Contacts of the helix formed by residues 62 - 82 (chain B) in PDB entry 5I1U
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 SER 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 3.9 8.3 - - - -
60B GLU 3.9 0.8 + - - -
61B SER* 1.3 76.4 - - - +
63B ALA* 1.3 59.5 + - - +
64B GLU* 3.6 7.8 + - - +
65B ASP* 3.2 31.1 + - - +
66B LEU* 2.8 27.7 + - - +
188B LEU 5.2 0.4 + - - -
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Residues in contact with ALA 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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18B HIS* 3.6 34.1 + - + +
21B GLU* 3.4 41.3 - - + +
22B ALA* 4.0 4.3 - - - +
25B ARG* 4.3 4.3 - - - +
62B SER* 1.3 75.7 - - - +
64B GLU* 1.3 62.2 + - - +
66B LEU* 3.4 3.0 + - - +
67B ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.9 30.7 - - - +
62B SER* 3.2 6.8 + - - +
63B ALA* 1.3 78.9 - - - +
65B ASP* 1.3 71.6 + - - +
67B ALA* 3.4 5.6 + - - +
68B LEU* 3.2 19.1 + - - +
126B ARG* 4.8 2.4 + - - -
187B ARG* 5.0 7.6 + - - -
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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
----------------------------------------------------------
61B SER* 3.9 13.5 - - - -
62B SER* 3.2 21.3 + - - +
64B GLU* 1.3 86.4 - - - +
66B LEU* 1.3 60.1 + - - +
68B LEU* 3.2 8.4 + - - +
69B ALA* 3.0 23.9 + - - +
187B ARG* 2.9 29.8 + - - -
188B LEU* 3.5 26.3 - - + +
190B HIS* 2.7 32.5 + - - -
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Residues in contact with LEU 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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16B ASN* 3.4 28.9 - - + +
18B HIS* 3.7 13.2 - - + -
19B GLN* 3.9 0.2 - - - -
22B ALA* 3.6 21.8 - - + -
51B THR 5.5 0.2 - - - +
54B ALA* 3.5 39.5 - - + +
55B SER* 3.6 20.0 - - - +
58B TYR 4.2 1.3 - - - +
61B SER* 3.5 17.1 + - - +
62B SER 2.8 17.7 + - - +
63B ALA* 3.7 4.5 - - - +
65B ASP* 1.3 76.4 - - - +
67B ALA* 1.3 56.1 + - - +
69B ALA* 3.1 8.3 + - + +
70B ALA* 2.9 27.3 + - + +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.8 13.4 - - - +
25B ARG* 3.7 36.3 - - + +
26B HIS 4.9 1.1 - - - +
63B ALA 3.0 13.6 + - - +
64B GLU* 3.5 10.8 - - - +
65B ASP 3.2 0.2 - - - -
66B LEU* 1.3 77.0 - - - +
68B LEU* 1.3 56.0 + - - +
70B ALA* 3.2 4.0 + - - +
71B ASP* 2.9 39.6 + - - +
126B ARG* 4.1 5.8 - - - +
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Residues in contact with LEU 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 GLU 3.2 9.4 + - - +
65B ASP* 3.2 11.7 + - - +
67B ALA* 1.3 78.0 - - - +
69B ALA* 1.3 58.7 + - - +
71B ASP* 3.3 1.1 + - - +
72B LEU* 2.9 29.3 + - + +
123B LEU* 4.0 15.3 - - + -
126B ARG* 3.4 49.9 - - + +
127B ILE* 4.4 18.8 - - + -
184B MET* 5.6 2.0 - - - -
187B ARG* 3.6 37.9 - - + +
188B LEU* 3.9 15.0 - - + -
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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
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54B ALA* 4.1 10.1 - - + -
58B TYR* 3.5 35.4 - - + -
65B ASP 3.0 13.3 + - - +
66B LEU* 3.1 12.5 + - + +
68B LEU* 1.3 77.0 - - - +
70B ALA* 1.3 56.4 + - - +
72B LEU* 3.4 8.9 + - - +
73B MET* 2.9 33.8 + - - +
188B LEU* 3.8 11.4 - - + +
