Contacts of the helix formed by residues 58 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ILE* 4.6 5.5 - - - +
57B THR* 1.3 87.2 + - - +
59B LYS* 1.3 65.9 + - - -
60B ALA 3.3 2.2 - - - -
61B GLU* 3.1 15.0 + - - +
62B LEU* 3.2 20.8 + - - +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 3.2 44.4 + - - +
34B ARG* 4.3 6.7 + - - +
36B LEU* 3.3 38.0 + - + +
37B THR* 6.0 0.2 - - - +
58B GLY* 1.3 70.1 - - - -
60B ALA* 1.3 65.9 + - - +
62B LEU* 3.0 9.1 + - + +
63B LEU* 2.9 36.5 + - + +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 3.3 0.4 - - - -
59B LYS* 1.3 79.4 - - - +
61B GLU* 1.3 77.0 + - - +
63B LEU* 3.5 12.0 + - - +
64B GLY* 3.2 18.2 + - - -
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 3.3 23.5 - - + +
58B GLY* 3.1 26.6 + - - +
59B LYS 3.2 0.2 - - - -
60B ALA* 1.3 88.6 + - - +
62B LEU* 1.3 60.6 + - - +
64B GLY* 3.4 2.2 + - - +
65B ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.8 27.1 - - + +
21B VAL* 4.8 7.9 - - + -
24B ALA* 3.9 27.4 - - + -
36B LEU* 4.2 18.6 - - + -
41B LEU* 3.9 24.5 - - + -
56B ILE* 4.9 12.3 - - + -
58B GLY 3.2 13.2 + - - +
59B LYS* 3.0 12.4 + - + +
61B GLU* 1.3 75.1 - - - +
63B LEU* 1.3 66.6 + - - +
65B ALA* 3.2 7.8 + - + +
66B ALA* 2.9 22.9 + - + +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.8 23.3 - - + -
33B GLU* 4.4 13.2 - - + +
36B LEU* 3.7 25.8 - - + -
59B LYS* 2.9 39.2 + - + +
60B ALA* 3.7 9.2 - - - +
62B LEU* 1.3 76.8 - - - +
64B GLY* 1.3 57.9 + - - +
66B ALA* 3.3 5.1 + - - +
67B THR* 2.9 34.3 + - - -
106B TRP* 5.0 0.3 - - - -
110B GLN* 4.0 38.4 - - + +
114B GLN* 5.5 0.2 - - - -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA 3.2 11.5 + - - -
61B GLU* 3.4 3.8 + - - -
62B LEU 3.2 0.6 - - - -
63B LEU* 1.3 79.6 - - - +
65B ALA* 1.3 56.4 + - - +
67B THR* 3.3 2.4 + - - -
68B ASP* 2.9 30.9 + - - +
114B GLN* 4.1 24.7 - - - +
122B THR* 5.1 1.1 + - - -
123B VAL* 4.2 3.3 - - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 4.0 24.9 - - - +
21B VAL* 3.7 19.8 - - + +
61B GLU 3.0 17.4 + - - +
62B LEU* 3.2 10.0 + - + +
64B GLY* 1.3 76.1 - - - +
66B ALA* 1.3 57.8 + - - +
68B ASP* 3.8 5.7 - - - +
69B ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.7 13.2 - - + +
24B ALA* 4.7 7.2 - - + -
25B VAL* 4.0 13.5 - - + -
28B LEU* 3.8 27.8 - - + -
62B LEU 2.9 16.0 + - - +
63B LEU* 3.6 4.9 - - - +
65B ALA* 1.3 75.4 - - - +
67B THR* 1.3 65.3 + - - +
69B ALA* 3.4 1.4 + - - +
70B VAL* 3.1 30.0 + - - +
106B TRP* 4.1 3.4 - - + -
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU 2.9 23.0 + - - -
64B GLY* 3.3 6.2 + - - -
66B ALA* 1.3 75.4 - - - +
68B ASP* 1.3 58.7 + - - +
70B VAL* 3.8 1.7 - - - +
71B VAL* 3.0 34.2 + - + +
106B TRP* 3.8 5.4 - - - -
107B LEU* 3.5 24.9 - - + +
110B GLN* 3.2 29.8 - - + +
111B LEU* 3.7 23.6 - - + -
114B GLN* 4.8 6.5 + - - +
123B VAL* 4.0 13.5 - - + -
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 2.9 18.2 + - - +
65B ALA* 3.8 7.2 - - - +
67B THR* 1.3 78.4 - - - +
69B ALA* 1.3 59.9 + - - +
71B VAL* 3.4 1.4 + - - +
72B THR* 2.9 44.6 + - - -
122B THR* 2.7 21.9 + - - +
123B VAL* 3.8 16.5 + - + +
