Contacts of the helix formed by residues 65 - 82 (chain B) in PDB entry 2E4Y
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 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 4.5 2.9 - - - +
46B PRO* 3.5 23.6 - - - -
47B ILE* 3.9 11.0 - - - -
61B ASN* 3.4 15.8 + - - -
63B ASP 3.4 0.2 - - - -
64B ARG* 1.3 79.9 - - - +
66B ILE* 1.3 65.9 + - - +
67B GLN 3.3 0.5 + - - -
68B ARG* 3.5 1.6 + - - +
69B LEU* 3.0 24.2 + - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.7 24.2 - - + -
60B ILE* 3.4 26.5 - - + -
61B ASN 3.1 5.4 + - - +
62B GLU 3.3 9.4 + - - +
65B GLY* 1.3 70.1 - - - +
67B GLN* 1.3 63.9 + - - +
69B LEU* 3.4 6.3 - - + +
70B GLU* 3.0 24.8 + - + +
337B PHE* 4.1 12.3 - - + -
348B ASN* 4.4 9.9 - - - +
350B TRP* 4.0 17.3 - - + +
351B PHE* 4.6 8.3 - - + -
354B PHE* 3.8 45.1 - - + -
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLU 3.3 5.1 + - - +
63B ASP* 3.0 39.8 + - - +
65B GLY 3.3 0.6 - - - -
66B ILE* 1.3 74.0 - - - +
68B ARG* 1.3 69.8 + - - +
70B GLU* 2.9 6.4 + - - +
71B ALA 2.7 20.8 + - - -
333B PHE* 3.6 20.6 - - + -
337B PHE* 3.8 22.9 - - + -
384B TYR* 3.2 30.3 - - - -
385B GLU 3.5 5.3 + - - -
386B GLN* 3.4 2.3 - - - -
387B GLU* 2.6 33.6 + - - +
390B ILE* 3.4 12.1 - - + +
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Residues in contact with ARG 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 3.2 23.6 - - + -
46B PRO* 5.0 0.2 - - - +
63B ASP 3.9 0.6 + - - +
64B ARG* 2.9 44.8 - - - +
65B GLY 3.5 0.6 + - - -
67B GLN* 1.3 78.4 - - - +
69B LEU* 1.3 65.2 + - - +
71B ALA* 3.2 10.4 + - - +
72B MET 3.2 6.6 + - - -
149B SER* 2.5 31.3 + - - -
171B TYR* 4.0 15.3 - - - -
172B ALA* 4.2 1.7 - - - +
387B GLU* 2.7 36.1 + - - +
389B LYS* 3.3 17.6 - - - +
390B ILE* 3.3 22.8 - - + +
393B VAL* 3.7 12.4 - - + +
2001B 52A 2.7 37.0 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.1 7.6 - - + -
45B PHE* 3.6 16.3 - - + -
47B ILE* 3.3 31.4 - - + -
65B GLY 3.0 18.1 + - - +
66B ILE* 3.4 9.9 - - + +
68B ARG* 1.3 75.1 - - - +
70B GLU* 1.3 70.1 + - - +
72B MET* 2.7 17.3 + - - +
73B LEU* 3.2 34.1 + - + -
95B ILE* 4.1 13.9 - - + -
348B ASN* 3.7 19.1 - - - +
350B TRP* 3.5 17.9 - - + -
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Residues in contact with GLU 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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66B ILE* 3.0 14.2 + - + +
67B GLN 2.9 7.9 + - - +
69B LEU* 1.3 80.1 - - - +
71B ALA* 1.3 54.3 + - - +
73B LEU* 2.7 17.8 + - - +
74B PHE* 2.6 34.3 + - - +
333B PHE* 3.9 11.4 - - + -
336B TYR* 2.7 34.5 + - + -
337B PHE* 4.0 12.3 - - + -
340B LEU* 3.7 14.7 - - + +
345B ASN* 3.2 21.7 + - - +
347B ARG* 4.2 0.3 + - - -
348B ASN* 2.7 33.5 + - - +
351B PHE* 5.0 0.4 - - + -
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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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67B GLN 2.7 13.7 + - - +
68B ARG 3.2 11.9 - - - +
69B LEU 3.0 0.2 + - - -
70B GLU* 1.3 72.1 - - - +
72B MET* 1.3 57.3 + - - +
74B PHE* 3.4 4.9 - - - +
75B ALA* 2.9 28.2 + - - +
333B PHE* 3.2 26.2 - - + -
390B ILE* 3.8 24.2 - - + -
393B VAL* 3.8 15.2 - - + +
394B VAL* 4.2 4.9 - - + +
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Residues in contact with MET 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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41B LEU* 4.0 11.7 - - + +
42B GLY 3.8 17.3 - - - +
43B GLY* 4.2 1.8 - - - -
45B PHE* 3.6 35.0 - - + -
68B ARG 3.2 1.8 + - - +
69B LEU 2.7 16.8 + - - +
71B ALA* 1.3 72.4 - - - +
73B LEU* 1.3 63.8 + - - +
75B ALA* 3.2 6.1 + - - +
76B ILE* 2.9 27.8 + - + +
93B VAL* 3.8 24.2 - - + -
95B ILE* 3.6 24.0 - - + -
146B ILE* 3.9 20.6 - - + -
393B VAL* 4.0 7.8 - - + +
397B VAL* 3.9 14.1 - - + -
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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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33B ILE* 4.4 13.2 - - + -
35B ILE* 6.2 2.2 - - + -
69B LEU* 3.2 17.2 + - + -
70B GLU* 2.7 39.2 + - - +
72B MET* 1.3 73.2 - - - +
74B PHE* 1.3 52.9 + - - +
76B ILE* 3.1 8.2 + - - +
