4.1 3.2 - - - +
97C THR* 3.5 21.7 - - - -
98C GLU* 2.9 47.8 + - - +
99C ASP* 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET* 3.4 32.8 - - + -
83B ALA 3.1 15.3 + - - +
84B ALA* 3.5 4.7 - - - +
85B VAL 3.1 0.4 - - - -
86B ASP* 1.3 78.3 - - - +
88B SER* 1.3 59.1 + - - +
90B PHE* 3.2 19.3 - - + +
91B LEU* 3.0 35.6 + - + +
114B ILE* 3.8 37.5 - - + -
118B GLN* 3.9 18.8 - - - +
120B TYR* 4.6 5.6 - - + -
124B TRP* 4.5 9.9 - - + -
141B TRP* 4.3 10.1 - - + -
96C ARG 4.5 5.6 + - - +
97C THR* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA 3.0 14.1 + - - -
85B VAL 2.9 8.8 + - - -
87B LEU* 1.3 72.1 - - - +
89B HIS* 1.3 67.7 + - - +
90B PHE 3.0 1.7 + - - -
91B LEU* 3.1 2.4 + - - -
92B LYS* 2.9 25.4 + - - +
140B GLY 3.6 0.3 + - - -
141B TRP* 3.3 14.1 - - - -
142B CYS* 3.1 44.1 + - - -
143B TYR* 3.9 17.0 + - - -
185B PHE* 4.5 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.0 35.8 + - + +
86B ASP* 3.8 10.9 + - - +
88B SER* 1.3 79.9 - - - +
90B PHE* 1.3 52.9 + - - +
92B LYS* 3.5 6.0 - - + +
93B GLU* 2.7 54.6 + - + +
142B CYS* 5.2 5.7 - - - -
185B PHE* 4.4 20.8 - + - -
187B SER* 5.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP 3.0 15.6 + - - +
87B LEU* 3.2 22.2 - - + +
88B SER 3.0 0.4 - - - -
89B HIS* 1.3 76.9 - - - +
91B LEU* 1.3 74.0 + - + +
92B LYS 3.1 0.2 - - - -
93B GLU* 3.5 13.8 + - + +
94B LYS* 3.0 62.2 + - + +
113B TRP* 4.3 8.7 - + - -
118B GLN* 4.8 2.5 - - - -
94C GLU* 4.8 6.3 - - - -
96C ARG* 3.7 50.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.0 21.9 + - + +
88B SER 3.1 3.8 + - - +
90B PHE* 1.3 90.8 - - + +
92B LYS* 1.3 58.2 + - - +
94B LYS* 3.9 9.3 - - + +
95B GLY* 3.1 22.7 + - - -
96B GLY 4.7 0.3 + - - -
97B LEU* 3.8 23.6 + - + +
98B GLU* 5.3 0.9 + - - +
110B LEU* 4.4 13.2 - - + -
113B TRP* 3.7 29.8 - - + -
114B ILE* 4.6 5.4 - - + -
141B TRP* 3.5 35.2 - - + -
143B TYR* 3.5 13.5 + - + +
----------------------------------------------------------
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 SER 2.9 15.8 + - - +
89B HIS* 3.5 6.7 - - + +
91B LEU* 1.3 76.7 - - - +
93B GLU* 1.3 67.1 + - + +
94B LYS 3.2 0.7 - - - -
95B GLY* 3.2 12.6 + - - -
98B GLU* 3.5 35.5 + - + +
143B TYR* 3.4 5.4 + - - +
185B PHE* 3.5 48.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP 5.1 0.2 - - - +
89B HIS* 2.7 47.0 + - + +
90B PHE* 3.7 14.6 + - + +
92B LYS* 1.3 74.1 - - + +
94B LYS* 1.3 62.5 + - - +
95B GLY* 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.0 56.4 + - + +
91B LEU* 4.2 8.5 - - + +
93B GLU* 1.3 78.7 - - - +
95B GLY* 1.3 70.5 + - - +
113B TRP* 4.2 19.0 - - + -
----------------------------------------------------------
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