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Residues in contact with ALA 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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22B ALA* 5.0 2.7 - - + +
26B HIS* 3.3 20.2 - - + -
50B ILE* 3.3 7.6 - - + +
51B THR* 3.7 31.4 - - + -
54B ALA* 3.8 14.0 - - + +
66B LEU* 2.9 13.9 + - + +
67B ALA* 3.6 8.7 - - - +
69B ALA* 1.3 73.4 - - - +
71B ASP* 1.3 61.9 + - - +
74B GLY 2.9 25.3 + - - -
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Residues in contact with ASP 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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25B ARG 4.9 1.7 - - - +
26B HIS* 2.7 39.0 + - - -
29B TRP* 3.2 42.8 - - + +
67B ALA* 2.9 20.1 + - - +
68B LEU 3.7 2.2 - - - +
70B ALA* 1.3 75.7 - - - +
72B LEU* 1.3 57.7 + - - +
74B GLY* 3.5 0.5 + - - -
75B PHE* 2.9 28.4 + - - +
123B LEU* 3.7 19.7 - - + -
126B ARG* 2.9 31.2 + - - +
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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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58B TYR* 5.3 3.8 - - + +
68B LEU* 2.9 21.1 + - + +
69B ALA* 3.6 8.1 - - - +
71B ASP* 1.3 76.5 - - - +
73B MET* 1.3 66.5 + - + +
75B PHE* 3.1 6.4 + - + +
76B TYR* 3.0 42.2 + - + +
123B LEU* 3.8 20.3 - - + +
127B ILE* 4.6 7.2 - - + -
143B TRP* 3.5 36.6 - - + -
180B SER* 5.8 0.4 - - - -
181B ILE* 5.3 4.9 - - + -
184B MET* 3.8 36.3 - - + -
188B LEU* 6.5 0.2 - - + -
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Residues in contact with MET 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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50B ILE* 3.9 16.8 - - + -
53B LEU* 4.2 28.9 - - + -
54B ALA* 4.8 7.4 - - + -
57B VAL* 4.1 9.0 - - + -
58B TYR* 4.1 25.1 - - + +
69B ALA* 2.9 22.4 + - + +
70B ALA 4.6 0.2 - - - -
72B LEU* 1.3 79.4 - - + +
74B GLY* 1.3 61.9 + - - +
76B TYR* 3.3 21.5 + - - +
77B PHE* 2.9 35.4 + - + -
181B ILE* 4.3 16.6 - - + -
299B TRP* 4.1 25.1 - - + +
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Residues in contact with GLY 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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26B HIS* 4.3 2.5 - - - -
29B TRP* 5.0 0.9 - - - -
45B TYR* 3.5 24.5 - - - -
50B ILE* 3.5 9.7 - - - +
70B ALA 2.9 16.0 + - - -
71B ASP 3.8 1.6 - - - -
73B MET* 1.3 74.9 - - - +
75B PHE* 1.3 62.1 + - - +
77B PHE* 3.3 3.3 + - - +
78B LEU* 2.9 33.6 + - - +
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Residues in contact with PHE 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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29B TRP* 4.2 8.1 - - + -
36B LEU* 4.2 7.0 - - + -
71B ASP 2.9 9.2 + - - +
72B LEU 3.1 8.7 + - - +
74B GLY* 1.3 73.3 - - - +
76B TYR* 1.3 74.0 + + - +
78B LEU* 3.2 4.4 + - - +
79B PHE* 2.7 62.0 + + + +
101B LEU* 4.8 1.3 - - + -
116B SER* 3.6 27.1 - - - -
119B ALA* 4.0 18.8 - - + -
120B PHE* 3.9 22.4 - + + -
123B LEU* 3.4 27.1 - - + -
143B TRP* 4.1 30.7 - + - -
146B TYR* 4.9 0.2 - + - -
147B PHE* 4.5 8.7 - + - -
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Residues in contact with TYR 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 LEU* 3.0 38.1 + - + +
73B MET* 3.3 21.0 + - - +
75B PHE* 1.3 81.4 - + - +
77B PHE* 1.3 68.7 + - + +
79B PHE* 4.0 0.3 - - - +
