Contacts of the helix formed by residues 67 - 79 (chain A) in PDB entry 2EEJ
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 PRO 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 6.0 2.5 - - - -
65A ASP 3.5 3.8 - - - +
66A GLU* 1.3 97.7 - - + +
68A TYR* 1.3 63.0 + - - +
69A GLU* 4.1 10.5 - - + +
70A LYS* 3.6 30.3 - - + +
71A VAL* 3.0 23.2 + - - +
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Residues in contact with TYR 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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24A LEU* 3.7 38.6 + - + +
25A ASN 4.5 0.4 - - - -
26A ALA* 4.1 31.9 - - + -
32A GLY 5.9 0.7 - - - +
33A SER* 3.5 21.5 - - - +
67A PRO* 1.3 74.4 - - - +
69A GLU* 1.3 66.4 + - + +
70A LYS 3.3 0.2 - - - -
71A VAL* 3.2 6.8 - - - +
72A VAL* 2.7 55.4 + - + +
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Residues in contact with GLU 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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67A PRO* 3.3 9.6 - - + +
68A TYR* 1.3 90.6 - - + +
70A LYS* 1.3 60.7 + - + +
72A VAL* 2.9 21.5 - - - +
73A ASP* 3.2 13.9 + - - +
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Residues in contact with LYS 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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63A VAL* 5.9 0.2 - - - -
66A GLU* 4.1 22.7 + - + +
67A PRO* 3.6 33.9 + - + +
68A TYR 3.3 0.4 - - - -
69A GLU* 1.3 78.5 - - + +
71A VAL* 1.3 66.1 + - - +
73A ASP* 3.4 6.6 + - + +
74A ARG* 3.1 34.8 + - + +
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Residues in contact with VAL 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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24A LEU* 4.2 8.7 - - + -
32A GLY* 5.2 5.2 - - - -
33A SER* 3.5 18.6 - - - +
55A ILE* 5.4 6.3 - - + -
58A VAL* 5.0 1.1 - - - +
63A VAL* 3.4 49.1 - - + +
66A GLU* 3.9 4.9 - - + +
67A PRO 3.0 18.1 + - - +
68A TYR* 3.2 19.5 - - - +
70A LYS* 1.3 75.0 - - - +
72A VAL* 1.3 76.5 + - - +
74A ARG* 3.2 10.9 + - - +
75A ILE* 3.2 26.6 + - + +
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Residues in contact with VAL 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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24A LEU* 4.5 14.6 - - + -
68A TYR* 2.7 46.0 - - + +
69A GLU* 2.9 18.6 - - - +
71A VAL* 1.3 81.8 - - + +
73A ASP* 1.3 76.0 + - + +
75A ILE* 2.9 8.0 + - + +
76A GLN* 2.8 53.7 + - + +
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Residues in contact with ASP 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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69A GLU 3.2 17.3 + - - +
70A LYS* 3.4 7.2 + - + +
72A VAL* 1.3 81.7 - - + +
74A ARG* 1.3 54.0 + - + +
76A GLN* 3.8 14.8 + - - +
77A SER* 2.8 43.4 + - - -
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Residues in contact with ARG 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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58A VAL* 3.4 33.4 - - + -
59A ASN* 4.1 11.4 + - - +
61A VAL* 4.1 21.9 - - - +
63A VAL* 3.9 15.5 - - - +
66A GLU* 5.8 3.2 + - - +
70A LYS* 3.1 23.3 + - + +
71A VAL 3.3 10.3 - - - +
72A VAL 3.1 0.4 - - - -
73A ASP* 1.3 76.9 - - + +
75A ILE* 1.3 57.1 + - - +
77A SER* 4.0 4.6 - - - -
78A SER* 3.0 27.5 + - - -
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Residues in contact with ILE 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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20A TYR* 3.7 31.1 + - + -
22A PHE* 5.2 4.7 - - + -
24A LEU* 4.2 18.4 - - + -
55A ILE* 4.1 20.6 - - + -
58A VAL* 4.0 6.5 - - + -
71A VAL* 3.5 13.7 - - + +
72A VAL* 2.9 8.3 + - + +
74A ARG* 1.3 73.6 - - - +
76A GLN* 1.3 64.0 + - + +
78A SER* 2.8 21.5 + - - -
82A VAL* 3.9 20.4 - - + -
84A LEU* 3.7 38.8 - - + -
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Residues in contact with GLN 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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15A LYS* 4.5 7.1 + - - +
20A TYR* 5.5 3.8 - - + -
72A VAL* 2.8 48.5 + - + +
73A ASP* 3.7 15.7 + - - +
75A ILE* 1.3 76.9 - - + +
77A SER* 1.3 65.1 + - - +
79A GLY* 3.4 14.2 + - - +
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Residues in contact with SER 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 ASP* 2.8 28.4 + - - -
74A ARG* 4.0 4.7 - - - -
76A GLN* 1.3 68.6 - - - +
78A SER* 1.3 70.1 + - - +
79A GLY* 2.7 7.5 + - - -
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Residues in contact with SER 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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20A TYR* 3.3 4.2 + - - -
59A ASN* 4.6 9.9 - - - +
74A ARG 3.0 15.8 + - - -
75A ILE 2.8 18.0 + - - -
77A SER* 1.3 76.5 + - - +
79A GLY* 1.3 60.2 + - - +
80A LYS 4.1 1.4 + - - -
81A ASN* 3.1 28.4 + - - +
82A VAL* 3.3 19.0 - - - +
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Residues in contact with GLY 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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15A LYS* 2.5 34.2 + - - -
20A TYR* 3.1 7.0 + - - -
76A GLN 3.4 7.3 + - - +
77A SER 2.7 10.0 + - - -
78A SER* 1.3 79.1 + - - +
80A LYS* 1.3 59.4 + - - -
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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
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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