Contacts of the helix formed by residues 79 - 89 (chain B) in PDB entry 1AGQ
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 MET 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 3.8 43.7 - - + -
58A TYR* 5.3 6.3 - - - +
123A ILE 5.9 0.2 - - - +
124A LEU* 4.1 15.7 - - + -
125A ARG 3.5 22.7 - - - +
126A LYS 3.6 1.1 - - - +
127A HIS* 3.6 24.5 - - + -
78B THR* 1.3 76.3 + - - +
80B TYR* 1.3 64.6 + - - +
82B LYS* 3.2 16.0 + - + +
83B ILE* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.9 12.8 - + - -
67A ARG 3.6 20.4 - - - -
68A TYR* 3.4 5.4 - - - +
69A CYS* 2.9 32.6 + - - +
104A ARG* 3.7 14.4 - - - -
105A PRO* 3.4 33.7 - - + +
108A PHE* 4.0 9.4 - + + -
126A LYS 3.3 16.3 + - - +
127A HIS 3.8 23.8 - - - +
129A ALA 4.2 5.6 - - - -
78B THR* 3.6 8.3 - - + +
79B MET* 1.3 79.0 - - - +
81B ASP* 1.3 66.0 + - - +
83B ILE* 3.2 6.2 + - - +
84B LEU* 3.0 50.1 + - + +
98B VAL* 4.2 0.2 - - - +
99B GLY 4.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 2.8 40.4 + - - -
76B ALA* 3.9 22.2 - - + -
77B GLU* 4.5 3.7 + - - +
78B THR* 2.8 30.3 + - + +
80B TYR* 1.3 76.1 - - - +
82B LYS* 1.3 65.7 + - - +
84B LEU* 3.4 11.3 + - - +
85B LYS* 3.1 32.2 + - - +
100B GLN* 4.8 0.9 - - - -
101B ALA* 4.0 17.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
56A LEU* 4.9 6.7 - - + -
76B ALA* 3.6 25.2 + - + -
77B GLU 4.4 3.4 + - - -
78B THR* 3.1 31.6 + - - +
79B MET* 3.5 24.3 - - + +
81B ASP* 1.3 76.2 - - - +
83B ILE* 1.3 58.9 + - - +
85B LYS* 3.3 6.2 + - - +
86B ASN* 3.0 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.8 50.9 - - + +
56A LEU* 4.6 3.1 - - + -
66A PHE* 3.6 25.1 - - + -
127A HIS* 3.6 36.3 - - + +
79B MET* 3.0 26.1 + - + +
80B TYR 3.4 6.7 - - - +
82B LYS* 1.3 77.8 - - - +
84B LEU* 1.3 57.2 + - - +
86B ASN* 3.0 2.8 + - - +
87B LEU* 2.8 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.0 16.2 - - + -
68A TYR* 4.2 3.1 - - + -
80B TYR* 3.0 40.7 + - + +
81B ASP* 3.6 18.2 - - - +
82B LYS 3.3 0.2 - - - -
83B ILE* 1.3 77.0 - - - +
85B LYS* 1.3 61.5 + - - +
87B LEU* 3.3 3.4 + - - +
88B SER* 3.0 26.0 + - - -
93B LEU* 3.7 23.9 - - + +
98B VAL* 3.2 39.0 - - + -
99B GLY 3.8 10.3 - - - +
100B GLN* 5.1 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B CYS 5.3 1.4 + - - -
74B GLU 3.2 23.0 + - - -
75B ALA* 4.2 0.4 - - - +
76B ALA* 3.2 40.3 - - + +
81B ASP* 3.1 21.4 + - - +
82B LYS* 3.5 9.9 - - - +
84B LEU* 1.3 75.7 - - - +
86B ASN* 1.3 67.6 + - - +
88B SER* 3.4 5.4 + - - -
89B ARG* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP 5.0 1.3 - - - +
54A LEU 2.7 34.0 + - - +
55A GLY* 3.3 24.3 + - - +
56A LEU* 4.2 7.5 - - - +
82B LYS* 3.0 23.3 + - - +
83B ILE 3.0 3.8 + - - +
85B LYS* 1.3 81.4 - - - +
87B LEU* 1.3 58.6 + - - +
89B ARG* 3.3 7.7 + - - +
90B SER* 3.0 29.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
47A ILE* 5.3 2.2 - - + -
49A LEU* 3.9 20.6 - - + -
53A ASP* 3.4 29.2 - - + +
66A PHE* 3.5 37.7 - - + -
83B ILE* 2.8 32.2 + - + +
84B LEU* 3.3 4.0 + - - +
86B ASN* 1.3 73.7 - - - +
88B SER* 1.3 61.3 + - - +
90B SER* 3.2 8.5 + - - +
91B ARG 3.1 2.4 + - - -
92B ARG* 2.9 39.7 + - + -
93B LEU* 3.2 28.4 + - + +
----------------------------------------------------------
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 LEU 3.0 18.4 + - - -
85B LYS* 3.7 6.7 - - - -
87B LEU* 1.3 76.2 - - - +
89B ARG* 1.3 66.4 + - - +
91B ARG* 3.1 26.3 + - - -
93B LEU 3.1 17.0 + - - -
94B THR* 4.4 2.3 - - - +
95B SER* 3.2 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS 3.1 14.2 + - - +
86B ASN* 3.7 9.2 - - - +
88B SER* 1.3 76.6 - - - +
90B SER* 1.3 60.2 + - - +
91B ARG* 3.2 23.2 + - - +
----------------------------------------------------------
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