Contacts of the helix formed by residues 93 - 108 (chain R) in PDB entry 2X86
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 ASN 93 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77R ALA* 3.4 13.2 - - + +
78R CYS* 2.8 46.8 + - - -
89R MET* 2.9 29.6 + - - +
92R ASN* 1.3 84.6 + - - +
94R TYR* 1.3 63.9 + - - +
97R SER* 2.8 33.5 + - - -
140R PHE* 4.0 7.9 - - - -
143R SER* 3.2 29.0 + - - +
144R LYS* 4.6 7.0 - - + +
147R PHE* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R MET 3.7 0.2 + - - -
90R MET* 3.2 37.3 + - + +
93R ASN* 1.3 77.3 - - - +
95R GLN* 1.3 72.2 + - - +
97R SER* 3.2 6.3 + - - -
98R LYS* 2.9 40.1 + - + +
143R SER* 4.1 9.4 - - - +
146R LEU* 3.5 45.8 - - + +
147R PHE* 3.6 27.1 - + + -
150R TYR* 3.7 16.6 - - + +
48S ALA 4.3 0.7 + - - -
49S ASP* 2.5 39.8 + - - -
50S TYR* 3.7 14.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R MET 2.8 15.0 + - - +
91R ASP* 3.3 26.7 - - - +
94R TYR* 1.3 77.5 - - + +
96R TYR* 1.3 65.2 + - - +
98R LYS* 3.0 42.0 + - - +
99R GLU* 3.0 47.0 + - - +
50S TYR 4.0 9.9 - - - +
51S MET* 5.5 6.7 - - - +
55S ASP* 5.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R THR* 5.4 0.4 - - + -
30R VAL* 4.1 0.2 - - - +
53R LYS* 2.7 41.9 + - + +
54R GLU* 5.4 1.3 - - - -
56R PHE* 3.5 18.6 - + - -
57R LEU* 3.6 35.3 + - + -
74R HIS* 3.9 15.5 - + - -
91R ASP 2.9 12.2 + - - +
92R ASN* 3.0 26.9 - - - +
93R ASN 4.0 0.2 - - - +
94R TYR 3.3 0.4 - - - -
95R GLN* 1.3 73.6 - - - +
97R SER* 1.3 65.0 + - - +
99R GLU* 3.0 17.8 + - - +
100R LEU* 3.0 31.9 + - + +
400R NAP 3.4 37.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R HIS* 2.8 32.9 + - - -
76R GLY 5.2 0.5 + - - -
93R ASN* 2.8 21.2 + - - -
94R TYR 3.5 4.0 - - - -
96R TYR* 1.3 80.1 - - - +
98R LYS* 1.3 63.0 + - - +
100R LEU* 3.3 3.7 + - - +
101R LEU* 2.9 24.6 + - - +
111R PHE* 4.1 1.0 - - - -
113R TYR* 5.9 0.3 - - - -
144R LYS* 5.6 3.1 + - - -
147R PHE* 3.6 34.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R TYR* 2.9 26.6 + - + +
95R GLN* 3.0 43.3 + - - +
97R SER* 1.3 76.4 - - - +
99R GLU* 1.3 64.1 + - - +
101R LEU* 3.2 3.0 + - - +
102R HIS* 3.0 37.3 + - + +
147R PHE* 3.7 12.6 - - + -
150R TYR* 3.6 44.8 + - + +
49S ASP* 2.8 35.8 + - - +
50S TYR 4.2 2.0 + - - -
51S MET* 5.3 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R LEU* 4.0 15.0 - - + -
60R ILE* 3.9 7.5 - - + +
61R MET* 3.4 43.7 - - + +
95R GLN* 3.0 38.2 + - - +
96R TYR 3.2 9.9 - - - +
98R LYS* 1.3 79.8 - - - +
100R LEU* 1.3 61.8 + - - +
102R HIS* 3.5 8.0 + - - +
103R TYR* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R THR* 4.1 14.6 - - + -
56R PHE* 3.7 24.7 - - + -
57R LEU* 5.2 2.5 - - + -
60R ILE* 3.9 17.9 - - + -
72R ILE* 4.5 12.6 - - + -
74R HIS* 3.3 46.0 - - + +
96R TYR* 3.0 24.2 + - + +
