Contacts of the helix formed by residues 70 - 89 (chain B) in PDB entry 2ODG
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 70 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LYS* 5.2 5.6 - - - +
68B GLY 3.5 7.8 - - - +
69B ALA* 1.3 80.7 - - - +
71B ALA* 1.3 68.1 + - - +
72B LYS* 3.0 11.6 + - + +
73B GLN* 3.2 20.8 + - + +
74B SER* 3.1 20.9 + - - -
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Residues in contact with ALA 71 (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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60B ARG* 5.0 6.5 - - - +
64B LYS* 5.0 13.1 - - - +
70B ASN* 1.3 73.1 - - - +
72B LYS* 1.3 60.2 + - - +
74B SER* 2.9 21.1 + - - -
75B ARG* 3.3 22.1 + - - +
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Residues in contact with LYS 72 (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 ASN* 4.0 8.7 - - + +
71B ALA* 1.3 79.7 - - - +
73B GLN* 1.3 68.8 + - + +
75B ARG* 3.2 21.9 + - - +
76B ASP* 3.5 14.0 + - - +
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Residues in contact with GLN 73 (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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25B GLY* 3.6 18.7 + - - +
26B ILE* 6.2 0.2 - - - -
27B GLY* 5.3 3.4 - - - +
30B LEU* 2.8 32.7 - - - +
69B ALA* 4.3 7.3 - - + -
70B ASN* 3.2 30.2 + - + +
72B LYS* 1.3 82.1 - - + +
74B SER* 1.3 63.4 + - - +
76B ASP* 3.3 17.9 + - - +
77B CYS* 3.3 18.3 + - - -
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Residues in contact with SER 74 (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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59B PHE* 4.2 7.4 - - - -
60B ARG* 3.3 41.5 - - - +
63B LEU* 5.0 6.1 - - - -
64B LYS* 5.8 2.0 - - - -
69B ALA* 4.7 9.8 - - - +
70B ASN 3.1 10.2 + - - -
71B ALA* 2.9 22.9 + - - -
73B GLN* 1.3 79.2 - - - +
75B ARG* 1.3 62.3 + - - +
77B CYS* 3.2 8.6 + - - +
78B PHE* 2.9 23.8 + - - +
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Residues in contact with ARG 75 (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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56B GLU* 5.1 5.6 - - - +
60B ARG* 4.0 25.8 - - - +
71B ALA* 3.3 21.0 + - - +
72B LYS* 3.2 11.7 + - - +
74B SER* 1.3 84.1 + - - +
76B ASP* 1.3 66.2 + - - +
78B PHE* 3.3 6.6 + - - +
79B GLY* 3.1 20.6 + - - -
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Residues in contact with ASP 76 (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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1B MET* 5.1 5.4 - - - +
3B THR* 3.8 29.1 - - + +
7B HIS* 4.6 1.4 + - - -
24B ALA* 3.7 6.7 - - + +
25B GLY* 3.7 20.7 + - - +
72B LYS* 3.5 15.3 + - - +
73B GLN* 3.3 10.6 + - - +
74B SER 3.2 0.8 - - - -
75B ARG* 1.3 79.9 - - - +
77B CYS* 1.3 58.2 + - - +
80B CYS* 2.7 33.5 + - - +
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Residues in contact with CYS 77 (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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23B LEU* 5.1 2.0 - - - -
24B ALA 2.9 22.4 - - - -
25B GLY* 3.7 1.6 - - - -
26B ILE* 3.1 38.4 - - - -
59B PHE* 3.9 21.1 - - + -
63B LEU* 5.5 1.3 - - - -
73B GLN 3.3 12.3 + - - +
74B SER* 3.2 9.5 + - - +
76B ASP* 1.3 78.2 - - - +
78B PHE* 1.3 60.2 + - - +
80B CYS* 4.1 2.0 - - - -
81B LEU* 2.7 42.7 + - + +
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Residues in contact with PHE 78 (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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49B PHE* 3.7 24.0 - + - -
54B LYS* 3.5 26.5 - - + -
56B GLU* 3.5 48.2 - - + -
59B PHE* 4.1 16.0 - + + -
60B ARG* 5.5 1.3 - - + -
74B SER 2.9 16.0 + - - +
75B ARG* 3.7 8.7 - - - +
76B ASP 3.3 0.2 - - - -
77B CYS* 1.3 77.5 - - - +
79B GLY* 1.3 59.9 + - - +
81B LEU* 3.9 0.7 - - - +
82B ARG* 2.7 75.3 + - - +
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Residues in contact with GLY 79 (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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1B MET* 6.0 6.5 - - - -
7B HIS* 4.0 7.4 - - - -
75B ARG 3.1 10.8 + - - -
76B ASP* 5.5 0.2 - - - -
78B PHE* 1.3 88.3 - - - +
80B CYS* 1.3 57.8 + - - +
82B ARG* 4.2 4.5 - - - -
83B GLU* 2.7 38.9 + - - +
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Residues in contact with CYS 80 (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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7B HIS* 3.5 25.2 - - - +
