Contacts of the helix formed by residues 84 - 99 (chain B) in PDB entry 1QO0
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 84 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.8 19.7 - - + -
20B THR* 3.9 29.6 - - + +
58B GLY* 3.7 25.8 - - - +
63B TYR* 5.5 0.6 + - - +
83B TYR* 1.3 79.6 - - + +
85B SER* 1.3 55.4 + - - +
86B HIS* 3.3 31.9 - - + +
87B THR* 2.6 45.1 + - + +
88B ARG 3.4 2.1 + - - -
150B TYR* 3.7 17.0 - - + +
179B LEU* 3.9 29.8 - - + -
206B VAL* 4.3 1.3 - - + -
500B BMD 3.2 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR 3.4 0.4 + - - -
84B MET* 1.3 71.1 - - - +
86B HIS* 1.3 59.8 + - - +
88B ARG* 3.1 26.7 + - - +
89B LYS* 2.9 28.8 + - - +
104B TYR* 4.0 1.1 - - - -
109B GLU* 2.5 35.6 + - - -
150B TYR* 4.0 1.2 - - - -
151B ILE* 3.8 17.5 - - - -
152B TYR* 4.2 1.1 - - - +
500B BMD 3.0 25.4 + - - -
88E TYR* 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 5.0 0.2 + - - -
60B PRO* 3.8 36.1 - - + +
84B MET* 3.4 44.6 - - + +
85B SER* 1.3 74.1 - - - +
87B THR* 1.3 56.6 + - + +
89B LYS* 3.8 4.8 - - + +
90B ALA* 3.2 25.3 + - - +
150B TYR* 3.4 32.9 - + + +
151B ILE* 4.5 2.4 - - + +
179B LEU* 4.6 7.4 - - + +
88E TYR* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 4.2 12.8 - - - +
60B PRO* 4.3 10.1 - - + -
63B TYR* 3.3 42.5 - - + +
82B CYS* 3.6 4.3 - - - +
83B TYR 3.2 20.6 + - - -
84B MET* 2.6 40.0 + - + +
86B HIS* 1.3 72.1 - - + +
88B ARG* 1.3 63.9 + - - +
90B ALA* 3.6 6.6 + - - +
91B VAL* 3.3 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B CYS* 3.9 10.1 - - + -
84B MET 3.4 0.4 + - - -
85B SER* 3.1 28.7 + - - +
87B THR* 1.3 80.3 + - - +
89B LYS* 1.3 69.8 + - - +
91B VAL* 3.2 2.9 + - - +
92B MET* 2.9 28.8 + - + +
102B LEU* 4.9 4.0 - - + +
104B TYR* 3.0 67.8 + - + -
108B TYR* 3.6 14.6 - - - -
109B GLU* 3.1 22.2 + - - -
110B GLY 5.2 0.2 + - - -
112B GLU* 2.7 42.4 + - - +
117B ILE* 4.1 17.7 - - + -
119B TYR* 4.4 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER 2.9 14.0 + - - +
86B HIS* 3.9 7.4 - - - +
87B THR 3.4 0.2 - - - -
88B ARG* 1.3 82.3 - - - +
90B ALA* 1.3 56.2 + - - +
92B MET* 4.0 19.3 - - + +
93B PRO* 3.1 27.2 - - - +
109B GLU* 4.9 0.2 - - - -
111B PHE 5.1 3.4 + - - -
112B GLU* 2.8 37.7 + - - +
113D HIS* 5.3 1.4 + - - -
87E GLU* 3.4 22.4 + - + +
88E TYR* 3.4 52.2 - - + +
89E GLU* 5.2 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PRO* 3.4 33.4 - - + +
61B ASP* 5.8 0.9 - - - +
64B ARG* 3.6 30.3 - - + +
86B HIS 3.2 18.2 + - - +
87B THR 3.7 5.4 - - - +
88B ARG 3.3 0.2 - - - -
89B LYS* 1.3 76.2 - - - +
91B VAL* 1.3 60.4 + - - +
93B PRO* 4.0 6.5 - - - +
94B VAL* 4.3 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 4.0 21.5 - - + -
63B TYR* 3.6 36.8 - - + +
64B ARG* 4.9 0.2 - - - +
67B ALA* 4.0 11.0 - - + -
79B LEU* 5.3 1.6 - - + -
