Contacts of the helix formed by residues 63 - 78 (chain E) in PDB entry 2GZJ
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 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E ASP* 2.7 22.5 + - - -
62E ASP* 1.3 81.9 + - - +
64E PRO* 1.3 74.6 - - - +
65E SER* 3.4 10.8 + - - -
66E GLY 3.0 14.7 + - - -
67E ILE* 2.9 22.3 + - - +
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Residues in contact with PRO 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E LEU* 3.8 9.2 - - + -
19E VAL* 3.8 18.0 - - + +
20E THR* 3.4 32.1 - - + +
23E CYS* 4.1 24.7 - - + -
24E ASN* 5.9 1.6 - - - +
62E ASP 4.5 0.2 - - - +
63E SER* 1.3 86.9 - - - +
65E SER* 1.3 60.6 + - - +
67E ILE* 3.4 2.4 + - - +
68E VAL* 3.1 27.7 + - - +
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E LEU* 3.8 17.1 - - - +
61E ASP* 4.8 1.9 + - - -
63E SER* 3.4 9.4 + - - -
64E PRO* 1.3 78.6 - - - +
66E GLY* 1.3 62.9 + - - +
68E VAL* 3.4 4.4 + - - +
69E ASN* 3.0 24.7 + - - +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ASP* 3.3 40.4 - - - +
63E SER* 3.0 12.1 + - - -
65E SER* 1.3 77.1 + - - +
67E ILE* 1.3 60.9 + - - +
69E ASN* 3.3 7.7 + - - +
70E THR* 3.0 26.3 + - - -
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Residues in contact with ILE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E VAL* 4.0 14.6 - - + -
23E CYS* 3.7 23.3 - - - -
40E PHE* 3.9 29.8 - - + -
52E LEU* 3.7 31.0 - - + +
53E ILE* 3.9 13.5 - - + +
61E ASP 4.0 1.3 - - - +
62E ASP* 3.5 28.5 - - - +
63E SER 2.9 13.7 + - - +
64E PRO 3.7 3.6 - - - +
66E GLY* 1.3 73.4 - - - +
68E VAL* 1.3 66.4 + - - +
70E THR* 3.3 7.8 + - - -
71E VAL* 3.0 25.2 + - + +
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Residues in contact with VAL 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLU* 4.1 32.5 - - + +
15E PHE* 3.9 24.2 - - + -
16E LEU* 3.8 32.1 - - + -
19E VAL* 4.0 9.6 - - + -
64E PRO 3.1 17.8 + - - +
65E SER* 3.9 6.3 - - - +
66E GLY 3.4 0.2 - - - -
67E ILE* 1.3 74.6 - - - +
69E ASN* 1.3 56.8 + - - +
71E VAL* 3.3 6.7 + - - +
72E LYS* 2.9 29.8 + - + +
83E PHE* 4.2 6.0 - - + -
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Residues in contact with ASN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E SER 3.0 17.4 + - - +
66E GLY* 3.6 7.6 - - - +
67E ILE 3.3 0.4 - - - -
68E VAL* 1.3 76.3 - - - +
70E THR* 1.3 61.8 + - - +
72E LYS* 3.3 7.6 + - - +
73E GLN* 2.9 53.7 + - - +
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E HIS* 4.2 11.4 - - + -
52E LEU* 4.0 28.3 - - + -
60E ASP* 4.8 18.7 + - - +
61E ASP* 4.9 5.0 + - - +
66E GLY 3.0 14.2 + - - -
67E ILE* 3.3 11.4 + - - -
69E ASN* 1.3 80.4 + - - +
71E VAL* 1.3 58.6 + - - +
73E GLN* 4.1 3.6 - - - +
74E TRP* 3.0 32.4 + - + +
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 4.1 5.2 - - + -
15E PHE* 4.1 15.7 - - + -
40E PHE* 4.1 10.3 - - + -
44E THR* 3.9 34.8 - - + -
46E HIS* 5.0 4.0 - - + +
52E LEU* 3.9 21.5 - - + -
67E ILE 3.0 20.8 + - - +
68E VAL 3.7 4.0 - - - +
70E THR* 1.3 73.9 - - - +
72E LYS* 1.3 61.5 + - - +
74E TRP* 3.3 5.2 + - - +
75E ARG* 2.9 53.3 + - + +
83E PHE* 4.8 3.1 - - + -
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Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E GLU* 2.7 39.2 + - - +
68E VAL* 2.9 20.5 + - + +
69E ASN* 3.6 9.2 - - - +
71E VAL* 1.3 75.7 - - - +
73E GLN* 1.3 72.9 + - - +
75E ARG* 3.5 5.6 + - - +
76E ALA* 3.0 29.9 + - + +
83E PHE* 4.1 22.0 - - + -
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Residues in contact with GLN 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ASN* 2.9 42.9 + - - +
70E THR* 4.2 3.4 - - - +
72E LYS* 1.3 91.0 - - - +
74E TRP* 1.3 66.9 + - - +
76E ALA* 3.4 11.1 + - - +
77E ALA* 3.0 25.9 + - - +
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Residues in contact with TRP 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR 3.8 14.6 - - - -
45E GLU 3.3 24.0 - - - -
46E HIS* 3.4 33.4 - + + +
47E PRO* 3.5 26.7 - - + +
70E THR 3.0 20.3 + - - +
71E VAL* 3.8 1.8 - - - +
73E GLN* 1.3 76.2 - - - +
75E ARG* 1.3 74.1 + - + +
77E ALA* 3.2 1.8 + - - -
78E ASN* 2.8 70.0 + - + +
80E LYS* 4.0 30.7 - - + -
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Residues in contact with ARG 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE* 3.2 32.6 - - - +
43E MET 3.4 7.9 + - - -
44E THR 3.0 23.3 + - - +
45E GLU* 2.9 28.3 + - - +
71E VAL* 2.9 35.4 + - + +
72E LYS* 3.8 5.2 - - - +
74E TRP* 1.3 91.3 - - + +
76E ALA* 1.3 63.1 + - - +
78E ASN 3.3 5.2 + - - -
80E LYS* 3.0 52.7 + - + +
81E SER* 2.8 44.0 + - - +
82E GLY* 4.9 4.7 - - - -
83E PHE* 6.1 0.9 - - - -
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Residues in contact with ALA 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LYS* 3.0 18.7 + - + +
73E GLN* 3.5 15.9 - - - +
75E ARG* 1.3 76.7 - - - +
77E ALA* 1.3 62.4 + - - +
78E ASN 3.5 0.7 + - - -
79E GLY* 4.0 5.9 + - - -
80E LYS 4.9 3.1 - - - -
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Residues in contact with ALA 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLN 3.0 16.4 + - - +
74E TRP* 4.7 1.1 - - - -
76E ALA* 1.3 77.3 - - - +
78E ASN* 1.3 73.0 + - - +
79E GLY 3.6 1.4 + - - -
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Residues in contact with ASN 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E TRP* 2.8 75.4 + - + +
75E ARG 3.3 0.9 + - - +
76E ALA 3.3 0.4 - - - -
77E ALA* 1.3 93.4 - - - +
79E GLY* 1.3 61.6 + - - +
80E LYS* 3.3 18.5 + - - +
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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