Contacts of the helix formed by residues 59 - 81 (chain X) in PDB entry 2OU0
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 THR 59 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X LEU* 3.6 6.0 - - - +
52X ARG* 4.7 5.6 - - - +
58X ILE* 1.3 77.7 - - - +
60X LYS* 1.3 59.8 + - - +
61X ASP* 3.7 8.5 + - - +
62X GLU* 2.9 38.7 + - - +
63X ALA* 2.9 28.4 + - - +
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Residues in contact with LYS 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ARG* 6.2 0.2 - - - +
13X LEU* 4.0 29.8 - - + -
15X LEU* 3.8 21.3 - - + +
59X THR* 1.3 72.0 - - - +
61X ASP* 1.3 63.0 + - - +
63X ALA* 3.2 2.3 + - - +
64X GLU* 2.9 54.7 + - + +
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Residues in contact with ASP 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X THR* 3.3 7.9 + - - +
60X LYS* 1.3 79.5 - - - +
62X GLU* 1.3 58.6 + - + +
64X GLU* 3.3 15.3 + - - +
65X LYS* 2.9 29.7 + - - +
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Residues in contact with GLU 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X ILE* 3.6 24.3 - - + +
52X ARG* 2.8 48.6 + - - -
58X ILE* 3.3 14.4 - - + +
59X THR* 2.9 35.7 + - - +
60X LYS 3.3 0.4 - - - -
61X ASP* 1.3 76.5 - - + +
63X ALA* 1.3 62.5 + - - +
65X LYS* 3.3 11.6 + - + +
66X LEU* 3.1 27.0 + - - +
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Residues in contact with ALA 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 3.7 26.7 - - + -
15X LEU* 4.0 2.9 - - + -
28X GLY* 3.9 12.1 - - - -
29X ILE* 4.4 5.8 + - - +
58X ILE* 3.7 18.5 - - + +
59X THR 2.9 13.8 + - - +
60X LYS 3.2 8.7 + - - +
62X GLU* 1.3 77.6 - - - +
64X GLU* 1.3 56.4 + - - +
66X LEU* 3.4 6.1 + - - +
67X PHE* 3.0 28.6 + - - +
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Residues in contact with GLU 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LEU* 5.7 0.9 - - + -
29X ILE* 4.3 14.4 - - + -
60X LYS* 2.9 49.5 + - + +
61X ASP* 3.8 17.0 - - - +
63X ALA* 1.3 72.4 - - + +
65X LYS* 1.3 60.8 + - - +
67X PHE* 3.4 11.0 - - + +
68X ASN* 2.9 30.0 + - - +
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Residues in contact with LYS 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X ALA 6.2 0.4 - - - -
61X ASP 2.9 17.2 + - - +
62X GLU* 3.5 11.2 - - + +
63X ALA 3.3 0.2 - - - -
64X GLU* 1.3 76.1 - - - +
66X LEU* 1.3 66.2 + - + +
68X ASN* 3.3 7.1 + - - +
69X GLN* 3.2 47.2 + - + +
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Residues in contact with LEU 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27X ILE* 4.4 14.1 - - + -
31X HIS* 3.9 43.5 - - + +
46X LEU* 4.8 1.6 - - + -
49X ALA* 4.0 31.0 - - + +
50X ILE* 3.7 23.1 - - + -
58X ILE* 4.7 4.5 - - + -
62X GLU 3.1 16.5 + - - +
63X ALA* 3.4 6.7 + - - +
65X LYS* 1.3 79.0 - - + +
67X PHE* 1.3 57.0 + - - +
69X GLN* 3.2 22.8 + - - +
70X ASP* 2.8 36.5 + - - +
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Residues in contact with PHE 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X PHE* 3.4 49.4 - + + -
7X LEU* 3.6 24.0 - - + -
8X ARG* 4.7 3.1 - - + -
29X ILE* 3.5 56.1 - - + -
31X HIS* 5.8 0.6 - - - +
63X ALA 3.0 17.3 + - - +
64X GLU* 3.4 9.2 - - + +
65X LYS 3.2 0.2 - - - -
66X LEU* 1.3 76.7 - - - +
68X ASN* 1.3 56.6 + - - +
70X ASP* 3.3 5.8 + - - +
71X VAL* 2.9 53.5 + - + +
104X PHE* 4.1 12.3 - + - -
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Residues in contact with ASN 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X PHE* 3.8 21.0 - - + -
64X GLU 2.9 17.5 + - - +
65X LYS* 3.7 7.0 - - - +
66X LEU 3.3 0.2 - - - -
67X PHE* 1.3 75.7 - - - +
69X GLN* 1.3 63.6 + - + +
71X VAL* 4.0 0.9 - - - +
72X ASP* 3.0 22.6 + - - +
304X MR3 3.3 25.5 - - - -
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Residues in contact with GLN 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X HIS* 6.2 0.6 - - - -
49X ALA 5.2 3.4 + - - -
65X LYS* 3.2 38.7 + - + +
66X LEU* 3.2 28.4 + - - +
68X ASN* 1.3 75.9 - - + +
70X ASP* 1.3 57.2 + - - +
72X ASP* 3.4 7.2 + - - +
73X ALA* 2.8 35.3 + - - +
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Residues in contact with ASP 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ILE 5.1 0.2 - - - +
31X HIS* 2.6 51.6 + - - +
66X LEU* 2.8 20.0 + - - +
