Contacts of the helix formed by residues 109 - 129 (chain C) in PDB entry 2OX6
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 LEU 109 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 3.7 26.5 - - + -
25C GLN* 4.0 28.3 - - + +
28C GLN* 4.2 17.9 - - - +
29C LEU* 4.0 20.0 - - + -
93C GLN* 3.5 22.4 - - + +
96C TYR* 3.6 7.0 - - - -
107C LEU 3.2 1.3 - - - +
108C PRO* 1.3 87.2 - - + +
110C THR* 1.3 65.8 + - - +
111C GLU* 3.6 12.6 - - - +
112C LEU* 3.0 29.2 + - + +
113C TYR 3.5 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 2.6 30.0 + - - +
91C PRO 4.7 2.7 - - - +
92C THR* 3.9 3.6 - - - -
93C GLN* 2.9 33.9 + - + +
96C TYR* 3.4 39.6 - - - +
109C LEU* 1.3 72.4 - - - +
111C GLU* 1.3 71.0 + - - +
113C TYR* 3.1 3.5 + - - +
114C ASN* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU 4.3 5.4 - - - +
20C SER* 3.6 26.0 - - - +
21C LEU* 4.4 8.1 - - + -
25C GLN* 3.1 30.5 + - - +
93C GLN* 4.4 2.4 - - - +
109C LEU* 3.1 13.2 - - - +
110C THR* 1.3 85.6 + - - +
112C LEU* 1.3 55.6 - - - +
114C ASN* 3.4 1.6 + - - +
115C THR* 2.8 32.9 + - - -
14D TYR* 3.5 23.1 - - - +
17D GLN* 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.6 28.7 - - + +
21C LEU* 3.8 14.6 - - + -
29C LEU* 4.6 7.2 - - + -
58C ILE* 3.9 37.5 - - + -
62C ILE* 3.7 11.2 - - + +
107C LEU* 3.9 21.0 - - + +
108C PRO* 3.8 28.5 - - + -
109C LEU* 3.0 22.9 + - + +
111C GLU* 1.3 74.7 - - - +
113C TYR* 1.3 59.2 + - - +
115C THR* 3.2 6.3 + - - -
116C ALA* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLN* 3.4 30.4 + - - -
87C PHE* 3.6 25.7 - + - -
88C VAL 3.6 21.9 + - - -
89C VAL* 4.8 6.1 - - + -
90C TYR* 3.9 24.5 + + - -
96C TYR* 3.5 28.0 + + + +
103C PHE* 3.3 43.3 - + - -
107C LEU* 4.6 8.6 - - + +
109C LEU 3.5 1.6 + - - -
110C THR* 3.1 6.6 + - - +
112C LEU* 1.3 77.5 - - - +
114C ASN* 1.3 59.3 + - - +
116C ALA* 3.2 6.8 + - - +
117C ALA* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 3.4 25.4 - - + +
90C TYR 3.8 20.6 + - - +
91C PRO* 5.3 3.6 + - - +
110C THR* 2.8 24.2 + - - +
111C GLU 3.7 0.4 - - - +
113C TYR* 1.3 76.3 - - - +
115C THR* 1.3 57.4 + - - +
117C ALA* 3.2 7.6 + - - +
118C TRP* 2.8 29.8 + - - +
134C LEU* 4.8 1.9 - - - +
10D ILE* 4.0 12.0 - - + +
14D TYR* 3.0 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER 3.5 22.4 - - - +
19C LEU* 3.3 8.6 + - - -
20C SER* 2.8 22.6 + - - +
62C ILE* 4.1 11.2 - - + -
111C GLU 2.8 24.3 + - - -
112C LEU* 3.4 7.6 - - - -
113C TYR 3.2 0.2 - - - -
114C ASN* 1.3 72.8 - - - +
116C ALA* 1.3 64.7 + - - +
118C TRP* 3.3 5.4 + - + +
119C ARG* 3.0 46.3 + - + +
14D TYR* 4.1 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ILE* 3.8 26.6 - - + +
65C GLN* 3.8 34.5 - - + +
66C VAL* 3.9 2.7 - - + +
107C LEU* 5.3 0.2 - - + -
112C LEU 3.0 12.4 + - - +
113C TYR* 3.2 9.4 + - - +
115C THR* 1.3 76.2 - - - +
117C ALA* 1.3 57.7 + - - +
119C ARG* 3.2 2.4 + - - +
120C ILE* 2.8 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 3.7 23.8 - - + -
89C VAL* 3.4 33.0 - - + -
113C TYR 2.9 12.0 + - - +
114C ASN 3.2 7.8 + - - +
116C ALA* 1.3 77.4 - - - +
118C TRP* 1.3 61.6 + - - +
120C ILE* 3.2 6.3 + - - +
121C LYS* 3.0 23.2 + - - +
134C LEU* 3.7 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASN 2.8 16.0 + - - +
115C THR* 3.7 6.5 - - + +
117C ALA* 1.3 77.9 - - - +
119C ARG* 1.3 66.8 + - + +
121C LYS* 3.2 42.1 + - + +
122C LYS* 2.9 46.1 + - + +
134C LEU* 3.9 12.1 - - + +
7D LEU* 4.5 9.2 - - + -
11D GLU* 3.8 24.0 - - + -
14D TYR* 4.0 22.7 - - + -
15D LEU* 3.7 42.4 - - + -
