Contacts of the helix formed by residues 109 - 129 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.7 25.1 - - + -
25B GLN* 3.9 28.5 - - + +
28B GLN* 3.9 18.6 - - - +
29B LEU* 4.1 23.6 - - + -
93B GLN* 3.4 17.7 - - + +
96B TYR* 3.7 6.0 - - - -
107B LEU 3.2 1.4 + - - +
108B PRO* 1.3 88.8 - - + +
110B THR* 1.3 66.6 + - - +
111B GLU* 3.7 10.5 - - - +
112B LEU* 3.0 29.0 + - + +
113B TYR 3.7 2.1 + - - -
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 2.7 29.7 + - - +
91B PRO 5.0 2.7 - - - +
92B THR* 4.1 2.7 - - - -
93B GLN* 3.0 30.7 + - + +
96B TYR* 3.5 40.0 - - - +
109B LEU* 1.3 71.4 - - - +
111B GLU* 1.3 72.8 + - - +
113B TYR* 3.0 5.0 + - - +
114B ASN* 2.9 35.2 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.6 24.3 - - - +
17A GLN* 5.6 0.7 - - - +
19B LEU 4.3 2.2 - - - +
20B SER* 3.7 26.0 - - - +
21B LEU* 4.6 8.1 - - + -
25B GLN* 2.9 31.5 + - - +
93B GLN* 4.5 1.9 - - - +
109B LEU* 3.2 8.2 + - + +
110B THR* 1.3 92.0 + - + +
112B LEU* 1.3 52.2 + - - +
114B ASN* 3.5 2.1 + - - +
115B THR* 2.7 37.7 + - - -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.7 27.4 - - + +
21B LEU* 4.0 15.7 - - + -
29B LEU* 4.8 4.5 - - + -
58B ILE* 3.7 34.3 - - + -
62B ILE* 3.8 9.6 - - + +
107B LEU* 3.9 23.3 - - + +
108B PRO* 3.6 32.3 - - + -
109B LEU* 3.0 22.1 + - + +
111B GLU* 1.3 73.8 - - - +
113B TYR* 1.3 62.1 + - - +
115B THR* 3.3 6.7 + - - -
116B ALA* 3.0 26.7 + - - +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN* 3.5 25.7 + - - -
87B PHE* 3.8 22.5 - + - -
88B VAL 3.5 24.3 + - - -
89B VAL* 4.3 7.0 - - + -
90B TYR* 3.9 24.1 - + - -
96B TYR* 3.5 36.1 + + + +
100B ASN* 4.8 1.8 - - - -
103B PHE* 3.8 31.0 - + - -
107B LEU* 4.5 6.0 - - + +
109B LEU 3.7 1.2 + - - -
110B THR* 3.0 7.2 + - - +
112B LEU* 1.3 76.5 - - - +
114B ASN* 1.3 60.1 + - - +
116B ALA* 3.2 5.3 + - - +
117B ALA* 2.9 25.8 + - - +
155B ARG* 3.8 14.9 + - - -
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Residues in contact with ASN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.1 4.9 - - + -
14A TYR* 2.9 51.0 + - + +
89B VAL* 3.3 27.8 - - - +
90B TYR 4.2 9.9 + - - +
91B PRO* 6.0 1.0 + - - +
110B THR* 2.9 28.4 + - - +
111B GLU* 3.7 5.2 - - - +
113B TYR* 1.3 75.7 - - - +
115B THR* 1.3 57.8 + - - +
117B ALA* 3.1 8.6 + - - +
118B TRP* 2.8 30.0 + - - +
134B LEU* 4.7 1.6 - - - +
136B ASN* 5.0 1.3 + - - +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 4.4 6.1 - - - -
18B SER 3.4 24.5 - - - +
19B LEU* 3.3 10.6 + - - -
20B SER* 2.9 21.5 + - - +
62B ILE* 4.5 6.5 - - + -
111B GLU 2.7 22.0 + - - -
112B LEU* 3.4 8.7 - - - -
114B ASN* 1.3 76.1 - - - +
116B ALA* 1.3 63.2 + - - +
118B TRP* 3.3 6.7 + - + +
119B ARG* 2.9 45.8 + - + +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE* 3.8 27.1 - - + +
65B GLN* 4.0 33.7 - - + +
66B VAL* 3.9 2.1 - - - +
107B LEU* 5.1 0.4 - - + -
112B LEU 3.0 13.1 + - - +
113B TYR* 3.5 10.1 - - - +
115B THR* 1.3 76.1 - - - +
117B ALA* 1.3 58.2 + - - +
119B ARG* 3.3 2.8 + - - +
120B ILE* 2.8 37.4 + - + +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.7 22.6 - - + -
89B VAL* 3.4 33.4 - - + -
113B TYR 2.9 9.4 + - - +
114B ASN 3.3 8.7 - - - +
116B ALA* 1.3 75.8 - - - +
118B TRP* 1.3 62.5 + - - +
120B ILE* 3.2 5.6 + - - +
121B LYS* 2.9 23.6 + - - +
134B LEU* 3.8 15.4 - - + +
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Residues in contact with TRP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.4 8.3 - - + -
11A GLU* 3.9 31.0 - - + -
14A TYR* 3.8 26.5 - - + -
15A LEU* 3.6 43.3 - - + -
18A SER* 4.1 19.6 + - - -
56A LEU* 4.9 6.5 - - + -
59A ASP* 4.6 6.7 + - - -
114B ASN 2.8 17.9 + - - +
115B THR* 3.8 6.5 - - + +
117B ALA* 1.3 72.2 - - - +
119B ARG* 1.3 74.7 + - + +
121B LYS* 3.2 38.0 + - + +