97R SER 3.6 7.2 - - - +
99R GLU* 1.3 75.1 - - - +
101R LEU* 1.3 67.1 + - - +
103R TYR* 3.1 6.6 + - - +
104R CYS* 2.9 26.3 + - - -
111R PHE* 3.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R SER 2.9 16.9 + - - +
98R LYS 3.5 4.3 - - - +
100R LEU* 1.3 77.7 - - - +
102R HIS* 1.3 60.5 + - + +
104R CYS* 3.3 1.6 + - - +
105R LEU* 2.8 43.5 + - + +
111R PHE* 3.8 31.8 - - + -
147R PHE* 4.0 21.3 - - + -
150R TYR* 4.0 28.3 - - + -
151R VAL* 4.3 9.6 - - + -
154R ILE* 4.3 13.5 - - + -
162R ILE* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98R LYS* 3.0 34.7 + - + +
99R GLU* 3.9 9.0 - - - +
101R LEU* 1.3 77.8 - - + +
103R TYR* 1.3 63.6 - - - +
105R LEU* 3.5 13.7 - - + +
106R GLU* 3.0 30.4 + - - +
150R TYR* 2.6 38.3 + + - -
154R ILE* 4.5 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R ILE* 6.0 0.2 - - + -
60R ILE* 3.5 59.0 - - + -
63R GLY* 4.3 0.4 - - - -
64R GLU 2.6 28.4 + - - -
65R GLU* 3.8 5.2 + - - -
66R PHE* 3.3 17.7 + + - -
69R VAL* 5.6 2.9 - - + +
72R ILE* 4.7 7.2 - - + -
99R GLU 3.2 12.7 + - - +
100R LEU 3.1 8.9 + - - +
102R HIS* 1.3 77.3 - - - +
104R CYS* 1.3 71.7 + - - +
106R GLU* 4.8 1.8 - - - -
107R ARG* 3.1 79.8 + - - +
109R ILE* 4.1 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ILE* 3.4 37.0 - - - -
100R LEU 2.9 15.0 + - - +
101R LEU* 3.6 7.4 - - + +
103R TYR* 1.3 78.3 - - - +
105R LEU* 1.3 55.3 + - + +
107R ARG 3.0 2.3 + - - -
108R GLU 2.7 31.4 + - - -
109R ILE* 2.9 41.7 + - - +
111R PHE* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R LEU* 2.8 31.9 + - + +
102R HIS* 3.5 15.9 - - - +
104R CYS* 1.3 77.2 - - + +
106R GLU* 1.3 63.1 + - - +
108R GLU* 3.3 17.8 + - - +
109R ILE 6.0 0.2 - - - +
111R PHE* 6.3 0.2 - - + -
154R ILE* 3.6 32.8 - - + -
158R ALA* 4.4 14.1 - - + -
159R ASN* 5.2 2.4 - - - +
160R SER* 4.2 14.4 + - - +
162R ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260N GLU* 5.4 8.5 - - - +
102R HIS* 3.0 19.0 + - - +
103R TYR* 3.8 6.1 - - - +
105R LEU* 1.3 78.5 - - - +
107R ARG* 1.3 77.3 + - + +
108R GLU* 3.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R GLY* 3.5 29.5 + - - -
65R GLU* 3.3 38.2 + - - +
103R TYR* 3.1 64.1 + - - +
104R CYS 3.0 2.6 + - - -
106R GLU* 1.3 100.3 + - + +
108R GLU* 1.3 72.2 + - - +
109R ILE* 3.2 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194N ASN 5.3 1.9 - - - +
195N GLY 5.2 0.6 - - - +
196N GLU* 3.3 42.9 - - - +
197N SER 4.4 0.7 + - - -
199N LYS* 5.1 2.8 + - - -
104R CYS 2.7 7.6 + - - -
105R LEU 3.3 10.8 + - - +
106R GLU 4.9 2.7 - - - +
107R ARG* 1.3 81.8 - - - +
109R ILE* 1.3 58.0 + - - +
110R PRO* 3.4 10.9 - - - +
159R ASN* 3.9 21.4 - - + +
160R SER* 3.4 24.7 - - - +
----------------------------------------------------------
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