Contacts of the helix formed by residues 56 - 74 (chain B) in PDB entry 2H4U
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 HIS 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.5 28.8 - + + -
22A GLU* 3.7 29.0 + - - +
62A THR* 3.7 22.0 - - + +
65A ASP* 4.6 14.4 - - - -
66A ASN* 4.1 9.6 + - - -
48B HIS 2.8 22.7 + - - +
49B THR 4.1 1.8 - - - -
50B ASN* 3.7 28.4 - - + +
54B THR 3.1 3.8 + - - -
55B LEU* 1.3 70.6 - - - +
57B GLY* 1.3 57.6 + - - +
58B GLY* 2.9 29.4 + - - -
59B LEU* 2.7 26.4 + - + +
60B THR* 2.9 13.2 + - - -
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Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 4.0 14.5 + - - -
83A SER* 6.0 1.1 - - - -
86A MET* 4.7 0.6 - - - +
50B ASN* 4.8 3.0 - - - +
55B LEU 3.3 5.2 + - - -
56B HIS* 1.3 73.2 + - - +
58B GLY* 1.3 55.8 + - - +
60B THR* 3.5 4.0 - - - -
61B ALA* 3.1 20.1 + - - +
90B TYR* 2.9 42.0 + - - -
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.9 1.6 - - - -
58A GLY 3.7 0.9 - - - +
61A ALA 4.7 1.8 - - - -
62A THR* 3.3 37.1 + - - -
65A ASP* 4.2 2.8 + - - -
56B HIS* 2.9 17.1 + - - -
57B GLY* 1.3 73.4 - - - +
59B LEU* 1.3 62.4 + - - +
61B ALA* 3.5 5.9 + - - +
62B THR* 2.8 25.5 + - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.6 34.3 - - + -
24B VAL* 4.0 9.9 - - + +
25B LEU* 3.7 27.8 - - + -
42B MET* 4.5 7.2 - - + -
48B HIS* 3.4 49.4 - - + -
55B LEU* 3.8 13.5 - - + -
56B HIS* 2.7 18.8 + - + +
58B GLY* 1.3 69.5 - - - +
60B THR* 1.3 54.2 + - - +
62B THR* 2.7 27.4 + - - -
63B LEU* 2.7 25.2 + - + +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.5 24.0 + - - +
56B HIS 2.9 10.0 + - - -
57B GLY* 3.5 12.8 - - - -
59B LEU* 1.3 75.6 - - - +
61B ALA* 1.3 57.1 + - - +
63B LEU* 3.2 16.0 + - - +
64B VAL* 3.0 27.0 + - + +
88B ILE* 4.3 7.9 - - + -
90B TYR* 3.8 22.5 - - + -
120B LEU* 3.8 20.6 - - + +
129B ILE* 5.5 1.2 - - - +
130B ALA* 4.0 16.2 - - + -
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Residues in contact with ALA 61 (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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58A GLY* 4.5 1.7 - - - -
61A ALA* 3.4 33.2 - - + -
86A MET* 4.4 1.3 - - + -
57B GLY 3.1 17.5 + - - +
58B GLY 3.6 3.6 - - - +
59B LEU 3.1 0.2 - - - -
60B THR* 1.3 72.1 - - - +
62B THR* 1.3 64.7 + - - +
64B VAL* 3.4 6.3 + - - +
65B ASP* 3.1 23.9 + - - +
86B MET* 3.6 17.2 - - + +
88B ILE* 4.1 13.9 - - + -
90B TYR* 4.6 0.2 + - - -
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Residues in contact with THR 62 (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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21A PHE* 4.3 1.7 - - - -
56A HIS* 3.8 22.7 - - + -
58A GLY* 3.6 16.2 + - - -
21B PHE* 3.6 21.6 - - + -
22B GLU* 5.9 0.7 - - + -
24B VAL* 4.0 6.1 - - + -
25B LEU* 3.9 22.9 - - + -
58B GLY 2.8 20.6 + - - -
59B LEU* 2.7 25.2 + - - -
61B ALA* 1.3 71.6 - - - +
63B LEU* 1.3 55.1 + - - -
65B ASP* 3.4 3.0 + - - +
66B ASN* 2.9 29.2 + - - +
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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
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25B LEU* 3.6 24.7 - - + -
28B ILE* 3.7 22.4 - - + -
42B MET* 4.2 14.8 - - + -
55B LEU* 4.7 3.8 - - + -
59B LEU* 2.7 32.7 + - + +
60B THR* 3.4 15.0 - - - +
62B THR* 1.3 74.1 - - - +
64B VAL* 1.3 55.8 + - - +
66B ASN* 4.5 1.1 - - - +
67B ILE* 3.0 45.2 + - + +
100B ILE* 4.6 4.5 - - + -
102B ILE* 4.3 28.9 - - + +
120B LEU* 4.2 16.2 - - + -
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Residues in contact with VAL 64 (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 THR 3.0 18.0 + - - +
61B ALA* 3.7 7.2 - - - +
62B THR 3.3 0.2 - - - -
63B LEU* 1.3 73.2 - - - +
65B ASP* 1.3 58.9 + - - +
68B SER* 2.5 39.7 + - - -
86B MET* 3.5 26.5 - - + -
87B ASN 5.1 0.2 - - - +
88B ILE* 4.5 13.2 - - + -
118B VAL* 3.8 34.3 - - + +
120B LEU* 4.3 11.4 - - + -
132B GLY* 4.4 21.1 - - - +
134B HIS* 4.3 10.3 - - + -
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Residues in contact with ASP 65 (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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56A HIS* 4.5 19.9 + - + -
57A GLY* 3.8 20.6 + - - -
58A GLY 4.7 2.0 - - - +
90A TYR* 4.5 3.3 + - - -
61B ALA 3.1 16.6 + - - +
62B THR* 3.7 4.9 - - - +
64B VAL* 1.3 76.1 - - - +
66B ASN* 1.3 56.6 + - - +
68B SER* 3.1 11.1 + - - -