77B ASP* 2.8 40.6 + - - +
93B VAL* 4.6 10.3 - - + -
95B ILE* 3.5 29.6 - - + -
336B TYR* 4.0 1.1 - - - +
347B ARG* 3.2 48.0 - - + +
348B ASN* 4.9 1.3 - - + -
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Residues in contact with PHE 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 GLU 2.6 10.1 + - - +
71B ALA* 3.4 14.1 - - - +
73B LEU* 1.3 73.8 - - - +
75B ALA* 1.3 60.3 + - - +
77B ASP* 3.1 9.1 + - + +
78B GLU* 2.8 67.9 + - + +
330B VAL* 4.3 4.7 - - + -
332B GLN* 3.7 30.1 - - + -
333B PHE* 3.8 24.2 - + + -
336B TYR* 3.2 50.1 - + + -
394B VAL* 4.4 8.1 - - + -
444B PHE* 3.8 27.4 - + - -
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Residues in contact with ALA 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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71B ALA 2.9 19.1 + - - +
72B MET* 3.2 5.8 + - - +
74B PHE* 1.3 81.1 - - - +
76B ILE* 1.3 57.8 + - - +
78B GLU* 3.2 6.5 + - - +
79B ILE* 2.8 35.6 + - - +
394B VAL* 4.2 14.6 - - + -
397B VAL* 4.1 23.8 - - + -
398B TYR* 4.1 15.0 - - + -
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Residues in contact with ILE 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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35B ILE* 6.0 2.7 - - + -
41B LEU* 3.8 23.1 - - + -
72B MET* 2.9 22.8 + - + +
73B LEU* 3.4 9.0 - - - +
75B ALA* 1.3 72.9 - - - +
77B ASP* 1.3 74.4 + - - +
79B ILE* 2.7 18.8 + - + +
80B ASN* 2.9 33.4 + - - +
91B LEU* 3.5 39.0 - - + +
93B VAL* 3.4 28.7 - - + -
397B VAL* 4.3 7.0 - - + -
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Residues in contact with ASP 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 LEU 2.8 19.3 + - - +
74B PHE* 3.1 13.7 - - + +
76B ILE* 1.3 76.5 - - - +
78B GLU* 1.3 60.4 + - + +
80B ASN* 3.2 10.2 + - - +
81B LYS* 3.0 28.8 + - - +
336B TYR* 4.4 8.8 + - - -
347B ARG* 3.0 38.8 + - - -
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Residues in contact with GLU 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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74B PHE* 2.8 42.5 + - + +
75B ALA* 3.4 6.7 - - - +
76B ILE 3.0 0.2 - - - -
77B ASP* 1.3 74.3 - - + +
79B ILE* 1.3 59.9 + - - +
80B ASN 3.0 1.8 - - - -
81B LYS* 2.8 33.1 + - - +
82B ASP* 2.9 29.3 + - - +
332B GLN* 5.4 1.7 - - - +
398B TYR* 3.3 20.1 + - - +
444B PHE* 3.4 26.5 - - + -
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Residues in contact with ILE 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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75B ALA 2.8 18.2 + - - +
76B ILE* 2.7 15.3 + - - +
78B GLU* 1.3 71.9 - - - +
80B ASN* 1.3 58.8 + - - +
82B ASP* 3.7 11.6 + - - +
85B LEU* 3.5 33.9 - - + +
86B LEU* 3.7 10.9 - - + +
91B LEU* 4.0 26.0 - - + -
397B VAL* 4.0 18.8 - - + -
398B TYR* 3.4 36.3 - - + -
401B ALA* 3.5 26.0 - - + -
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Residues in contact with ASN 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 ILE* 2.9 41.1 + - - +
77B ASP* 3.5 9.7 + - - +
79B ILE* 1.3 79.3 - - - +
81B LYS* 1.3 62.2 + - - +
82B ASP 3.1 8.3 + - - +
86B LEU 5.2 2.6 - - - +
87B PRO* 6.1 0.2 - - - +
89B VAL 4.7 0.7 - - - +
90B LYS* 3.6 21.6 - - + +
91B LEU* 3.0 34.3 + - - +
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Residues in contact with LYS 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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77B ASP 3.0 13.6 + - - +
78B GLU* 2.8 45.7 + - - +
80B ASN* 1.3 77.1 - - - +
82B ASP* 1.3 61.6 + - - +
83B ASN* 3.8 10.9 + - - +
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Residues in contact with ASP 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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78B GLU 2.9 14.9 + - - +
79B ILE* 3.7 18.4 - - - +
80B ASN 3.1 8.2 - - - +
81B LYS* 1.3 80.8 - - - +
83B ASN* 1.3 83.2 + - - +
84B TYR* 2.7 23.4 + - - +
85B LEU* 3.2 34.0 + - - +
86B LEU 4.3 4.0 - - - +
87B PRO* 4.6 4.5 - - - +
398B TYR* 5.1 5.6 - - - +
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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