18D SER* 3.9 20.9 + - - -
56D LEU* 4.7 7.4 - - + -
59D ASP* 4.7 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.0 36.2 + - - -
19C LEU* 4.0 3.4 - - - +
59C ASP* 2.8 29.7 + - - -
62C ILE* 3.5 19.9 - - - +
63C GLU* 3.0 28.3 + - - +
66C VAL* 3.5 20.3 - - + +
115C THR* 3.0 34.1 + - + +
116C ALA 3.7 0.2 - - - +
118C TRP* 1.3 80.8 - - + +
120C ILE* 1.3 60.2 + - - +
122C LYS* 3.4 7.5 + - + +
123C GLU* 2.9 31.4 + - - +
122D LYS* 3.7 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C GLN* 4.2 12.6 - - + +
66C VAL* 3.8 26.2 - - - +
69C THR* 3.6 43.1 - - + +
70C THR* 4.5 2.9 - - - +
73C ILE* 4.3 4.9 - - + -
87C PHE* 3.9 28.7 - - + -
116C ALA 2.8 25.2 + - - +
117C ALA* 3.2 6.0 + - - +
119C ARG* 1.3 75.3 - - - +
121C LYS* 1.3 57.9 + - - +
123C GLU* 3.2 2.4 + - - +
124C CYS* 2.8 44.3 + - - +
132C VAL* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ALA 3.0 13.3 + - - +
118C TRP* 3.4 39.9 - - + +
120C ILE* 1.3 76.0 - - - +
122C LYS* 1.3 62.9 + - - +
124C CYS* 3.5 1.7 + - - +
125C LYS* 3.0 26.3 + - + +
130C VAL 4.6 1.2 - - - +
131C ASP* 3.3 17.2 + - - -
132C VAL* 2.9 45.0 + - + +
133C SER* 4.5 0.6 + - - +
134C LEU* 4.1 9.2 - - + -
7D LEU* 3.9 14.1 - - - +
11D GLU* 3.4 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C TRP* 2.9 36.8 + - + +
119C ARG* 3.7 8.3 - - + +
121C LYS* 1.3 76.4 - - - +
123C GLU* 1.3 58.9 + - - +
125C LYS* 3.3 9.4 + - - +
126C LEU* 2.9 32.7 + - + +
59D ASP* 2.9 40.1 + - - +
60D ASP* 5.1 4.9 + - - -
63D GLU* 4.0 37.8 - - - +
119D ARG* 4.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C VAL* 4.1 14.8 - - + +
67C LEU* 4.7 9.1 - - + +
70C THR* 3.5 29.9 - - + +
119C ARG 2.9 18.2 + - - +
120C ILE 3.6 2.9 - - - +
122C LYS* 1.3 77.3 - - - +
124C CYS* 1.3 56.9 + - - +
126C LEU* 3.2 10.5 + - - +
127C VAL* 2.9 51.7 + - + +
170C MG 2.2 31.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR* 4.0 20.2 - - - -
73C ILE* 3.7 31.4 - - - -
120C ILE* 2.8 25.7 + - - +
121C LYS 3.9 1.1 - - - +
123C GLU* 1.3 72.9 - - - +
125C LYS* 1.3 61.8 + - - +
128C LEU* 3.1 20.9 + - - +
129C GLU 3.0 18.7 + - - -
130C VAL* 3.1 16.7 + - + +
132C VAL* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LYS* 3.0 20.5 + - + +
122C LYS* 3.5 7.6 - - - +
124C CYS* 1.3 76.6 - - - +
126C LEU* 1.3 63.8 + - - +
129C GLU* 3.2 24.0 + - - +
130C VAL 3.3 13.4 + - - +
131C ASP* 5.8 1.8 - - - -
56D LEU* 4.8 23.2 - - - +
60D ASP* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS* 2.9 19.7 + - + +
123C GLU* 3.8 10.8 - - - +
125C LYS* 1.3 81.2 - - - +
127C VAL* 1.3 74.9 - - + +
129C GLU* 4.7 6.4 + - - +
63D GLU* 5.4 12.3 - - + +
67D LEU* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR* 4.2 7.4 - - + -
123C GLU* 2.9 53.2 + - + +
126C LEU* 1.3 91.5 - - + +
128C LEU* 1.3 81.4 + - + +
129C GLU* 3.7 1.5 - - - +
170C MG 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C THR* 4.0 17.0 - - + +
73C ILE* 3.9 28.5 - - + -
74C GLU* 3.9 44.6 - - + +
77C PHE* 5.0 10.2 - - + -
83C ARG* 3.0 15.9 + - - -
124C CYS* 3.1 17.4 + - - +
127C VAL* 1.3 97.1 - - + +
129C GLU* 1.3 67.7 + - - +
130C VAL* 3.3 16.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ARG* 3.1 34.7 + - - +
124C CYS 3.0 3.4 + - - -
125C LYS* 3.2 19.1 + - - +
126C LEU 4.7 6.5 - - - +
127C VAL 5.4 1.1 - - - -
128C LEU* 1.3 79.8 - - - +
130C VAL* 1.3 58.5 + - - +
131C ASP 4.3 0.5 + - - -
169C MG 2.3 30.3 - - - -
----------------------------------------------------------
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