10B PHE* 4.0 28.5 - - - -
11B VAL* 3.8 3.1 - - - +
23B LEU* 4.9 2.0 - - - -
24B ALA* 3.5 33.7 - - + +
76B ASP 2.7 24.1 + - - +
77B CYS* 3.8 4.0 - - - +
79B GLY* 1.3 76.6 - - - +
81B LEU* 1.3 65.2 + - + +
84B TRP* 3.1 22.9 + - - +
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Residues in contact with LEU 81 (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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10B PHE* 4.7 4.9 - - + -
23B LEU* 3.6 37.9 - - + -
45B VAL* 4.5 12.8 - - + +
46B LEU* 4.2 27.7 - - + +
49B PHE* 4.3 18.6 - - + -
59B PHE* 3.7 32.5 - - + -
77B CYS* 2.7 32.8 + - + +
78B PHE 4.0 1.1 - - - +
80B CYS* 1.3 75.9 - - + +
82B ARG* 1.3 63.5 + - - +
84B TRP* 3.4 6.0 + - - +
85B CYS* 3.1 27.4 + - - -
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Residues in contact with ARG 82 (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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49B PHE* 3.8 22.6 - - + -
54B LYS* 4.6 17.9 - - + +
78B PHE* 2.7 56.1 + - - +
79B GLY* 4.0 3.8 - - - +
81B LEU* 1.3 75.3 - - - +
83B GLU* 1.3 58.7 + - + +
85B CYS* 3.2 5.5 + - + +
86B ASP* 2.9 44.7 + - - +
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Residues in contact with GLU 83 (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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1B MET* 5.9 4.3 - - - +
7B HIS* 3.5 21.5 + - + -
11B VAL* 3.9 20.4 - - + +
79B GLY* 2.7 33.4 + - - +
82B ARG* 1.3 71.6 - - + +
84B TRP* 1.3 69.0 + - - +
86B ASP* 3.0 23.2 + - + +
87B ALA* 3.1 13.0 + - - +
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Residues in contact with TRP 84 (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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84A TRP* 5.3 3.8 - + - -
88A PHE 3.8 11.4 - - - -
89A LEU* 3.5 33.4 - - + -
10B PHE* 3.1 44.7 + + + -
11B VAL* 3.4 8.8 - - + +
14B PRO* 5.2 0.7 - - + -
15B MET* 3.9 24.4 - - + +
46B LEU* 3.4 26.2 - - + -
50B LEU* 6.3 0.2 - - + -
80B CYS 3.1 19.0 + - - +
81B LEU* 3.5 4.7 - - - +
83B GLU* 1.3 76.7 - - - +
85B CYS* 1.3 66.2 + - - +
87B ALA 3.0 0.3 + - - -
88B PHE* 2.7 102.1 + + + +
89B LEU* 4.9 5.8 - - + -
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Residues in contact with CYS 85 (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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46B LEU* 3.7 22.9 - - - -
49B PHE* 4.3 7.0 - - + -
50B LEU* 3.8 9.4 - - - -
54B LYS* 4.5 11.7 - - - +
81B LEU 3.1 14.9 + - - +
82B ARG* 3.3 11.9 - - - +
84B TRP* 1.3 90.5 - - - +
86B ASP* 1.3 55.1 + - - +
89B LEU* 2.3 74.9 + - + +
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Residues in contact with ASP 86 (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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54B LYS* 5.4 4.3 + - - -
82B ARG* 2.9 42.9 + - - +
83B GLU* 3.0 20.5 + - - +
85B CYS* 1.3 78.5 - - - +
87B ALA* 1.3 60.6 + - - +
89B LEU 4.3 7.4 + - - +
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Residues in contact with ALA 87 (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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11B VAL* 4.4 11.4 - - + +
83B GLU 3.1 9.6 + - - +
84B TRP 3.0 6.5 + - - +
86B ASP* 1.3 78.1 - - - +
88B PHE* 1.3 79.2 + - + +
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Residues in contact with PHE 88 (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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14A PRO* 5.9 2.5 - - - +
84A TRP* 3.8 21.0 - - - -
88A PHE* 4.5 19.3 - + - +
10B PHE 3.9 0.7 - - - -
11B VAL 3.8 22.2 - - - -
12B ALA 4.5 1.3 - - - -
13B GLU* 3.4 29.2 - - - -
14B PRO* 3.7 24.2 - - + -
84B TRP* 2.7 77.6 + + + +
87B ALA* 1.3 91.8 - - + +
89B LEU* 1.3 58.7 + - - +
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Residues in contact with LEU 89 (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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14A PRO* 4.4 11.5 - - - +
15A MET* 3.1 35.1 - - + +
16A GLY* 3.7 29.8 + - - +
43A TYR* 4.2 12.3 - - + -
46A LEU* 4.6 4.5 - - + -
84A TRP* 3.5 26.0 - - + -
50B LEU* 3.4 34.8 - - + -
54B LYS* 4.5 13.8 + - - +
84B TRP* 4.9 4.5 - - + -
85B CYS* 2.3 58.8 + - + +
86B ASP* 4.3 7.4 - - - +
87B ALA 3.7 1.4 - - - -
88B PHE* 1.3 70.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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