Contacts of the helix formed by residues 93 - 108 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY 5.7 0.7 - - - -
77B ALA* 3.4 12.5 - - + +
78B CYS* 2.8 45.8 + - - +
89B MET* 2.9 29.0 + - - +
92B ASN* 1.3 84.9 + - - +
94B TYR* 1.3 63.2 + - - +
97B SER* 2.8 33.4 + - - -
140B PHE* 4.0 8.3 - - - -
143B SER* 3.2 28.4 + - - +
144B LYS* 4.6 6.9 - - + +
147B PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MET 3.7 0.2 + - - -
90B MET* 3.2 38.2 + - + +
93B ASN* 1.3 75.2 - - - +
95B GLN* 1.3 73.0 + - - +
97B SER* 3.2 6.5 + - - -
98B LYS* 2.9 40.1 + - + +
143B SER* 4.1 9.9 - - - +
146B LEU* 3.5 42.9 - - + +
147B PHE* 3.6 28.4 - + + -
150B TYR* 3.7 15.8 - - + +
48C ALA 4.3 0.7 + - - -
49C ASP* 2.4 39.6 + - - -
50C TYR* 3.7 13.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET 2.8 15.2 + - - +
91B ASP* 3.3 26.7 - - - +
94B TYR* 1.3 77.0 - - + +
96B TYR* 1.3 63.6 + - - +
98B LYS* 3.0 41.6 + - - +
99B GLU* 3.0 47.6 + - - +
50C TYR 4.1 9.9 - - - +
51C MET* 5.5 4.9 - - - +
55C ASP* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 5.4 0.4 - - + -
53B LYS* 2.7 41.4 + - + +
54B GLU* 5.4 1.8 - - - -
56B PHE* 3.5 19.1 - + - -
57B LEU* 3.6 33.0 + - + -
74B HIS* 3.9 15.5 - + - +
91B ASP 2.9 12.3 + - - +
92B ASN* 3.1 26.9 - - - +
93B ASN 4.0 0.2 - - - +
95B GLN* 1.3 73.8 - - - +
97B SER* 1.3 63.8 + - - +
99B GLU* 3.0 17.7 + - - +
100B LEU* 3.0 31.3 + - + +
400B NAP 3.3 36.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B HIS* 2.8 32.8 + - - -
76B GLY 5.2 0.2 + - - -
93B ASN* 2.8 21.3 + - - -
94B TYR 3.5 3.8 - - - -
96B TYR* 1.3 80.1 - - - +
98B LYS* 1.3 62.4 + - - +
100B LEU* 3.3 2.9 + - - +
101B LEU* 2.9 24.6 + - - +
111B PHE* 4.1 1.0 - - - -
113B TYR* 5.9 0.5 - - - -
144B LYS* 5.7 3.1 + - - -
147B PHE* 3.6 33.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 2.9 30.8 + - + +
95B GLN* 3.0 45.1 + - - +
97B SER* 1.3 76.4 - - - +
99B GLU* 1.3 64.3 + - - +
101B LEU* 3.2 3.1 + - - +
102B HIS* 3.0 37.5 + - + +
147B PHE* 3.5 13.2 - - + -
150B TYR* 3.6 45.9 + - + +
49C ASP* 2.9 30.9 + - - -
50C TYR 4.2 2.4 + - - -
51C MET* 5.2 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.0 14.4 - - + -
60B ILE* 3.9 8.0 - - + +
61B MET* 3.4 45.4 - - + +
95B GLN* 3.0 37.8 + - - +
96B TYR 3.0 10.5 + - - +
98B LYS* 1.3 80.4 - - - +
100B LEU* 1.3 61.9 + - - +
102B HIS* 3.4 8.1 + - - +
103B TYR* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 4.1 14.1 - - + -
56B PHE* 3.7 24.7 - - + -
57B LEU* 5.2 2.7 - - + -
60B ILE* 3.9 18.4 - - + -
72B ILE* 4.4 12.8 - - + -
74B HIS* 3.3 46.0 - - + +
96B TYR* 3.0 25.0 + - + +
97B SER 3.6 7.2 - - - +
