Contacts of the helix formed by residues 59 - 71 (chain R) 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 THR 59 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872E PHE 5.0 4.7 + - - +
874E LEU* 4.8 17.9 - - + -
58R LEU* 1.3 93.0 - - - +
60R LYS* 1.3 62.7 + - - +
61R LYS* 3.4 15.0 - - + +
62R LYS* 2.8 31.5 + - - +
63R LEU* 4.0 9.0 + - - +
85R LEU* 4.3 3.2 - - - +
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Residues in contact with LYS 60 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56R GLN* 4.4 24.8 - - - +
58R LEU 5.0 0.4 - - - +
59R THR* 1.3 73.6 - - - +
61R LYS* 1.3 57.3 + - - +
62R LYS 3.5 0.2 - - - -
63R LEU* 3.3 10.2 - - + +
64R GLN* 3.0 48.2 + - + +
78R GLU* 5.3 0.4 + - - -
82R GLU* 3.1 42.5 + - - +
85R LEU* 4.0 19.1 - - + -
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Residues in contact with LYS 61 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R THR* 3.1 14.5 - - + +
60R LYS* 1.3 78.2 - - - +
62R LYS* 1.3 59.0 + - - +
64R GLN* 3.3 6.2 + - + +
65R ASP* 2.8 67.9 + - - +
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Residues in contact with LYS 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870E GLU 3.8 9.9 + - - +
871E THR 3.6 7.9 + - - -
872E PHE* 3.4 62.4 + - + +
907E GLN* 5.8 2.9 - - + -
910E LEU* 6.5 1.3 - - + -
58R LEU* 4.4 7.0 - - + -
59R THR* 2.8 19.1 + - - +
61R LYS* 1.3 72.0 - - - +
63R LEU* 1.3 66.1 + - - +
65R ASP* 3.3 19.0 - - + +
66R LEU* 3.0 24.7 + - + +
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Residues in contact with LEU 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910E LEU* 4.9 22.7 - - + -
914E VAL* 5.9 2.7 - - + -
58R LEU* 5.2 3.4 - - + +
59R THR 4.0 10.0 + - - +
60R LYS* 3.3 17.2 - - + +
62R LYS* 1.3 76.5 - - - +
64R GLN* 1.3 60.7 + - + +
66R LEU* 3.1 7.1 + - + +
67R VAL* 2.9 44.6 + - + +
81R GLU* 3.7 35.4 - - + +
84R LEU* 5.7 8.5 - - + -
85R LEU* 3.7 41.5 - - + -
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Residues in contact with GLN 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60R LYS* 3.0 34.8 + - - +
61R LYS* 4.0 4.1 - - - +
63R LEU* 1.3 76.8 - - + +
65R ASP* 1.3 60.6 + - - +
67R VAL* 4.1 7.9 - - + -
68R ARG* 2.9 39.4 + - + +
78R GLU* 5.4 8.5 + - - +
81R GLU* 3.7 26.3 + - - +
82R GLU* 5.7 1.0 + - - -
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Residues in contact with ASP 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R LYS* 2.8 59.2 + - - +
62R LYS* 3.3 25.5 - - + +
64R GLN* 1.3 76.1 - - - +
66R LEU* 1.3 51.2 + - - +
68R ARG* 4.8 0.2 - - - +
69R GLU* 2.7 44.3 + - - +
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Residues in contact with LEU 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907E GLN* 3.6 30.3 - - + +
910E LEU* 4.7 4.9 - - + +
911E GLN* 4.3 20.2 - - + +
914E VAL* 3.7 32.8 - - + -
62R LYS* 3.0 18.0 + - + +
63R LEU* 3.8 4.5 - - + +
65R ASP* 1.3 76.1 - - - +
67R VAL* 1.3 57.7 + - - +
69R GLU* 3.3 24.0 + - - +
70R VAL* 3.0 43.5 + - + +
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Residues in contact with VAL 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914E VAL* 4.2 24.5 - - + +
917E ILE* 5.1 11.9 - - + -
63R LEU* 2.9 38.1 + - + +
64R GLN* 3.8 7.9 - - + +
65R ASP 3.3 0.2 - - - -
66R LEU* 1.3 75.7 - - - +
68R ARG* 1.3 64.7 + - + +
70R VAL* 3.1 4.0 + - - +
71R ASP* 2.7 40.2 + - + +
74R GLU* 5.3 0.4 - - - +
76R LEU* 3.7 29.8 - - + -
81R GLU* 4.1 11.9 - - + +
84R LEU* 6.4 0.7 - - + -
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Residues in contact with ARG 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R GLN* 2.9 25.5 + - + +
65R ASP* 4.8 0.4 - - - +
67R VAL* 1.3 76.8 - - + +
69R GLU* 1.3 62.3 + - - +
71R ASP 3.3 14.4 + - - -
72R PRO* 2.5 59.6 + - + +
74R GLU* 2.8 38.1 + - - +
76R LEU* 3.4 35.3 + - - +
81R GLU* 5.2 3.0 + - - -
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Residues in contact with GLU 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R ASP* 2.7 25.0 + - - +
66R LEU* 3.3 32.2 - - + +
68R ARG* 1.3 79.0 - - - +
70R VAL* 1.3 65.2 + - + +
72R PRO* 4.3 3.1 - - - +
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Residues in contact with VAL 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911E GLN* 6.0 2.5 - - + -
914E VAL* 3.7 29.6 - - + +
918E SER* 5.0 13.7 - - - -
66R LEU* 3.0 30.4 + - + +
67R VAL 3.8 0.2 - - - +
69R GLU* 1.3 82.0 - - + +
71R ASP* 1.3 63.3 + - + +
72R PRO* 3.4 8.2 - - - +
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Residues in contact with ASP 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914E VAL* 6.0 1.8 - - + -
917E ILE* 5.4 4.4 - - + +
918E SER* 5.2 6.9 - - - -
921E ALA* 3.6 20.3 - - - +
67R VAL* 2.7 25.1 + - + +
68R ARG* 3.3 16.6 + - - -
70R VAL* 1.3 77.8 - - + +
72R PRO* 1.3 61.5 - - - +
73R ASN* 3.0 27.9 + - - +
74R GLU* 3.1 33.4 - - - +
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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