126B ARG* 2.6 38.8 + - - -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.7 21.5 - - + -
25B VAL* 5.4 0.9 - - + -
65B ALA 3.0 19.4 + - - +
66B ALA 3.8 2.2 - - - +
67B THR 3.4 0.4 - - - -
68B ASP* 1.3 78.3 + - - +
70B VAL* 1.3 65.5 + - + +
72B THR* 3.9 4.3 - - - -
73B ALA* 3.1 25.6 + - - +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 4.1 17.7 - - + -
66B ALA 3.1 17.1 + - - +
67B THR 3.8 3.4 - - - +
69B ALA* 1.3 75.4 - - + +
71B VAL* 1.3 65.1 + - - +
73B ALA* 3.5 4.8 + - - +
74B ALA* 3.0 23.1 + - + +
100B ALA* 3.9 6.1 - - + -
104B HIS* 3.3 38.4 - - + +
106B TRP* 3.9 16.8 - - + -
107B LEU* 3.9 21.5 - - + -
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR 3.0 21.5 + - - +
68B ASP 3.8 2.9 - - - +
70B VAL* 1.3 74.4 - - - +
72B THR* 1.3 67.4 + - - +
74B ALA* 3.2 4.6 + - - +
75B VAL* 2.9 32.9 + - + +
97B LEU* 4.0 30.7 - - + -
100B ALA* 5.1 1.8 - - - -
107B LEU* 4.2 20.0 - - + -
111B LEU* 4.3 4.9 - - + -
123B VAL* 3.9 28.7 - - + -
126B ARG* 6.4 1.3 - - + -
127B ILE* 4.3 10.3 - - + -
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Residues in contact with THR 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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68B ASP* 2.9 35.7 + - - -
69B ALA* 3.9 4.9 - - - -
71B VAL* 1.3 78.8 - - - +
73B ALA* 1.3 55.4 + - - +
75B VAL* 4.9 1.8 - - - -
76B THR* 2.7 55.1 + - + +
126B ARG* 4.8 9.7 + - - -
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Residues in contact with ALA 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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69B ALA 3.1 16.9 + - - +
70B VAL* 3.8 5.6 - - - +
72B THR* 1.3 81.3 - - - +
74B ALA* 1.3 57.7 + - - +
76B THR* 4.3 2.9 - - - -
77B ALA* 2.9 40.6 + - + +
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Residues in contact with ALA 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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70B VAL* 3.0 19.5 + - + +
71B VAL* 3.8 2.9 - - - +
73B ALA* 1.3 80.5 - - - +
75B VAL* 1.3 61.1 + - - +
77B ALA 3.8 13.3 + - - +
92B ALA 5.1 0.5 - - - +
96B GLY* 3.2 36.7 - - - +
99B ASP* 5.8 1.3 - - + -
100B ALA* 3.6 14.1 - - + +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 2.9 34.3 + - + +
72B THR* 4.2 2.7 - - - +
74B ALA* 1.3 78.9 - - - +
76B THR* 1.3 65.7 + - + +
77B ALA 5.2 0.5 - - - -
92B ALA* 4.7 9.7 - - - +
93B VAL* 3.9 49.4 - - + +
96B GLY* 4.3 4.7 - - - -
97B LEU* 4.4 13.7 - - + +
127B ILE* 6.0 1.6 - - + -
130B SER* 4.8 9.4 - - - +
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Residues in contact with THR 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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72B THR* 2.7 38.5 + - + +
73B ALA* 4.1 2.9 + - - -
75B VAL* 1.3 84.7 - - + +
77B ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 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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73B ALA* 2.9 25.9 + - + +
74B ALA* 4.0 12.2 - - - +
75B VAL 3.5 0.6 - - - -
76B THR* 1.3 83.4 - - - +
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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