Contacts of the helix formed by residues 109 - 129 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU* 3.8 24.0 - - + -
25D GLN* 3.8 28.9 - - + +
28D GLN* 5.4 7.2 - - + -
29D LEU* 4.1 23.6 - - + -
93D GLN* 3.4 19.5 - - + +
96D TYR* 3.6 7.1 - - - -
107D LEU 3.2 1.7 + - - +
108D PRO* 1.3 87.8 - - + +
110D THR* 1.3 67.2 + - - +
111D GLU* 3.6 11.7 - - - +
112D LEU* 3.0 28.8 + - + +
113D TYR 3.7 2.4 + - - -
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Residues in contact with THR 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D TYR* 2.7 29.4 + - - +
91D PRO 4.8 2.7 - - - +
92D THR* 4.0 2.9 - - - -
93D GLN* 2.9 30.2 + - + +
96D TYR* 3.5 39.3 - - - +
109D LEU* 1.3 71.8 - - - +
111D GLU* 1.3 72.7 + - - +
113D TYR* 3.1 4.5 + - - +
114D ASN* 2.9 35.7 + - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 3.6 23.4 - - - +
17C GLN* 5.7 0.2 - - - +
19D LEU 4.3 3.8 - - - +
20D SER* 3.7 26.0 - - - +
21D LEU* 4.5 8.3 - - + -
25D GLN* 3.2 30.6 + - - +
93D GLN* 4.5 1.9 - - - +
109D LEU* 3.2 8.4 + - - +
110D THR* 1.3 91.9 + - - +
112D LEU* 1.3 52.4 + - - +
114D ASN* 3.6 2.4 - - - +
115D THR* 2.7 38.1 + - - -
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 3.6 28.7 - - + +
21D LEU* 3.9 19.7 - - + -
29D LEU* 4.6 5.6 - - + -
58D ILE* 3.8 35.9 - - + -
62D ILE* 3.8 9.5 - - + +
107D LEU* 3.9 20.9 - - + -
108D PRO* 3.7 31.9 - - + -
109D LEU* 3.0 18.5 + - + +
111D GLU* 1.3 77.1 - - - +
113D TYR* 1.3 58.2 + - - +
115D THR* 3.3 7.1 + - - -
116D ALA* 3.0 25.8 + - - +
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Residues in contact with TYR 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D GLN* 3.2 28.9 + - - -
87D PHE* 3.6 24.8 - + - -
88D VAL 3.5 24.0 + - - -
89D VAL* 4.5 6.1 - - + -
90D TYR* 3.8 19.7 - + - -
96D TYR* 3.4 37.1 + + + +
100D ASN* 4.3 6.7 - - - -
103D PHE* 3.9 29.6 - + - -
107D LEU* 4.6 3.1 - - + +
109D LEU 3.7 1.4 + - - -
110D THR* 3.1 6.5 + - - +
112D LEU* 1.3 76.5 - - - +
114D ASN* 1.3 60.8 + - - +
116D ALA* 3.2 5.7 + - - +
117D ALA* 2.9 25.6 + - - +
155D ARG* 3.9 13.3 + - - -
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Residues in contact with ASN 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.2 12.7 - - + +
14C TYR* 3.0 49.0 + - + +
89D VAL* 3.4 26.3 - - - +
90D TYR 4.1 11.9 + - - +
91D PRO* 5.7 2.6 + - - +
110D THR* 2.9 29.4 + - - +
111D GLU* 3.6 3.5 - - - +
113D TYR* 1.3 76.8 - - - +
115D THR* 1.3 56.4 + - - +
117D ALA* 3.2 7.8 + - - +
118D TRP* 2.9 30.1 + - - +
134D LEU* 4.7 2.4 - - + +
136D ASN* 5.2 0.8 + - - +
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Residues in contact with THR 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 4.3 5.8 - - + -
18D SER 3.4 25.1 - - - +
19D LEU* 3.3 10.1 + - - -
20D SER* 2.8 22.9 + - - +
62D ILE* 4.5 7.4 - - + -
111D GLU 2.7 20.0 + - - -
112D LEU* 3.4 9.9 - - - -
113D TYR 3.2 0.2 - - - -
114D ASN* 1.3 75.2 - - - +
116D ALA* 1.3 63.4 + - - +
118D TRP* 3.3 6.1 + - + +
119D ARG* 3.0 47.8 + - + +
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ILE* 3.8 25.0 - - + +
65D GLN* 4.0 32.5 - - + +
66D VAL* 3.8 3.7 - - + +
107D LEU* 5.1 0.4 - - + -
112D LEU 3.0 14.2 + - - +
113D TYR* 3.2 9.4 + - - +
115D THR* 1.3 77.0 - - - +
117D ALA* 1.3 51.8 + - - +
119D ARG* 3.3 2.9 + - - +
120D ILE* 2.8 42.9 + - + +
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 3.6 24.7 - - + -
89D VAL* 3.3 34.1 - - + -
113D TYR 2.9 10.7 + - - +
114D ASN 3.4 7.0 - - - +
116D ALA* 1.3 76.5 - - - +
118D TRP* 1.3 57.7 + - - +
120D ILE* 3.2 5.6 + - - +
121D LYS 2.9 24.3 + - - -
134D LEU* 3.6 17.7 - - + +
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Residues in contact with TRP 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 4.5 4.5 - - + -
11C GLU* 3.8 31.2 - - + -
14C TYR* 3.8 25.8 - - + -
15C LEU* 3.6 45.3 - - + -
18C SER* 4.0 20.2 + - - -
56C LEU* 4.6 11.7 - - + -
59C ASP* 4.7 6.6 + - - -
114D ASN 2.9 20.1 + - - +