82B CYS* 3.8 17.3 - - - -
87B THR 3.4 16.4 - - - +
88B ARG 3.2 4.2 + - - +
90B ALA* 1.3 76.1 - - - +
92B MET* 1.3 65.1 + - - +
93B PRO* 3.4 1.6 - - - -
94B VAL* 3.0 17.4 + - - +
95B VAL* 3.0 31.0 + - + +
102B LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 2.9 16.8 + - - +
89B LYS* 4.0 32.1 - - + +
91B VAL* 1.3 75.7 - - - +
93B PRO* 1.3 67.2 - - + +
95B VAL* 3.3 9.6 + - - +
96B GLU* 3.0 48.9 + - + +
112B GLU* 3.5 23.6 - - - +
114B SER* 3.9 3.8 - - - +
117B ILE* 3.8 22.0 - - + -
113D HIS* 3.6 35.4 - - + +
108E GLN 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS 3.1 21.3 - - - +
90B ALA 4.0 5.8 - - - +
91B VAL 3.5 3.4 - - - -
92B MET* 1.3 99.3 - - + +
94B VAL* 1.3 55.6 + - + +
96B GLU* 4.0 11.3 - - + +
97B ARG* 2.9 58.0 + - - +
109E PRO* 3.9 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 4.0 22.4 - - + +
67B ALA* 4.3 7.6 - - + +
68B GLU* 3.9 41.7 - - + +
71B ILE* 3.4 24.5 - - + -
72B ARG* 4.5 10.8 - - - +
90B ALA 4.3 4.3 - - - +
91B VAL 3.0 10.7 + - - +
93B PRO* 1.3 73.4 - - + +
95B VAL* 1.3 67.1 - - - +
97B ARG* 3.5 16.6 + - - +
98B ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 4.0 12.8 - - + -
79B LEU* 4.7 4.9 - - + -
91B VAL* 3.0 37.0 - - + +
92B MET* 3.3 11.2 - - - +
94B VAL* 1.3 75.5 - - + +
96B GLU* 1.3 62.3 + - + +
98B ALA 3.2 1.7 + - - -
99B ASP 3.1 3.6 + - - -
100B ALA* 3.0 45.1 + - + +
102B LEU* 4.1 18.2 - - + +
116B ASN* 3.5 32.0 + - + +
117B ILE* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 4.7 3.6 - - - -
92B MET* 3.0 29.8 + - + +
93B PRO* 4.0 8.8 - - - +
95B VAL* 1.3 74.9 - - + +
97B ARG* 1.3 64.2 + - + +
99B ASP* 3.1 19.9 + - - +
114B SER* 2.5 28.1 + - - +
115B PRO* 4.0 4.9 - - - +
116B ASN* 3.5 27.5 + - + +
111D ASP* 5.4 2.1 - - - +
113D HIS* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU 4.8 4.3 - - - -
97A ARG* 3.4 66.6 + - + +
98A ALA* 5.4 0.2 - - - -
99A ASP* 5.2 6.0 + - - -
64B ARG* 6.0 1.6 - - - +
68B GLU* 4.7 8.1 + - - -
72B ARG* 5.3 8.5 - - - +
93B PRO* 2.9 48.0 + - - +
94B VAL* 4.1 27.0 - - - +
96B GLU* 1.3 74.6 - - + +
98B ALA* 1.3 59.1 + - - +
99B ASP* 3.5 4.5 + - - +
109E PRO* 4.4 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG 5.2 0.9 - - - -
71B ILE* 3.3 38.6 - - + -
77B ARG* 3.6 21.7 + - - +
94B VAL 3.1 15.1 + - - +
95B VAL 3.2 3.5 + - - +
97B ARG* 1.3 75.2 - - - +
99B ASP* 1.3 71.1 + - - +
100B ALA* 3.3 5.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 2.6 40.1 + - - +
97A ARG* 5.1 6.6 - - - -
77B ARG* 4.5 2.4 - - - -
95B VAL 3.1 3.2 + - - -
96B GLU 3.1 10.9 + - - +
97B ARG 4.4 4.5 - - - +
98B ALA* 1.3 81.8 - - - +
100B ALA* 1.3 61.2 + - - +
116B ASN* 3.6 14.5 + - - +
308B VAL* 3.5 23.5 - - - +
----------------------------------------------------------
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