Contacts of the helix formed by residues 70 - 89 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS* 4.2 2.2 - - - -
68A GLY 3.5 8.0 - - - +
69A ALA* 1.3 80.8 - - - +
71A ALA* 1.3 68.3 + - - +
72A LYS* 2.9 12.0 + - + +
73A GLN* 3.2 20.6 + - + +
74A SER* 3.1 20.1 + - - -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ARG* 5.0 7.4 - - - +
64A LYS* 4.2 18.6 - - - +
70A ASN* 1.3 74.5 - - - +
72A LYS* 1.3 59.4 + - - +
74A SER* 2.9 20.7 + - - -
75A ARG* 3.3 22.2 + - - +
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASN* 4.0 8.7 - - + +
71A ALA* 1.3 79.1 - - - +
73A GLN* 1.3 70.4 + - + +
75A ARG* 3.2 18.9 + - - +
76A ASP* 3.5 16.5 + - - +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY* 3.6 18.8 + - - +
27A GLY* 5.3 3.8 - - - +
30A LEU* 2.8 32.3 - - - +
63A LEU* 5.1 0.2 - - - -
69A ALA* 4.3 7.4 - - + -
70A ASN* 3.2 29.9 + - + +
72A LYS* 1.3 81.5 - - + +
74A SER* 1.3 62.7 + - - +
76A ASP* 3.3 19.1 + - - +
77A CYS* 3.3 17.4 + - - -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.2 3.2 - - - -
60A ARG* 3.4 37.5 - - - +
63A LEU* 4.1 22.9 - - - -
64A LYS* 4.7 7.7 - - - +
69A ALA* 4.7 1.4 - - - +
70A ASN 3.1 9.9 + - - -
71A ALA* 2.9 23.6 + - - -
73A GLN* 1.3 79.9 - - - +
75A ARG* 1.3 62.0 + - - +
77A CYS* 3.1 2.6 + - - +
78A PHE* 2.9 24.0 + - - +
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Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 5.1 5.2 - - - +
60A ARG* 4.0 27.7 - - - +
71A ALA* 3.3 19.2 + - - +
72A LYS* 3.2 12.8 + - - +
74A SER* 1.3 83.8 + - - +
76A ASP* 1.3 65.7 + - - +
78A PHE* 3.4 6.6 + - - +
79A GLY* 3.2 21.0 + - - -
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.1 5.2 - - - +
3A THR* 3.8 28.6 - - + +
7A HIS* 4.6 1.4 + - - -
24A ALA* 3.7 7.4 - - + +
25A GLY* 3.7 21.8 - - - +
72A LYS* 3.5 15.4 + - - +
73A GLN* 3.3 10.8 + - - +
74A SER 3.2 0.4 - - - -
75A ARG* 1.3 81.8 - - - +
77A CYS* 1.3 57.2 + - - +
79A GLY* 5.5 0.2 - - - -
80A CYS* 2.7 33.1 + - - +
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Residues in contact with CYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 5.1 2.0 - - - -
24A ALA 3.0 22.9 - - - -
25A GLY* 3.8 1.8 - - - -
26A ILE* 3.1 38.4 - - - -
59A PHE* 3.9 20.6 - - + -
63A LEU* 4.1 5.2 - - + -
73A GLN 3.3 12.3 + - - +
74A SER 3.1 7.7 + - - +
76A ASP* 1.3 77.6 - - - +
78A PHE* 1.3 61.8 + - - +
80A CYS* 4.1 1.8 - - - -
81A LEU* 2.7 43.2 + - + +
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.7 23.8 - + - -
54A LYS* 3.5 26.5 - - + -
56A GLU* 3.5 49.1 - - + +
59A PHE* 4.1 16.1 - + + -
60A ARG* 5.5 1.1 - - + -
74A SER 2.9 17.3 + - - +
75A ARG* 3.7 7.9 - - - +
76A ASP 3.3 0.2 - - - -
77A CYS* 1.3 77.2 - - - +
79A GLY* 1.3 58.9 + - - +
81A LEU* 4.0 0.2 - - - +
82A ARG* 2.7 75.6 + - - +
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 6.0 6.5 - - - -
7A HIS* 4.1 7.0 - - - -
75A ARG 3.2 10.9 + - - -
76A ASP 4.3 0.2 - - - -
78A PHE* 1.3 88.2 - - - +
80A CYS* 1.3 58.6 + - - +
82A ARG* 4.2 4.9 - - - -
83A GLU* 2.8 38.9 + - - +
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Residues in contact with CYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A HIS* 3.5 29.9 - - - +
10A PHE* 4.0 24.9 - - - -
11A VAL* 3.8 3.6 - - - +
23A LEU* 4.9 1.8 - - - -
