Contacts of the helix formed by residues 54 - 68 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48D SER* 4.1 1.8 - - - -
53D LEU* 1.3 76.0 - - - +
55D GLU* 1.3 59.2 + - - +
56D SER* 3.1 11.4 - - - +
57D THR* 2.9 33.6 + - - +
58D ILE* 3.2 11.3 + - - +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.8 45.1 - - + +
45D ARG* 3.5 30.0 + - - +
48D SER* 3.8 11.7 + - - -
53D LEU 3.8 1.4 + - - -
54D ALA* 1.3 69.8 - - - +
56D SER* 1.3 63.8 + - - +
58D ILE* 4.0 7.6 - - - -
59D HIS* 3.4 23.0 + - - +
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Residues in contact with SER 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D ALA* 3.1 7.5 - - - +
55D GLU* 1.3 81.0 - - - +
57D THR* 1.3 65.8 + - - +
59D HIS* 3.7 5.1 + - - +
60D GLU* 3.4 22.3 + - - +
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Residues in contact with THR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 4.2 19.3 - - + +
54D ALA* 2.9 29.5 + - - +
56D SER* 1.3 79.7 + - - +
58D ILE* 1.3 59.5 + - - +
60D GLU* 3.6 9.0 + - + +
61D ARG* 3.1 51.8 + - + +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ILE* 4.3 15.0 - - + -
44D LEU* 3.8 20.6 - - + +
47D ILE* 3.7 22.7 - - + -
48D SER* 3.4 40.4 - - - +
51D THR* 3.5 14.8 - - - +
53D LEU* 3.9 13.9 - - + -
54D ALA 3.2 14.9 + - - +
55D GLU* 3.9 3.6 + - - +
56D SER 3.4 0.2 - - - -
57D THR* 1.3 76.0 - - - +
59D HIS* 1.3 66.2 + - - +
61D ARG* 3.1 6.6 + - - +
62D ILE* 2.9 37.6 + - + +
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Residues in contact with HIS 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.9 28.7 - - + +
55D GLU 3.4 17.7 + - - +
56D SER* 3.9 6.7 + - - +
57D THR 3.5 0.2 - - - -
58D ILE* 1.3 79.6 - - - +
60D GLU* 1.3 60.4 + - - +
62D ILE* 3.6 8.0 + - + +
63D ARG* 3.0 36.2 + - + +
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Residues in contact with GLU 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D SER 3.4 12.6 + - - +
57D THR* 3.7 13.7 - - + +
58D ILE 3.2 0.4 - - - -
59D HIS* 1.3 80.9 + - - +
61D ARG* 1.3 73.0 + - + +
63D ARG* 2.5 49.6 + - - +
64D LYS* 3.0 39.7 + - - +
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Residues in contact with ARG 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP* 3.0 23.8 + - - -
28D ILE* 3.2 44.4 - - - +
29D ASP* 2.9 31.5 + - - +
32D ILE* 3.6 25.6 - - + -
53D LEU* 4.9 5.4 - - - +
57D THR* 3.1 39.6 + - + +
58D ILE* 3.1 6.7 + - - +
60D GLU* 1.3 83.2 - - + +
62D ILE* 1.3 56.8 + - - +
64D LYS* 3.1 9.5 + - + +
65D LEU* 2.9 34.0 + - + +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 5.8 3.8 - - - -
32D ILE* 3.8 20.0 - - + -
36D LEU* 3.9 19.5 - - + -
44D LEU* 4.3 13.2 - - + -
47D ILE* 4.5 6.5 - - + -
58D ILE* 2.9 36.9 + - + +
59D HIS* 3.7 6.7 - - + +
61D ARG* 1.3 74.1 - - - +
63D ARG* 1.3 58.1 + - - +
65D LEU* 3.3 8.1 + - - +
66D ARG* 2.9 41.4 + - - +
71D ILE* 4.3 4.6 - - + +
74D PHE* 4.3 22.2 - - + -
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Residues in contact with ARG 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D HIS* 3.0 26.2 + - + +
60D GLU* 2.5 54.2 + - - +
62D ILE* 1.3 77.3 - - - +
64D LYS* 1.3 74.3 + - - +
66D ARG* 3.8 6.6 - - - +
67D GLU* 3.2 41.5 + - - +
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D GLU* 3.0 32.3 + - - +
61D ARG* 3.1 11.2 + - - +
63D ARG* 1.3 98.5 - - - +
65D LEU* 1.3 54.5 + - + +
66D ARG 3.3 0.4 - - - -
67D GLU* 3.9 10.5 - - - +
68D SER* 2.7 38.9 + - - -
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.6 3.8 - - + -
29D ASP* 3.8 42.0 - - + +
32D ILE* 4.8 9.9 - - + -
33D ILE* 4.0 23.6 - - + -
61D ARG* 2.9 23.5 + - + +
62D ILE* 3.8 5.8 - - - +
64D LYS* 1.3 73.7 - - + +
66D ARG* 1.3 62.7 + - - +
68D SER* 3.3 4.6 + - - +
69D GLY 3.3 2.3 + - - -
70D VAL* 2.9 55.4 + - + -
71D ILE* 3.0 25.5 + - + -
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASP* 3.8 13.1 + - - -
41C LYS* 3.7 33.0 + - - +
62D ILE* 2.9 24.0 + - - +
63D ARG* 3.8 8.1 - - - +
65D LEU* 1.3 77.2 - - - +
67D GLU* 1.3 61.8 + - - +
69D GLY* 3.3 10.2 + - - -
71D ILE* 3.7 24.1 - - + +
73D LYS* 5.8 2.3 - - - +
74D PHE* 3.3 35.4 - - + +
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ARG* 3.2 32.7 + - + +
64D LYS* 3.9 10.4 - - - +
65D LEU 3.4 0.2 - - - -
66D ARG* 1.3 80.7 - - - +
68D SER* 1.3 60.1 + - - +
69D GLY 3.2 1.5 + - - -
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D LYS* 2.7 23.4 + - - -
65D LEU* 3.3 13.3 + - - +
67D GLU* 1.3 77.1 - - - +
69D GLY* 1.3 59.3 + - - +
70D VAL* 3.4 15.3 + - - +
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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