69B THR* 2.6 34.3 + - - -
83B SER* 3.1 19.6 + - - -
86B MET* 4.0 8.1 - - + +
134B HIS* 3.8 16.4 + - - -
136B LYS* 4.4 3.5 + - - -
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Residues in contact with ASN 66 (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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56A HIS* 4.0 7.9 + - - +
22B GLU* 3.2 36.3 + - - +
25B LEU* 3.4 26.9 - - + +
28B ILE* 5.3 2.8 - - - +
62B THR* 2.9 17.9 + - + +
63B LEU 4.4 0.9 - - - +
65B ASP* 1.3 78.3 + - - +
67B ILE* 1.3 70.7 + - + +
69B THR* 3.2 10.4 + - - -
70B MET* 3.0 32.6 + - - +
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.8 20.6 - - + -
38B VAL* 3.7 23.3 - - + -
40B CYS* 3.8 25.4 - - + -
63B LEU* 3.0 27.2 + - + +
64B VAL 4.8 0.2 - - - +
66B ASN* 1.3 78.1 - - + +
68B SER* 1.3 65.9 + - - +
70B MET* 3.2 9.5 + - - +
71B ALA 3.1 17.8 + - - -
102B ILE* 3.7 29.8 - - + +
104B ALA* 3.6 27.1 - - + +
118B VAL* 4.8 1.3 - - + -
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Residues in contact with SER 68 (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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64B VAL 2.5 24.9 + - - -
65B ASP 3.1 2.1 + - - -
67B ILE* 1.3 76.1 - - - +
69B THR* 1.3 64.4 + - - +
71B ALA* 3.2 13.7 + - - +
72B LEU* 3.2 11.6 + - - +
104B ALA* 4.0 9.8 - - - +
116B THR* 3.2 36.6 - - - +
118B VAL* 3.7 13.7 - - - +
134B HIS* 2.8 23.6 + - - -
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Residues in contact with THR 69 (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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65B ASP* 2.6 22.1 + - - -
66B ASN* 3.2 12.0 + - - -
68B SER* 1.3 77.4 + - - +
70B MET* 1.3 50.8 + - - +
72B LEU* 3.2 9.5 + - - +
73B LEU* 2.8 42.8 + - + +
80B PRO* 3.7 26.9 - - + +
136B LYS* 2.9 32.7 + - - +
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Residues in contact with MET 70 (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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28B ILE* 5.0 6.5 - - - -
30B LEU* 4.0 31.0 - - + -
33B ALA* 5.8 2.2 - - + -
38B VAL* 3.9 12.6 - - + -
40B CYS* 4.2 23.6 - - - -
66B ASN* 3.0 28.5 + - - +
67B ILE* 3.3 16.6 - - - +
69B THR* 1.3 75.8 - - - +
71B ALA* 1.3 62.8 + - - +
73B LEU* 3.3 16.2 + - + +
74B CYS* 3.2 31.2 + - - -
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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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36B GLY 5.1 3.5 + - - -
37B LYS 4.9 3.6 - - - +
38B VAL* 3.5 25.3 - - + +
67B ILE 3.1 8.7 + - - +
68B SER* 3.2 8.9 + - - +
70B MET* 1.3 75.4 - - - +
72B LEU* 1.3 67.8 + - - +
74B CYS* 3.6 15.7 + - - +
75B THR* 4.0 2.8 - - - +
104B ALA* 4.1 17.9 - - + +
105B HIS 5.0 0.7 - - - -
106B VAL* 3.7 26.4 - - + +
116B THR* 5.2 0.9 - - + -
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Residues in contact with LEU 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 SER 3.2 9.6 + - - +
69B THR* 3.3 8.5 - - - +
71B ALA* 1.3 73.4 - - - +
73B LEU* 1.3 53.2 + - - +
74B CYS 2.7 14.7 + - - -
75B THR* 2.7 30.4 + - - -
77B ARG 3.9 0.6 - - - +
79B ALA 3.8 15.9 - - - +
80B PRO 3.5 23.3 - - - +
106B VAL* 3.9 13.0 - - + -
109B GLN* 4.4 13.0 - - + +
114B ALA* 3.9 28.7 - - + -
115B PHE 4.9 0.2 - - - +
116B THR* 3.5 28.7 - - + -
136B LYS* 3.7 25.8 - - + -
138B LEU* 4.6 3.1 - - + -
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Residues in contact with LEU 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 THR* 2.8 35.7 + - + +
70B MET* 3.3 17.5 + - + +
72B LEU* 1.3 70.2 - - - +
74B CYS* 1.3 60.2 + - - +
75B THR 3.3 3.4 + - - +
78B GLY* 3.5 40.5 - - - +
79B ALA 4.3 0.4 + - - -
80B PRO* 3.9 25.8 - - + -
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Residues in contact with CYS 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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33B ALA* 4.2 26.5 - - + -
34B ALA 5.1 6.1 - - - +
35B PRO* 4.6 14.0 - - - +
36B GLY 4.8 0.7 + - - -
38B VAL* 5.0 3.4 - - + -
70B MET* 3.2 22.7 + - - +
71B ALA* 3.8 8.5 - - - +
72B LEU 2.7 7.9 + - - -
73B LEU* 1.3 75.8 - - - +
75B THR* 1.3 63.0 + - - +
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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
------------------------------------------------------------
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