122B LYS* 3.0 41.4 + - + +
134B LEU* 3.9 6.6 - - + +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 4.6 6.7 - - - +
18B SER* 3.0 39.4 + - - -
19B LEU* 4.2 2.2 - - - +
59B ASP* 2.9 29.3 + - - -
62B ILE* 3.6 24.2 - - - +
63B GLU* 3.5 23.8 + - - -
66B VAL* 3.5 19.2 - - + +
115B THR* 2.9 31.7 + - + +
118B TRP* 1.3 84.4 - - + +
120B ILE* 1.3 57.8 + - - +
122B LYS* 3.3 9.4 + - + +
123B GLU* 2.9 30.7 + - - +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLN* 4.2 14.6 - - + +
66B VAL* 3.8 26.0 - - - +
69B THR* 3.8 37.0 - - + +
70B THR* 4.5 2.9 - - - +
73B ILE* 4.5 4.7 - - + -
87B PHE* 3.9 31.9 - - + -
116B ALA* 2.8 26.3 + - + +
117B ALA* 3.5 5.4 - - - +
118B TRP 3.2 0.2 - - - -
119B ARG* 1.3 73.8 - - - +
121B LYS* 1.3 67.0 + - - +
123B GLU* 3.8 1.1 - - - -
124B CYS* 2.9 40.9 + - - +
132B VAL* 5.0 5.6 - - + -
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 5.4 7.1 + - - +
6A GLY 5.2 2.8 + - - -
7A LEU* 3.6 22.2 - - - +
11A GLU* 3.3 37.8 + - + +
117B ALA 2.9 12.9 + - - +
118B TRP* 3.5 28.3 - - + +
120B ILE* 1.3 75.9 - - - +
122B LYS* 1.3 64.2 + - - +
124B CYS* 3.5 1.9 + - - +
125B LYS* 3.1 24.2 + - + +
130B VAL 4.6 1.0 - - - +
131B ASP* 5.9 0.6 - - - +
132B VAL* 2.8 49.6 + - + +
133B SER* 4.5 4.0 + - - +
134B LEU* 4.5 7.2 - - + -
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 3.1 32.0 + - - +
60A ASP* 5.1 5.9 + - - -
63A GLU* 3.9 28.8 - - - +
119A ARG* 4.7 3.8 - - - +
118B TRP* 3.0 40.2 + - + +
119B ARG* 3.7 8.5 - - + +
120B ILE 3.2 0.2 - - - -
121B LYS* 1.3 77.7 - - - +
123B GLU* 1.3 58.5 + - - +
125B LYS* 3.2 5.6 + - - +
126B LEU* 3.0 58.1 + - + +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B VAL* 4.0 15.4 - - + +
67B LEU* 4.7 14.9 - - + +
70B THR* 3.7 25.6 - - + +
119B ARG 2.9 17.3 + - - +
120B ILE 3.8 2.7 - - - +
122B LYS* 1.3 76.4 - - - +
124B CYS* 1.3 60.3 + - - +
126B LEU* 4.5 7.9 - - - +
127B VAL* 2.8 60.3 + - + +
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Residues in contact with CYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR* 3.8 26.2 - - - -
73B ILE* 3.7 31.2 - - - -
120B ILE* 2.9 22.0 + - - +
121B LYS 3.8 2.9 - - - +
123B GLU* 1.3 75.3 - - - +
125B LYS* 1.3 62.1 + - - +
128B LEU* 3.0 22.8 + - - +
130B VAL* 3.0 34.0 + - + +
132B VAL* 3.8 15.9 - - + -
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS* 3.1 19.1 + - + +
122B LYS* 3.7 6.1 - - - +
123B GLU 3.2 0.2 - - - -
124B CYS* 1.3 77.1 - - - +
126B LEU* 1.3 69.2 + - + +
129B GLU* 3.2 37.7 + - - +
130B VAL 3.4 12.1 + - - +
131B ASP* 2.8 34.6 + - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP* 5.7 4.7 - - - +
63A GLU* 5.1 7.6 - - + +
122B LYS* 3.0 51.6 + - + +
123B GLU* 4.1 6.5 - - - +
125B LYS* 1.3 85.7 - - + +
127B VAL* 1.3 67.1 + - + +
129B GLU* 4.7 5.4 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 5.2 2.9 - - + -
123B GLU* 2.8 49.7 + - + +
126B LEU* 1.3 80.6 - - + +
128B LEU* 1.3 73.7 + - + +
129B GLU* 3.6 1.4 - - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B THR* 3.5 43.1 - - + +
71B ASP* 5.8 1.6 - - - +
73B ILE* 4.1 14.1 - - + -
74B GLU* 3.7 46.7 - - + +
82B LYS* 3.8 9.2 + - - +
124B CYS* 3.0 15.5 + - - +
127B VAL* 1.3 91.0 - - + +
129B GLU* 1.3 70.7 + - - +
130B VAL* 3.3 18.8 + - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS* 3.7 22.6 + - - +
124B CYS 3.1 2.0 + - - -
125B LYS* 3.2 34.1 + - - +
126B LEU 5.0 5.8 - - - +
127B VAL 5.5 0.7 - - - -
128B LEU* 1.3 80.0 - - - +
130B VAL* 1.3 57.8 + - - +
131B ASP* 4.2 1.9 + - - +
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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) + - + + + + + -
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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