Contacts of the helix formed by residues 55 - 69 (chain A) in PDB entry 1ZU1
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 1.7 - - - +
51A ALA 3.0 13.0 + - - -
52A HIS* 3.1 19.5 + - - -
54A GLN* 1.3 79.1 - - - +
56A ARG* 1.3 65.2 + - - +
57A LYS* 3.2 22.8 + - - +
58A HIS* 3.4 8.0 + - - +
59A ALA* 3.2 21.7 + - - +
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Residues in contact with ARG 56 (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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11A LEU* 3.6 33.3 - - - +
13A LEU* 3.6 20.0 - - - +
54A GLN* 3.1 24.9 + - - +
55A SER* 1.3 73.4 + - - +
57A LYS* 1.3 66.0 + - + +
59A ALA* 3.5 2.2 + - - +
60A ASN* 2.8 37.9 + - - +
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Residues in contact with LYS 57 (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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39A CYS* 5.5 0.4 - - - -
55A SER* 3.2 11.6 + - - +
56A ARG* 1.3 78.1 - - + +
58A HIS* 1.3 58.8 + - - +
60A ASN* 3.4 9.5 + - + +
61A LYS* 3.0 29.4 + - - +
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Residues in contact with HIS 58 (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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13A LEU* 6.5 0.2 - - + -
14A PRO* 6.1 0.2 - - + -
23A LEU* 4.9 4.8 - - + +
31A PHE* 3.6 27.0 - + - -
36A CYS* 3.7 0.2 - - - -
39A CYS* 3.6 10.0 - - - -
52A HIS* 3.1 27.9 + - + +
53A TYR* 3.6 45.3 + + - -
55A SER* 3.4 8.2 + - - +
57A LYS* 1.3 76.9 - - - +
59A ALA* 1.3 61.6 + - + +
61A LYS* 3.2 3.1 + - - +
62A VAL* 2.9 49.1 + - + +
129A ZN 2.1 36.5 - - - -
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Residues in contact with ALA 59 (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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13A LEU* 3.6 43.1 - - + -
55A SER 3.2 3.4 + - - +
56A ARG* 3.7 9.0 - - - +
57A LYS 3.4 0.2 - - - -
58A HIS* 1.3 84.6 - - + +
60A ASN* 1.3 57.5 + - - +
62A VAL* 3.4 5.7 + - - +
63A ARG* 3.0 31.6 + - - +
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Residues in contact with ASN 60 (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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56A ARG* 2.8 35.2 + - - +
57A LYS* 3.7 7.5 - - + +
59A ALA* 1.3 75.4 - - - +
61A LYS* 1.3 62.5 + - - +
63A ARG* 2.9 42.3 + - - +
64A ARG* 3.1 30.8 + - + +
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Residues in contact with LYS 61 (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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38A VAL* 2.8 32.4 + - + +
39A CYS* 3.8 23.8 - - - +
57A LYS 3.0 14.1 + - - +
58A HIS 3.5 7.4 - - - +
60A ASN* 1.3 76.1 - - - +
62A VAL* 1.3 55.2 + - - +
64A ARG* 3.4 8.6 + - + +
65A TYR* 2.9 38.4 + - + +
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Residues in contact with VAL 62 (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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31A PHE* 3.8 17.5 - - + -
38A VAL* 3.9 18.6 - - + -
58A HIS* 2.9 53.1 + - + +
59A ALA* 3.7 6.5 - - - +
61A LYS* 1.3 71.5 - - - +
63A ARG* 1.3 56.6 + - - +
65A TYR* 3.7 1.2 - - - +
66A MET* 2.8 49.3 + - + +
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Residues in contact with ARG 63 (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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59A ALA* 3.0 15.6 + - - +
60A ASN* 2.9 48.5 + - - +
62A VAL* 1.3 75.4 - - - +
64A ARG* 1.3 83.7 + - - +
66A MET* 3.6 6.3 + - - +
67A ALA* 3.2 22.9 + - - +
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Residues in contact with ARG 64 (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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60A ASN* 3.1 20.1 + - + +
61A LYS* 3.7 11.7 - - + +
63A ARG* 1.3 91.5 - - + +
65A TYR* 1.3 64.6 + - - +
67A ALA* 3.2 9.0 + - - +
68A ILE* 3.0 36.5 + - + +
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Residues in contact with TYR 65 (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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29A HIS* 5.8 0.7 - - - -
30A ILE* 3.8 24.3 - - + +
38A VAL* 3.8 40.6 - - + -
61A LYS* 2.9 25.3 + - + +
62A VAL* 3.3 4.0 + - + +
64A ARG* 1.3 75.5 - - - +
66A MET* 1.3 81.0 + - + +
68A ILE* 3.2 15.1 + - + +
69A ASN* 2.9 55.3 + - + +
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Residues in contact with MET 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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27A ASN* 5.3 5.2 - - - +
29A HIS* 5.8 3.4 - - + +
30A ILE* 4.2 18.6 - - + -
31A PHE* 6.2 0.2 - - + -
62A VAL* 2.8 39.3 + - + +
63A ARG* 3.8 7.6 - - - +
65A TYR* 1.3 92.1 - - + +
67A ALA* 1.3 60.8 + - - +
69A ASN* 3.6 23.1 + - - +
70A GLN* 3.7 13.9 - - - +
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Residues in contact with ALA 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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63A ARG 3.2 13.2 + - - +
64A ARG* 3.2 12.4 + - - +
66A MET* 1.3 76.3 - - - +
68A ILE* 1.3 62.5 + - + +
70A GLN* 2.9 33.1 + - - +
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Residues in contact with ILE 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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64A ARG* 3.0 26.7 + - + +
65A TYR* 3.2 14.3 + - + +
67A ALA* 1.3 72.8 - - + +
69A ASN* 1.3 52.0 + - - +
70A GLN* 2.8 18.4 + - - +
71A GLY 3.8 14.4 + - - +
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Residues in contact with ASN 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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29A HIS* 6.0 1.4 + - - -
65A TYR* 2.9 45.7 + - + +
66A MET* 3.9 18.8 - - - +
67A ALA 3.4 0.8 - - - -
68A ILE* 1.3 72.4 - - - +
70A GLN* 1.3 62.1 + - - +
71A GLY 3.9 1.6 - - - -
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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