Contacts of the helix formed by residues 58 - 76 (chain A) in PDB entry 2HXO
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 GLY 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ILE* 5.8 1.1 - - - +
57A THR* 1.3 89.0 + - - +
59A LYS* 1.3 64.2 + - - -
60A ALA 3.3 2.0 - - - -
61A GLU* 3.4 14.5 + - - +
62A LEU* 3.2 21.0 + - - +
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Residues in contact with LYS 59 (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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33A GLU* 3.3 44.3 + - - +
34A ARG* 4.4 9.3 + - - +
36A LEU* 3.6 33.2 + - + +
58A GLY* 1.3 70.1 - - - -
60A ALA* 1.3 68.5 + - - +
62A LEU* 3.0 9.6 + - + +
63A LEU* 2.9 34.9 + - + +
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Residues in contact with ALA 60 (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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58A GLY 3.3 0.2 - - - -
59A LYS* 1.3 80.4 - - - +
61A GLU* 1.3 76.3 + - - +
63A LEU* 3.5 12.4 + - - +
64A GLY* 3.2 18.2 + - - -
117A ARG* 6.0 4.0 - - - +
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Residues in contact with GLU 61 (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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57A THR* 3.2 26.0 - - + +
58A GLY* 3.4 21.5 + - - +
59A LYS 3.2 0.2 - - - -
60A ALA* 1.3 87.5 - - - +
62A LEU* 1.3 61.3 + - - +
64A GLY* 3.4 2.0 + - - +
65A ALA* 3.0 27.0 + - - +
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Residues in contact with LEU 62 (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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20A ILE* 4.1 25.6 - - + +
21A VAL* 4.9 6.7 - - + -
24A ALA* 4.0 26.9 - - + -
36A LEU* 4.3 15.9 - - + -
41A LEU* 3.7 29.2 - - + -
56A ILE* 5.6 8.5 - - + -
58A GLY 3.2 14.0 + - - +
59A LYS* 3.0 12.8 + - + +
61A GLU* 1.3 75.2 - - - +
63A LEU* 1.3 64.6 + - - +
65A ALA* 3.2 7.0 + - + +
66A ALA* 2.9 24.4 + - - +
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Residues in contact with LEU 63 (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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28A LEU* 4.0 23.6 - - + -
33A GLU* 3.9 24.9 - - + +
36A LEU* 3.6 25.6 - - + -
59A LYS* 2.9 30.8 + - + +
60A ALA* 3.7 11.9 - - - +
62A LEU* 1.3 76.6 - - - +
64A GLY* 1.3 58.8 + - - +
66A ALA* 3.3 5.8 + - - +
67A THR* 2.9 34.7 + - - -
106A TRP* 4.9 0.2 - - - -
110A GLN* 3.5 35.8 - - - +
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Residues in contact with GLY 64 (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 ALA 3.2 11.1 + - - -
61A GLU* 3.4 4.5 + - - -
62A LEU 3.2 0.4 - - - -
63A LEU* 1.3 80.7 - - - +
65A ALA* 1.3 56.2 + - - +
67A THR* 3.4 1.7 + - - -
68A ASP* 2.9 30.9 + - - +
114A GLN* 3.8 26.8 + - - -
122A THR* 5.1 1.4 + - - -
123A VAL* 5.6 0.5 - - - +
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Residues in contact with ALA 65 (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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17A ARG* 4.7 17.7 - - - +
21A VAL* 3.8 22.0 - - + +
61A GLU 3.0 16.3 + - - +
62A LEU* 3.2 9.6 + - + +
64A GLY* 1.3 75.5 - - - +
66A ALA* 1.3 58.3 + - - +
68A ASP* 3.7 6.8 - - - +
69A ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 66 (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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21A VAL* 3.8 14.1 - - + +
24A ALA* 4.7 8.3 - - + -
25A VAL* 4.1 13.8 - - + +
28A LEU* 4.0 26.2 - - + -
62A LEU 2.9 17.9 + - - +
63A LEU 3.5 4.3 - - - +
65A ALA* 1.3 74.5 - - - +
67A THR* 1.3 64.8 + - - +
69A ALA* 3.4 1.7 + - - +
70A VAL* 3.1 29.1 + - - +
106A TRP* 4.0 3.1 - - + -
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Residues in contact with THR 67 (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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63A LEU 2.9 18.3 + - - -
64A GLY* 3.7 5.3 - - - -
66A ALA* 1.3 78.3 - - - +
68A ASP* 1.3 57.5 + - - +
70A VAL* 3.4 2.1 + - - +