67X PHE* 3.6 4.9 + - - +
69X GLN* 1.3 76.8 + - - +
71X VAL* 1.3 60.3 + - - +
73X ALA* 3.4 6.4 + - - +
74X ALA* 2.9 29.1 + - - +
104X PHE* 3.5 25.8 - - + -
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Residues in contact with VAL 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ILE* 4.2 20.4 - - + -
4X PHE* 3.9 35.4 - - + -
7X LEU* 4.1 13.0 - - + -
67X PHE* 2.9 46.0 + - + +
68X ASN 4.0 3.1 - - - +
70X ASP* 1.3 72.4 - - - +
72X ASP* 1.3 66.9 + - - +
74X ALA* 3.1 7.3 + - - +
75X VAL* 3.1 32.0 + - + +
100X ILE* 4.6 2.5 - - + -
104X PHE* 4.4 3.4 - - + -
304X MR3 4.3 6.5 - - + -
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Residues in contact with ASP 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68X ASN* 3.0 19.4 + - - +
69X GLN* 3.4 8.4 - - - +
71X VAL* 1.3 77.7 - - - +
73X ALA* 1.3 56.9 + - - +
75X VAL* 3.4 1.7 + - - +
76X ARG* 2.9 46.6 + - - +
304X MR3 3.7 33.6 + - + -
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Residues in contact with ALA 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X GLN 2.8 21.0 + - - +
70X ASP* 3.6 9.6 - - - +
72X ASP* 1.3 73.2 - - - +
74X ALA* 1.3 56.2 + - - +
76X ARG* 3.8 5.8 - - - +
77X GLY* 2.8 27.5 + - - -
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Residues in contact with ALA 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X ASP 2.9 17.4 + - - +
71X VAL* 3.1 6.3 + - - +
73X ALA* 1.3 71.6 - - - +
75X VAL* 1.3 66.6 + - - +
77X GLY* 3.4 2.0 + - - -
78X ILE* 3.0 29.0 + - - +
100X ILE* 4.1 17.3 - - + -
103X VAL* 4.0 23.4 - - + +
104X PHE* 4.4 15.0 - - + +
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Residues in contact with VAL 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ILE* 6.2 0.2 - - + -
71X VAL* 3.1 17.8 + - + +
72X ASP 3.7 5.8 - - - +
74X ALA* 1.3 75.3 - - - +
76X ARG* 1.3 65.1 + - + +
78X ILE* 3.1 13.1 + - - +
79X LEU* 3.0 39.2 + - + +
88X TYR* 4.1 18.6 - - + +
100X ILE* 3.7 30.1 - - + -
304X MR3 3.8 25.4 - - - -
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Residues in contact with ARG 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X ASP* 2.9 38.2 + - - +
73X ALA* 4.0 5.2 - - - +
75X VAL* 1.3 80.0 - - + +
77X GLY* 1.3 60.8 + - - +
79X LEU* 3.4 20.7 + - + +
80X ARG* 3.1 70.6 + - - +
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Residues in contact with GLY 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X ALA 2.8 17.6 + - - -
74X ALA* 3.7 2.2 - - - -
76X ARG* 1.3 73.4 - - - +
78X ILE* 1.3 64.2 + - - +
80X ARG* 3.2 8.6 + - - +
81X ASN* 3.0 19.6 + - - +
103X VAL* 6.0 0.2 - - - -
108X GLU* 3.0 29.2 - - - +
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Residues in contact with ILE 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X ALA 3.0 20.7 + - - +
75X VAL* 3.4 7.4 - - - +
77X GLY* 1.3 73.9 - - - +
79X LEU* 1.3 60.4 + - + +
81X ASN* 3.1 25.5 + - - +
84X LEU* 4.1 21.1 - - + +
85X LYS 3.4 6.3 + - - +
88X TYR* 3.5 45.5 - - + -
99X ALA 4.0 4.5 - - - +
100X ILE* 3.9 34.5 - - + +
103X VAL* 3.6 30.5 - - + -
108X GLU* 5.3 0.4 - - - +
303X MR3 4.3 4.0 - - + -
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Residues in contact with LEU 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X VAL* 3.0 32.3 + - + +
76X ARG* 3.9 21.8 - - + +
77X GLY 3.3 0.2 - - - -
78X ILE* 1.3 77.0 - - + +
80X ARG* 1.3 60.8 + - + +
81X ASN 3.3 0.4 + - - -
85X LYS* 3.4 40.9 - - + +
88X TYR* 3.7 34.1 - - + -
89X ASP* 4.2 10.8 - - - +
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Residues in contact with ARG 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76X ARG* 3.1 70.4 + - - +
77X GLY* 3.2 8.0 + - - +
79X LEU* 1.3 78.2 - - + +
81X ASN* 1.3 60.1 + - - +
82X ALA* 3.6 2.8 + - - +
108X GLU* 5.2 1.3 - - - +
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Residues in contact with ASN 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X GLY 3.0 15.4 + - - +
78X ILE 3.1 6.6 + - - +
80X ARG* 1.3 77.3 - - - +
82X ALA* 1.3 59.4 + - - +
83X LYS* 2.9 33.3 + - - +
84X LEU* 3.1 25.4 + - + +
85X LYS* 2.9 35.0 + - - +
108X GLU* 2.7 35.8 + - - +
109X THR* 5.6 0.8 - - - +
112X ALA* 4.3 6.4 - - - +
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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