115D THR* 3.3 5.8 + - + +
117D ALA* 1.3 71.7 - - - +
119D ARG* 1.3 72.9 + - + +
121D LYS* 3.2 41.4 + - + +
122D LYS* 3.0 40.1 + - + +
134D LEU* 3.8 7.7 - - + +
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LYS* 4.5 7.0 - - - +
18D SER* 2.9 37.2 + - - -
19D LEU* 4.3 2.2 - - - +
59D ASP* 2.9 31.3 + - - -
62D ILE* 3.5 24.3 - - - +
63D GLU* 3.3 25.1 + - - -
66D VAL* 3.5 19.8 - - + +
115D THR* 3.0 31.5 + - + +
118D TRP* 1.3 84.5 - - + +
120D ILE* 1.3 57.5 + - - +
122D LYS* 3.5 5.7 + - - +
123D GLU* 2.9 31.0 + - - +
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D GLN* 4.3 13.2 - - + +
66D VAL* 3.8 25.8 - - - +
69D THR* 3.8 35.2 - - + +
70D THR* 4.5 2.7 - - - +
73D ILE* 4.4 4.5 - - + -
87D PHE* 3.7 36.1 - - + -
116D ALA 2.8 28.8 + - - +
117D ALA* 3.5 5.2 - - - +
119D ARG* 1.3 70.9 - - - +
121D LYS* 1.3 67.3 + - - +
123D GLU* 3.2 1.6 + - - +
124D CYS* 2.8 39.7 + - - +
132D VAL* 5.0 4.9 - - + -
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 5.3 8.1 + - - +
6C GLY 5.4 1.4 + - - -
7C LEU* 3.7 22.3 - - - +
11C GLU* 3.2 34.8 + - + +
117D ALA 2.9 13.5 + - - +
118D TRP* 3.4 31.6 - - + +
120D ILE* 1.3 76.8 - - - +
122D LYS* 1.3 62.9 + - - +
124D CYS* 3.7 2.3 - - - +
125D LYS* 3.1 24.2 + - + +
130D VAL 4.7 1.2 - - - +
132D VAL* 2.8 46.3 + - - +
133D SER* 4.4 4.4 + - - +
134D LEU* 4.3 9.0 - - + -
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASP* 3.0 37.0 + - - +
60C ASP* 5.8 3.4 - - - -
63C GLU* 3.5 29.9 + - - +
119C ARG* 3.7 6.3 - - - +
118D TRP* 3.0 35.8 + - + +
119D ARG* 3.9 6.1 - - - +
121D LYS* 1.3 75.3 - - - +
123D GLU* 1.3 65.2 + - - +
125D LYS* 3.4 5.3 + - - +
126D LEU* 3.1 50.5 + - + +
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Residues in contact with GLU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D VAL* 3.9 15.2 - - + +
67D LEU* 4.6 11.6 - - + +
70D THR* 3.5 29.6 - - + +
119D ARG 2.9 19.4 + - - +
120D ILE 3.8 1.1 - - - +
122D LYS* 1.3 77.4 - - - +
124D CYS* 1.3 58.3 + - - +
126D LEU* 4.7 6.8 - - - +
127D VAL* 2.9 51.7 + - - +
167D MG 2.2 32.5 - - - -
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Residues in contact with CYS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D THR* 4.0 24.0 - - - -
73D ILE* 3.7 38.6 - - - -
120D ILE* 2.8 22.5 + - - +
121D LYS 3.7 4.3 - - - +
123D GLU* 1.3 77.6 - - - +
125D LYS* 1.3 58.1 + - - +
128D LEU* 3.1 22.9 + - - +
130D VAL* 3.0 26.2 + - + +
132D VAL* 3.8 20.9 - - + -
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C ASN* 5.1 17.3 - - - +
121D LYS* 3.1 17.0 + - + +
122D LYS* 3.8 6.3 - - + +
123D GLU 3.3 0.2 - - - -
124D CYS* 1.3 77.6 - - - +
126D LEU* 1.3 63.3 + - + +
129D GLU* 3.1 38.9 + - - +
130D VAL 3.4 12.3 + - - +
131D ASP* 2.7 34.6 + - - +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASP* 5.4 8.5 - - - +
63C GLU* 5.6 5.4 - - + +
122D LYS* 3.1 51.2 + - + +
123D GLU* 4.4 7.4 - - - +
125D LYS* 1.3 85.3 - - + +
127D VAL* 1.3 65.3 + - + +
129D GLU* 4.8 3.6 + - - +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 5.0 4.5 - - + -
123D GLU* 2.9 45.4 + - + +
126D LEU* 1.3 81.5 - - + +
128D LEU* 1.3 79.3 + - + +
129D GLU* 3.7 1.5 - - - +
167D MG 4.2 3.6 - - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D THR* 3.7 40.4 - - + +
73D ILE* 4.2 13.7 - - + -
74D GLU* 3.8 47.6 - - + +
82D LYS* 3.2 15.8 + - - -
124D CYS* 3.1 16.7 + - - +
127D VAL* 1.3 93.4 - - + +
129D GLU* 1.3 72.0 + - - +
130D VAL* 3.3 14.6 + - + +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D LYS* 3.7 18.3 + - - +
124D CYS 3.1 2.8 + - - -
125D LYS* 3.1 35.3 + - - +
126D LEU 5.3 3.8 - - - +
127D VAL 3.7 1.7 - - - +
128D LEU* 1.3 79.6 - - - +
130D VAL* 1.3 58.9 + - - +
131D ASP* 4.1 2.1 + - - +
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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
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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