Contacts of the helix formed by residues 59 - 70 (chain A) in PDB entry 6MZL
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 ASP 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A LEU* 1.3 81.2 - - - +
60A ASP* 1.3 82.1 + - - +
61A GLU* 3.2 35.9 + - + +
62A CYS* 3.1 28.0 + - - +
63A LYS* 3.9 2.8 + - - +
131P LYS* 4.9 3.1 + - - -
305T PHE* 6.1 0.7 - - + -
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Residues in contact with ASP 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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58A LEU 3.9 0.4 + - - -
59A ASP* 1.3 87.8 - - - +
61A GLU* 1.3 60.7 + - - +
62A CYS 3.1 0.7 - - - -
63A LYS* 3.2 9.0 + - + +
64A LYS* 3.0 32.2 + - - +
131P LYS* 3.5 35.1 + - - +
148P GLN* 4.4 10.3 + - - +
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Residues in contact with GLU 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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59A ASP* 3.3 25.3 - - + +
60A ASP* 1.3 83.2 + - - +
62A CYS* 1.3 60.8 + - - +
64A LYS* 4.8 0.4 - - - -
65A HIS* 2.9 56.6 + - + +
126P ARG* 4.7 7.8 + - - -
131P LYS* 5.2 9.5 + - - +
288T PHE* 5.7 2.5 - - + -
289T PRO* 3.9 19.4 - - + +
305T PHE* 3.3 44.6 - - + +
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Residues in contact with CYS 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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43A PHE* 3.6 38.1 - - + -
52A LEU* 5.4 2.2 - - + -
58A LEU* 3.9 21.1 - - + -
59A ASP* 3.1 20.0 + - - +
60A ASP 3.1 0.2 - - - -
61A GLU* 1.3 78.7 - - - +
63A LYS* 1.3 49.8 + - - +
66A LEU* 2.6 42.8 + - - +
69A LEU* 5.2 1.2 - - - +
288T PHE* 6.2 1.6 - - - -
303T LEU* 6.5 0.4 - - - -
305T PHE* 4.4 25.6 - - - -
311T VAL* 5.7 0.9 - - - -
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Residues in contact with LYS 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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50A GLY 4.2 15.9 + - - +
51A GLN* 4.0 26.6 + - - +
52A LEU* 4.0 35.6 - - + +
59A ASP 3.9 1.5 + - - +
60A ASP* 3.2 13.9 + - + +
62A CYS* 1.3 76.2 - - - +
64A LYS* 1.3 67.5 + - - +
66A LEU* 3.2 12.9 - - + +
67A ALA* 3.1 21.8 + - - +
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Residues in contact with LYS 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 ASP 3.0 16.6 + - - +
63A LYS* 1.3 81.0 - - + +
65A HIS* 1.3 82.7 + - + +
67A ALA* 3.1 11.6 + - - +
68A GLY* 3.0 19.6 + - - -
131P LYS* 3.4 30.9 - - - +
148P GLN* 3.4 42.9 - - + +
149P ASN* 5.8 1.6 - - - +
151P VAL* 6.0 0.6 - - - +
152P ILE* 3.4 36.7 - - + +
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Residues in contact with HIS 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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61A GLU* 2.9 36.5 + - + +
62A CYS* 3.8 0.4 - - - -
64A LYS* 1.3 106.0 - - + +
66A LEU* 1.3 50.7 + - - +
68A GLY* 3.3 7.1 + - - +
69A LEU* 2.6 37.4 + - - +
131P LYS* 5.6 2.0 - - - -
152P ILE* 5.2 6.6 - - + +
286T GLU 5.2 2.4 + - - -
287T LEU 3.2 26.1 + - - -
288T PHE* 3.5 23.7 - + + -
289T PRO* 3.5 27.7 - - + +
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Residues in contact with LEU 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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39A ALA* 3.3 37.9 - - + +
40A GLY* 3.7 21.8 - - - +
43A PHE* 4.1 14.8 - - + -
46A ILE* 5.2 1.3 - - + -
50A GLY 6.0 1.6 - - - +
52A LEU* 3.9 26.7 - - + -
62A CYS 2.6 23.6 + - - +
63A LYS* 3.2 11.9 - - + +
64A LYS 3.1 0.2 - - - -
65A HIS* 1.3 72.7 - - - +
67A ALA* 1.3 60.0 + - - +
68A GLY 3.1 1.3 - - - -
69A LEU* 2.8 42.6 + - + +
70A GLY 3.1 10.0 + - - -
74A LEU* 6.2 0.2 - - + -
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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 LYS* 3.1 12.6 + - + +
64A LYS* 3.3 11.2 - - - +
66A LEU* 1.3 74.5 - - - +
68A GLY* 1.3 59.5 + - - +
70A GLY* 4.0 6.2 + - - -
71A ALA 5.4 0.2 + - - -
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Residues in contact with GLY 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 LYS 3.0 12.6 + - - -
65A HIS* 3.3 8.7 + - - -
66A LEU 3.1 0.4 - - - -
67A ALA* 1.3 76.0 - - - +
69A LEU* 1.3 59.1 + - - +
70A GLY 3.1 6.1 + - - -
71A ALA* 3.5 15.8 + - - +
72A LEU* 4.5 6.9 + - - +
287T LEU* 6.1 5.2 - - - +
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Residues in contact with LEU 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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39A ALA* 4.8 1.3 - - + -
43A PHE* 5.7 4.5 - - + -
62A CYS* 5.2 1.3 - - - +
65A HIS 2.6 23.2 + - - +
66A LEU* 2.8 37.7 + - + +
68A GLY* 1.3 67.0 - - - -
70A GLY* 1.3 63.4 + - - +
71A ALA 3.1 4.6 + - - -
72A LEU* 3.5 35.0 + - + -
74A LEU* 3.3 46.9 - - + +
288T PHE* 4.3 25.1 - - + -
303T LEU* 4.3 22.7 - - + -
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Residues in contact with GLY 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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37A SER* 6.2 2.7 - - - -
39A ALA* 4.3 15.0 - - - +
66A LEU 3.1 10.5 + - - -
67A ALA 4.0 5.1 + - - -
68A GLY 3.1 3.0 - - - -
69A LEU* 1.3 76.3 - - - +
71A ALA* 1.3 56.6 + - - +
75A GLY* 4.1 17.4 + - - -
78A ILE* 4.3 9.6 - - - +
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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