71A VAL* 3.0 36.1 + - + +
106A TRP* 3.7 3.9 - - - -
107A LEU* 3.6 23.8 - - + -
110A GLN* 3.2 29.7 - - + +
111A LEU* 3.8 24.0 - - + +
114A GLN* 4.4 12.2 + - - +
123A VAL* 4.5 6.5 - - + -
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Residues in contact with ASP 68 (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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64A GLY 2.9 18.2 + - - +
65A ALA* 3.7 7.9 - - - +
67A THR* 1.3 77.8 - - - +
69A ALA* 1.3 59.7 + - - +
71A VAL* 3.9 0.5 - - - +
72A THR* 2.9 42.2 + - - -
122A THR* 2.6 34.2 + - - +
123A VAL* 3.7 14.9 + - + +
126A ARG* 2.7 32.4 + - - -
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Residues in contact with ALA 69 (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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21A VAL* 3.7 22.0 - - + -
25A VAL* 5.5 1.6 - - + -
65A ALA 3.0 19.0 + - - +
66A ALA 3.8 2.0 - - - +
67A THR 3.4 0.2 - - - -
68A ASP* 1.3 79.1 + - - +
70A VAL* 1.3 64.2 + - + +
72A THR* 3.9 4.5 - - - -
73A ALA* 3.1 26.0 + - - +
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Residues in contact with VAL 70 (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 VAL* 4.2 12.1 - - + -
66A ALA 3.1 17.7 + - - +
67A THR 3.8 2.7 - - - +
69A ALA* 1.3 78.4 - - + +
71A VAL* 1.3 62.6 + - - +
73A ALA* 3.8 4.1 - - - +
74A ALA* 3.0 23.6 + - + +
100A ALA* 4.0 10.5 - - + -
104A HIS* 3.8 38.6 - - + +
106A TRP* 4.2 9.6 - - + -
107A LEU* 3.8 30.7 - - + -
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Residues in contact with VAL 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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67A THR* 3.0 26.4 + - + +
68A ASP 3.9 2.7 - - - +
70A VAL* 1.3 73.0 - - - +
72A THR* 1.3 67.9 + - - +
74A ALA* 3.2 4.5 + - - +
75A VAL* 2.9 28.8 + - + +
97A LEU* 3.8 20.6 - - + -
100A ALA* 5.3 0.9 - - - -
107A LEU* 4.2 20.2 - - + -
111A LEU* 4.3 4.0 - - + -
123A VAL* 3.8 19.7 - - + -
126A ARG* 6.4 0.4 - - + -
127A ILE* 3.4 33.2 - - + -
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Residues in contact with THR 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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68A ASP* 2.9 32.9 + - - -
69A ALA* 3.9 4.9 - - - -
71A VAL* 1.3 78.2 - - - +
73A ALA* 1.3 58.4 + - - +
75A VAL* 4.1 2.2 - - - -
76A THR* 2.5 48.2 + - + +
126A ARG* 4.7 11.3 + - - +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ALA 3.1 19.3 + - - +
70A VAL* 3.8 5.4 - - - +
71A VAL 3.2 0.2 - - - -
72A THR* 1.3 80.2 - - - +
74A ALA* 1.3 57.1 + - - +
76A THR* 3.9 3.7 + - - -
77A ALA* 3.0 30.4 + - - +
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Residues in contact with ALA 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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70A VAL* 3.0 19.0 + - + +
71A VAL 3.8 2.5 - - - +
73A ALA* 1.3 77.6 - - - +
75A VAL* 1.3 63.1 + - + +
77A ALA* 3.2 20.3 + - - +
78A GLY 4.6 0.7 + - - -
96A GLY* 3.5 32.5 - - - +
97A LEU* 5.6 0.2 - - - -
99A ASP* 6.1 0.7 - - + -
100A ALA* 3.7 15.3 - - + +
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Residues in contact with VAL 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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71A VAL* 2.9 33.7 + - + +
72A THR* 4.3 2.7 - - - +
74A ALA* 1.3 76.2 - - - +
76A THR* 1.3 66.6 + - + +
77A ALA 3.3 0.4 + - - -
78A GLY 5.4 1.0 + - - +
92A ALA* 4.8 10.3 - - - +
93A VAL* 4.1 45.3 - - + +
96A GLY* 4.5 5.8 - - - -
97A LEU* 4.3 14.4 - - + +
127A ILE* 4.7 4.7 - - + -
130A SER* 4.7 10.5 - - - +
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Residues in contact with THR 76 (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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72A THR* 2.5 34.6 + - + +
73A ALA* 3.9 4.0 + - - -
75A VAL* 1.3 85.4 - - + +
77A ALA* 1.3 67.1 + - - +
78A GLY 3.8 5.0 - - - +
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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