Contacts of the helix formed by residues 65 - 82 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.5 2.9 - - - +
46A PRO* 3.5 23.3 - - - -
47A ILE* 3.9 11.2 - - - -
61A ASN* 3.4 15.2 + - - -
63A ASP 3.3 0.4 - - - -
64A ARG* 1.3 79.8 - - - +
66A ILE* 1.3 66.4 + - - +
67A GLN 3.3 0.2 + - - -
68A ARG* 3.5 1.7 + - - +
69A LEU* 2.9 25.0 + - - +
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Residues in contact with ILE 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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47A ILE* 3.6 26.2 - - + +
60A ILE* 3.5 25.8 - - + -
61A ASN 3.0 5.3 + - - +
62A GLU 3.3 9.1 + - - +
65A GLY* 1.3 71.8 - - - +
67A GLN* 1.3 67.5 + - - +
69A LEU* 3.3 6.1 + - + +
70A GLU* 3.0 19.9 + - + +
337A PHE* 4.1 12.1 - - + -
348A ASN* 4.3 12.8 - - - +
350A TRP* 4.0 16.8 - - + +
351A PHE* 4.5 8.7 - - + +
354A PHE* 3.7 43.7 - - + -
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Residues in contact with GLN 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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62A GLU 3.3 5.6 + - - +
63A ASP* 3.0 39.6 + - - +
65A GLY 3.3 0.4 - - - -
66A ILE* 1.3 76.4 - - - +
68A ARG* 1.3 67.6 + - - +
70A GLU* 2.8 6.6 + - - +
71A ALA 2.8 20.6 + - - -
333A PHE* 3.7 15.6 - - + -
337A PHE* 3.9 26.3 - - + -
384A TYR* 3.2 29.8 - - - -
385A GLU 3.5 6.5 + - - -
386A GLN* 3.5 2.1 - - - -
387A GLU* 2.6 33.3 + - - +
390A ILE* 3.4 12.9 - - + +
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Residues in contact with ARG 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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45A PHE* 3.0 25.6 - - + -
63A ASP 3.9 0.8 + - - +
64A ARG* 2.9 43.5 - - - +
65A GLY 3.5 0.8 + - - -
67A GLN* 1.3 78.6 - - - +
69A LEU* 1.3 66.3 + - - +
71A ALA* 3.3 4.2 + - - +
72A MET 3.2 10.9 + - - -
149A SER* 2.5 31.9 + - - -
171A TYR* 3.9 17.3 - - - -
172A ALA* 4.2 0.8 - - - +
387A GLU* 2.6 42.3 + - - +
389A LYS* 3.5 19.6 - - - +
390A ILE* 3.4 16.8 - - + +
393A VAL* 3.7 11.2 - - + +
1001A 52A 2.7 32.7 + - - -
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Residues in contact with LEU 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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33A ILE* 4.1 4.3 - - + -
45A PHE* 3.5 16.0 - - + -
47A ILE* 3.5 30.3 - - + -
65A GLY 2.9 18.3 + - - +
66A ILE* 3.5 9.2 - - + +
68A ARG* 1.3 75.2 - - - +
70A GLU* 1.3 56.9 + - - +
72A MET* 2.7 27.5 + - - +
73A LEU* 3.3 36.3 + - + -
95A ILE* 3.9 18.2 - - + -
348A ASN* 3.7 19.5 - - - +
350A TRP* 3.6 18.2 - - + -
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Residues in contact with GLU 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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66A ILE* 3.0 14.1 + - + +
67A GLN 2.8 12.3 + - - +
69A LEU* 1.3 77.8 - - - +
71A ALA* 1.3 53.2 + - - +
73A LEU* 2.8 18.3 + - - +
74A PHE* 2.7 34.7 + - - +
333A PHE* 3.8 2.9 - - + -
336A TYR* 2.6 36.7 + - + -
337A PHE* 4.0 18.6 - - + -
340A LEU* 3.7 15.0 - - + +
345A ASN* 3.1 22.8 + - - +
347A ARG* 4.2 0.2 + - - -
348A ASN* 2.8 33.2 + - - +
351A PHE* 5.0 0.2 - - + -
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Residues in contact with ALA 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 GLN 2.8 13.5 + - - +
68A ARG 3.5 9.2 - - - +
69A LEU 3.1 0.2 + - - -
70A GLU* 1.3 72.4 - - - +
72A MET* 1.3 57.1 + - - +
74A PHE* 3.4 3.0 - - - +
75A ALA* 2.8 30.3 + - - +
333A PHE* 3.1 26.4 - - + -
390A ILE* 3.8 27.8 - - + -
393A VAL* 3.9 13.0 - - + -
394A VAL* 4.4 4.6 - - + +
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Residues in contact with MET 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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41A LEU* 4.1 12.3 - - + +
42A GLY 3.7 19.5 - - - +
43A GLY* 4.3 0.2 - - - -
45A PHE* 3.6 35.9 - - + -
68A ARG 3.2 4.2 + - - +
69A LEU 2.7 18.0 + - - +
71A ALA* 1.3 69.9 - - - +
73A LEU* 1.3 64.1 + - - +
75A ALA* 3.3 5.8 + - - +
76A ILE* 2.9 27.5 + - + +
93A VAL* 3.8 24.5 - - + -
95A ILE* 3.8 22.0 - - + -
146A ILE* 4.0 20.4 - - + -
393A VAL* 4.0 8.5 - - + +
397A VAL* 4.0 10.5 - - + -
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Residues in contact with LEU 73 (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 ILE* 4.5 12.8 - - + -