80B ASP* 3.2 31.3 + - - +
143B TRP* 3.5 35.6 - + - -
146B TYR* 3.5 27.6 - + - +
177B ALA* 3.5 24.1 + - + +
180B SER* 3.4 28.4 - - - -
181B ILE* 4.0 23.7 - - + +
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Residues in contact with PHE 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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48B TRP* 3.4 56.9 - + + -
50B ILE* 3.5 20.4 - - + -
53B LEU* 4.3 15.5 - - + -
73B MET* 2.9 27.3 + - + -
74B GLY 3.3 5.3 + - - +
75B PHE 3.2 0.6 - - - -
76B TYR* 1.3 85.4 - - + +
78B LEU* 1.3 62.5 + - - +
80B ASP* 4.0 3.0 - - - +
81B ASP* 3.1 22.9 + - - +
306B TRP* 4.5 22.4 - + - -
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Residues in contact with LEU 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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29B TRP* 4.6 3.4 - - + -
30B LEU* 4.0 26.5 - - + -
33B HIS 5.9 0.2 - - - +
36B LEU* 3.7 47.0 - - + +
37B ALA* 3.9 24.0 - - - +
39B VAL* 4.0 15.3 - - + +
40B VAL* 4.1 7.6 - - + -
45B TYR* 4.0 24.0 - - + -
48B TRP* 4.5 3.4 - - + -
74B GLY 2.9 24.8 + - - +
75B PHE 4.0 1.3 - - - +
77B PHE* 1.3 74.9 - - - +
79B PHE* 1.3 65.3 + - - +
81B ASP* 3.3 18.1 + - - +
82B GLN* 3.8 4.2 + - - +
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Residues in contact with PHE 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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36B LEU* 4.5 2.8 - - - +
75B PHE* 2.7 45.5 + + + +
76B TYR 4.0 1.3 - - - +
78B LEU* 1.3 73.6 - - - +
80B ASP* 1.3 64.2 + - - +
82B GLN* 3.0 51.4 - - - +
83B PHE* 3.6 22.0 - + - -
97B ILE* 4.4 1.8 - - + -
98B CYS* 4.3 6.1 - - - -
101B LEU* 3.4 32.3 - - + -
116B SER* 3.5 19.1 - - - -
146B TYR* 3.4 22.4 - + - -
147B PHE* 4.0 20.0 - + - -
150B HIS* 3.8 21.5 - + - -
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Residues in contact with ASP 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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76B TYR* 3.2 17.7 + - - +
77B PHE* 4.1 3.1 - - - +
79B PHE* 1.3 81.1 - - - +
81B ASP* 1.3 65.7 + - - +
83B PHE* 3.1 19.2 + - - +
84B ASP* 3.6 14.3 + - - +
146B TYR* 2.8 27.4 + - - -
150B HIS* 2.8 31.8 + - - -
153B GLU* 5.1 2.4 - - - +
175B THR 4.7 4.2 - - - +
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Residues in contact with ASP 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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39B VAL* 3.5 35.7 - - + +
40B VAL* 4.6 15.1 - - - +
48B TRP* 5.2 8.7 - - + -
77B PHE 3.1 14.1 + - - +
78B LEU* 3.4 13.9 - - - +
79B PHE 3.2 0.2 - - - -
80B ASP* 1.3 78.8 - - - +
82B GLN* 1.3 63.0 + - - +
84B ASP* 3.1 30.1 + - - +
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Residues in contact with GLN 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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36B LEU* 5.5 0.3 - - - +
39B VAL* 5.4 10.1 - - + +
78B LEU 3.8 3.8 + - - +
79B PHE* 3.0 34.3 + - - +
80B ASP 3.1 1.4 - - - -
81B ASP* 1.3 80.3 + - - +
83B PHE* 1.3 79.6 + - + +
84B ASP 3.3 0.4 + - - -
85B SER* 4.4 4.5 + - - -
89B ARG* 3.6 27.8 + - - +
97B ILE* 4.1 26.1 - - - +
116B SER* 3.1 25.3 + - - -
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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