24A ALA* 3.5 33.9 - - + -
76A ASP 2.7 23.3 + - - +
77A CYS* 3.8 4.0 - - - +
79A GLY* 1.3 78.0 - - - +
81A LEU* 1.3 65.4 + - + +
84A TRP* 3.2 22.2 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.7 4.9 - - + -
23A LEU* 3.6 37.5 - - + -
45A VAL* 4.5 13.2 - - + +
46A LEU* 4.2 27.8 - - + +
49A PHE* 4.3 18.2 - - + -
59A PHE* 3.7 32.5 - - + -
77A CYS* 2.7 33.4 + - + +
78A PHE 4.0 0.9 - - - +
80A CYS* 1.3 74.8 - - + +
82A ARG* 1.3 63.3 + - - +
84A TRP* 3.3 6.0 + - - +
85A CYS* 3.1 27.5 + - - -
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 3.8 23.7 - - + -
54A LYS* 4.6 17.9 - - + +
78A PHE* 2.7 55.9 + - - +
79A GLY* 4.1 3.6 - - - +
81A LEU* 1.3 74.7 - - - +
83A GLU* 1.3 62.5 + - + +
85A CYS* 3.2 5.6 + - + +
86A ASP* 3.0 37.9 + - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.9 4.0 - - - +
7A HIS* 3.6 20.9 + - + -
11A VAL* 3.9 21.3 - - + +
79A GLY* 2.8 32.0 + - - +
82A ARG* 1.3 71.8 - - + +
84A TRP* 1.3 68.3 + - - +
86A ASP* 3.0 23.4 + - + +
87A ALA* 3.1 13.7 + - - +
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Residues in contact with TRP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.3 49.0 + + + -
11A VAL* 3.4 7.5 - - - +
14A PRO* 5.1 0.7 - - + -
15A MET* 3.9 33.7 - - + +
46A LEU* 3.4 28.3 - - + -
50A LEU* 6.3 0.4 - - + -
80A CYS 3.2 10.2 + - - +
81A LEU* 3.6 8.7 - - - +
83A GLU* 1.3 76.2 - - - +
85A CYS* 1.3 64.3 + - - +
87A ALA* 3.1 2.2 + - - -
88A PHE* 2.6 104.7 + + + +
89A LEU* 4.7 6.1 - - + -
84B TRP* 5.3 3.6 - + - -
88B PHE 3.8 11.2 - - - -
89B LEU* 3.5 22.2 - - + -
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Residues in contact with CYS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.7 23.6 - - - -
49A PHE* 4.3 7.9 - - - -
50A LEU* 3.8 9.9 - - - -
54A LYS* 4.5 11.7 - - - +
81A LEU 3.1 15.3 + - - -
82A ARG* 3.4 11.9 - - - +
84A TRP* 1.3 88.4 - - - +
86A ASP* 1.3 55.2 + - - +
89A LEU* 2.4 74.2 + - + +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 5.4 4.3 + - - -
82A ARG* 3.0 35.7 + - - +
83A GLU* 3.0 19.8 + - + +
85A CYS* 1.3 80.0 - - - +
87A ALA* 1.3 59.8 + - - +
89A LEU 4.1 6.4 + - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.4 14.8 - - + +
83A GLU 3.1 9.3 + - - +
84A TRP* 3.1 6.7 + - - +
86A ASP* 1.3 77.5 - - - +
88A PHE* 1.3 77.2 + - + +
89A LEU 3.6 0.4 - - - -
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE 4.0 3.8 - - - -
11A VAL 4.0 13.9 - - - -
12A ALA 4.6 1.8 - - - -
13A GLU* 3.3 31.6 - - - -
14A PRO* 3.3 23.3 - - + -
84A TRP* 2.6 85.3 + + + +
87A ALA* 1.3 85.7 - - + +
89A LEU* 1.3 56.6 + - - +
14B PRO* 6.0 2.1 - - - +
84B TRP* 3.8 20.1 - - - -
88B PHE* 4.5 20.2 - + - +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.5 34.1 - - + -
54A LYS* 4.5 9.6 - - - +
84A TRP* 4.7 5.2 - - + -
85A CYS* 2.4 61.1 + - + +
86A ASP* 4.1 7.6 - - - +
87A ALA 3.6 1.2 - - - -
88A PHE* 1.3 72.5 - - - +
14B PRO* 4.1 15.0 - - - +
15B MET* 3.2 35.0 - - + +
16B GLY* 3.9 24.5 + - - +
43B TYR* 4.3 11.2 - - + -
46B LEU* 4.5 4.9 - - + -
84B TRP* 3.5 25.1 - - + -
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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
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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