99B GLU* 1.3 74.2 - - - +
101B LEU* 1.3 65.7 - - - +
103B TYR* 3.1 7.0 + - - +
104B CYS* 2.9 26.3 + - - -
111B PHE* 3.7 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B SER 2.9 18.5 + - - +
98B LYS 3.5 3.6 - - - +
100B LEU* 1.3 75.7 - - - +
102B HIS* 1.3 59.5 + - + +
104B CYS* 3.3 1.4 + - - +
105B LEU* 2.8 41.8 + - + +
111B PHE* 3.8 31.6 - - + -
147B PHE* 4.0 20.4 - - + -
150B TYR* 4.0 28.0 - - + -
151B VAL* 4.3 9.6 - - + -
154B ILE* 4.3 14.6 - - + -
162B ILE* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LYS* 3.0 33.8 + - + +
99B GLU* 3.9 8.5 - - - +
101B LEU* 1.3 78.0 - - + +
103B TYR* 1.3 63.8 + - - +
105B LEU* 3.5 13.4 - - + +
106B GLU* 3.0 30.0 + - - +
150B TYR* 2.6 37.0 + + - -
154B ILE* 4.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 3.5 58.1 - - + -
63B GLY* 4.3 1.1 - - - -
64B GLU 2.6 28.2 + - - -
65B GLU* 3.9 5.0 + - - -
66B PHE* 3.3 18.2 + + - -
69B VAL* 5.6 2.7 - - + +
72B ILE* 4.7 6.7 - - + -
99B GLU 3.2 13.4 + - - +
100B LEU 3.1 8.6 + - - +
102B HIS* 1.3 77.4 - - - +
104B CYS* 1.3 71.7 + - - +
106B GLU* 4.8 1.3 - - - -
107B ARG* 3.1 79.2 + - - +
109B ILE* 4.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.4 36.6 - - - -
100B LEU 2.9 14.8 + - - +
101B LEU* 3.6 7.6 - - + +
103B TYR* 1.3 79.1 - - - +
105B LEU* 1.3 55.9 + - + +
107B ARG 3.0 2.3 + - - -
108B GLU 2.7 31.5 + - - -
109B ILE* 2.9 42.4 + - - +
111B PHE* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 2.8 30.8 + - + +
102B HIS* 3.5 15.9 - - - +
104B CYS* 1.3 77.8 - - + +
106B GLU* 1.3 61.8 + - - +
108B GLU* 3.3 17.3 + - - +
109B ILE 6.1 0.2 - - - +
111B PHE* 6.3 0.4 - - + -
154B ILE* 3.5 33.0 - - + -
158B ALA* 4.3 13.2 - - + -
159B ASN* 5.2 3.5 + - - +
160B SER* 4.3 15.0 + - - +
161B GLN 5.7 0.2 - - - +
162B ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B HIS* 3.0 18.5 + - - +
103B TYR* 3.8 5.6 - - - +
104B CYS 3.1 0.2 - - - -
105B LEU* 1.3 77.4 - - - +
107B ARG* 1.3 79.2 + - + +
108B GLU* 3.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY* 3.5 29.1 + - - -
65B GLU* 3.3 37.6 + - - +
103B TYR* 3.1 64.2 + - - +
104B CYS 3.0 1.8 + - - -
106B GLU* 1.3 101.5 + - + +
108B GLU* 1.3 71.9 + - - +
109B ILE* 3.2 23.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B CYS 2.7 5.0 + - - -
105B LEU 3.3 10.4 + - - +
106B GLU 4.9 2.7 - - - +
107B ARG* 1.3 81.5 - - - +
109B ILE* 1.3 57.8 + - - +
110B PRO* 3.4 10.7 - - - +
159B ASN* 3.9 31.2 + - + +
160B SER* 3.4 26.6 - - - +
195G GLY 5.7 0.9 - - - +
----------------------------------------------------------
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