Contacts of the helix formed by residues 54 - 68 (chain G) in PDB entry 2ZNZ
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 ALA 54 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G SER* 4.2 2.0 - - - -
52G GLY 4.1 0.4 + - - -
53G LEU* 1.3 75.8 - - - +
55G GLU* 1.3 67.1 + - - +
56G SER* 3.2 6.7 - - - +
57G THR* 3.1 29.9 + - + +
58G ILE* 3.1 12.2 + - - +
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Residues in contact with GLU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 3.9 45.6 - - + +
45G ARG* 2.9 50.5 + - - +
48G SER* 4.1 9.4 + - - +
53G LEU 3.8 0.8 + - - -
54G ALA* 1.3 73.4 - - - +
56G SER* 1.3 61.7 + - - +
58G ILE* 3.5 11.1 + - - +
59G HIS* 3.1 23.6 + - - +
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Residues in contact with SER 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ALA* 3.2 5.3 - - - +
55G GLU* 1.3 78.1 - - - +
57G THR* 1.3 61.1 + - - +
59G HIS* 3.4 8.5 - - - +
60G GLU* 3.3 23.4 + - - +
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Residues in contact with THR 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G LEU* 3.4 20.5 - - + +
54G ALA* 3.2 38.6 - - + +
56G SER* 1.3 75.2 - - - +
58G ILE* 1.3 58.7 + - - +
60G GLU* 3.4 8.1 + - - +
61G ARG* 3.0 33.8 + - - +
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Residues in contact with ILE 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ILE* 4.6 6.7 - - + -
44G LEU* 3.9 20.4 - - + +
47G ILE* 3.7 24.0 - - + -
48G SER* 3.3 43.5 - - - +
51G THR* 3.7 7.9 - - - +
53G LEU* 3.6 19.5 - - + +
54G ALA 3.1 16.3 + - - +
55G GLU* 3.7 7.2 - - - +
57G THR* 1.3 73.9 - - - +
59G HIS* 1.3 60.6 + - - +
61G ARG* 2.9 11.4 + - - +
62G ILE* 2.9 40.7 + - + +
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Residues in contact with HIS 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G LEU* 4.5 22.0 - - + +
55G GLU 3.1 11.6 + - - +
56G SER* 3.4 14.1 - - - +
58G ILE* 1.3 80.4 - - - +
60G GLU* 1.3 65.0 + - - +
62G ILE* 3.5 8.6 + - - +
63G ARG* 3.2 30.0 + - + +
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Residues in contact with GLU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G SER 3.3 10.5 + - - +
57G THR* 3.7 11.2 - - - +
58G ILE 3.2 0.6 - - - -
59G HIS* 1.3 80.2 - - + +
61G ARG* 1.3 64.0 + - - +
63G ARG* 2.8 45.1 + - - +
64G LYS* 3.2 23.9 + - + +
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Residues in contact with ARG 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ASP* 2.8 34.7 + - - +
28G ILE* 3.5 26.5 - - - +
29G ASP* 2.9 34.8 + - - +
32G ILE* 3.9 17.9 - - + -
53G LEU* 3.8 18.1 - - + +
57G THR* 3.0 27.8 + - - +
58G ILE* 2.9 11.4 + - - +
60G GLU* 1.3 73.2 - - - +
62G ILE* 1.3 64.9 + - - +
64G LYS* 3.2 15.5 + - - +
65G LEU* 3.0 28.3 + - - +
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ILE* 3.8 22.2 - - + -
36G LEU* 3.9 19.1 - - + -
44G LEU* 4.6 6.5 - - + -
47G ILE* 4.4 11.0 - - + -
58G ILE* 2.9 34.1 + - + +
59G HIS* 3.7 11.2 - - - +
60G GLU 3.4 0.2 - - - -
61G ARG* 1.3 75.8 - - - +
63G ARG* 1.3 59.6 + - + +
65G LEU* 3.2 11.6 + - - +
66G ARG* 2.9 29.5 + - - +
71G ILE* 4.2 2.2 - - + +
74G PHE* 4.1 28.0 - - + -
41H LYS* 5.3 6.1 - - - -
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Residues in contact with ARG 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G HIS* 3.2 20.4 + - + +
60G GLU* 2.8 51.9 + - - +
62G ILE* 1.3 77.3 - - - +
64G LYS* 1.3 65.9 + - - +
66G ARG* 3.6 15.2 - - + +
67G GLU* 3.0 73.4 + - + +
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Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU* 5.8 2.6 - - - +
29G ASP* 3.6 23.1 + - - +
60G GLU* 3.2 16.8 + - + +
61G ARG* 3.2 17.9 + - - +
63G ARG* 1.3 83.8 - - - +
65G LEU* 1.3 76.0 + - - +
67G GLU* 3.2 5.0 + - - +
68G SER* 3.1 32.1 + - - +
70G VAL* 6.3 0.2 - - - +
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU* 4.5 5.8 - - + -
29G ASP* 3.6 38.6 - - + +
32G ILE* 4.5 10.8 - - + -
33G ILE* 3.9 26.9 - - + -
61G ARG 3.0 22.1 + - - +
62G ILE* 3.2 8.7 + - - +
64G LYS* 1.3 85.7 - - - +
66G ARG* 1.3 59.6 + - - +
68G SER* 3.4 7.1 + - - -
70G VAL* 2.9 51.9 + - + -
71G ILE* 3.0 22.5 + - + -
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Residues in contact with ARG 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ILE* 2.9 18.9 + - - +
63G ARG* 3.6 16.3 - - - +
65G LEU* 1.3 79.5 - - - +
67G GLU* 1.3 60.6 + - + +
68G SER 3.5 0.2 - - - -
69G GLY* 3.7 5.0 + - - -
71G ILE* 3.7 26.1 - - + +
73G LYS* 6.1 2.3 - - - +
74G PHE* 3.5 36.9 - - + +
39H ASP* 4.0 22.2 + - - -
41H LYS* 3.8 25.5 - - - +
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ARG* 3.0 50.0 + - + +
64G LYS* 3.2 5.8 + - - +
66G ARG* 1.3 75.7 - - + +
68G SER* 1.3 58.5 + - - +
69G GLY 3.2 5.7 + - - -
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Residues in contact with SER 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G LYS* 3.1 24.2 + - - -
65G LEU* 3.4 10.9 + - - -
67G GLU* 1.3 76.2 - - - +
69G GLY* 1.3 58.9 + - - +
70G VAL* 3.4 18.7 + - - +
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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