35A ILE* 6.2 2.2 - - + -
69A LEU* 3.3 17.4 + - + -
70A GLU* 2.8 34.7 + - - +
72A MET* 1.3 76.4 - - + +
74A PHE* 1.3 54.7 + - - +
76A ILE* 2.9 10.1 + - - +
77A ASP* 2.7 40.0 + - - +
93A VAL* 4.6 9.2 - - + -
95A ILE* 3.3 32.1 - - + -
336A TYR* 4.0 0.4 - - - +
347A ARG* 3.2 46.4 - - + +
348A ASN* 4.9 1.1 - - + -
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Residues in contact with PHE 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 GLU 2.7 14.3 + - - +
71A ALA* 3.4 8.3 - - - +
73A LEU* 1.3 73.6 - - - +
75A ALA* 1.3 73.3 + - - +
77A ASP* 3.1 10.1 + - + +
78A GLU* 2.8 55.0 + - + +
330A VAL* 4.3 3.4 - - + -
332A GLN* 3.7 29.4 - - + -
333A PHE* 3.7 27.1 - + + -
336A TYR* 3.2 50.3 - + + -
394A VAL* 4.5 8.5 - - + -
444A PHE* 3.9 26.7 - + - -
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Residues in contact with ALA 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 ALA 2.8 20.8 + - - +
72A MET* 3.5 6.3 - - - +
74A PHE* 1.3 78.9 - - - +
76A ILE* 1.3 58.1 + - - +
78A GLU* 3.2 7.2 + - - +
79A ILE* 2.9 34.7 + - - +
394A VAL* 4.2 20.6 - - + -
397A VAL* 4.1 24.9 - - + -
398A TYR* 4.2 7.9 - - + -
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Residues in contact with ILE 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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35A ILE* 6.1 2.9 - - + -
41A LEU* 3.8 14.4 - - + -
72A MET* 2.9 21.8 + - + +
73A LEU* 2.9 11.2 + - - +
75A ALA* 1.3 73.0 - - - +
77A ASP* 1.3 74.1 + - - +
79A ILE* 2.8 16.2 + - + +
80A ASN* 3.0 36.4 + - - +
91A LEU* 3.5 45.8 - - + +
93A VAL* 3.4 30.3 - - + -
397A VAL* 4.4 7.2 - - + -
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Residues in contact with ASP 77 (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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73A LEU* 2.7 18.1 + - - +
74A PHE* 3.2 13.2 - - + +
76A ILE* 1.3 79.2 - - - +
78A GLU* 1.3 60.4 + - + +
80A ASN* 3.3 8.3 + - - +
81A LYS* 3.1 27.9 + - - +
336A TYR* 4.4 8.8 + - - -
347A ARG* 3.1 39.6 + - - -
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Residues in contact with GLU 78 (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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74A PHE* 2.8 44.1 + - + +
75A ALA 3.4 5.6 - - - +
77A ASP* 1.3 71.8 - - + +
79A ILE* 1.3 59.8 + - - +
80A ASN 3.1 1.6 - - - -
81A LYS* 2.8 34.3 + - - +
82A ASP* 2.9 28.6 + - - +
332A GLN* 5.4 2.3 - - - +
398A TYR* 3.3 20.5 + - - +
444A PHE* 3.4 28.7 - - + -
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Residues in contact with ILE 79 (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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75A ALA 2.9 19.1 + - - +
76A ILE* 2.8 12.0 + - - +
78A GLU* 1.3 73.1 - - - +
80A ASN* 1.3 59.9 + - - +
82A ASP* 3.6 12.4 + - - +
85A LEU* 3.5 33.3 - - + +
86A LEU* 3.6 11.4 - - + +
91A LEU* 4.1 26.9 - - + -
397A VAL* 4.0 21.5 - - + -
398A TYR* 3.4 34.3 - - + -
401A ALA* 3.5 27.1 - - + -
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Residues in contact with ASN 80 (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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76A ILE* 3.0 42.9 + - - +
77A ASP* 3.6 8.9 + - - +
79A ILE* 1.3 78.9 - - - +
81A LYS* 1.3 63.5 + - - +
82A ASP 3.1 7.1 + - - +
86A LEU 5.2 2.7 - - - +
89A VAL 4.6 0.9 - - - +
90A LYS* 3.6 21.4 - - + +
91A LEU* 2.9 35.4 + - - +
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Residues in contact with LYS 81 (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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77A ASP 3.1 14.3 + - - +
78A GLU* 2.8 45.7 + - - +
80A ASN* 1.3 77.4 - - - +
82A ASP* 1.3 61.5 + - - +
83A ASN* 3.8 10.6 + - - +
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Residues in contact with ASP 82 (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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78A GLU 2.9 15.8 + - - +
79A ILE* 3.6 19.2 - - - +
80A ASN 3.1 5.6 - - - +
81A LYS* 1.3 80.1 - - - +
83A ASN* 1.3 80.0 + - - +
84A TYR* 2.8 22.9 + - - +
85A LEU* 3.2 34.9 + - - +
86A LEU 4.2 4.0 - - - +
87A PRO* 4.6 4.5 - - - +
398A TYR* 5.1 4.8 - - - +
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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