Contacts of the helix formed by residues 67 - 75 (chain H) 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 67 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489F PHE* 5.7 2.1 - - - -
58H MET* 6.3 0.7 - - + -
63H ARG* 6.1 2.7 - - - +
65H LYS* 5.2 7.0 - - + +
66H LEU* 1.3 77.9 - - - +
68H THR* 1.3 66.3 + - - +
69H SER* 3.2 16.1 + - - -
70H ASP* 2.8 39.9 + - - +
71H ILE* 3.8 5.9 + - - +
32L GLU* 4.8 16.8 - - - +
35L VAL* 3.6 16.4 - - - +
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Residues in contact with THR 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 4.6 17.4 + - - +
67H THR* 1.3 76.4 - - - +
69H SER* 1.3 61.0 + - - +
70H ASP 3.3 0.3 + - - -
71H ILE* 3.4 6.1 + - - +
72H ASP* 3.0 38.5 + - - +
32L GLU* 5.8 0.2 - - - +
34L ARG* 4.9 5.8 - - + -
35L VAL* 3.6 32.9 - - + +
38L GLN* 3.3 30.3 - - + +
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Residues in contact with SER 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C GLU* 6.1 0.9 - - - -
34C ARG* 5.7 4.9 - - - -
489F PHE* 4.6 15.3 - - - -
67H THR* 3.2 12.5 + - - -
68H THR* 1.3 80.4 + - - +
70H ASP* 1.3 65.2 + - - +
72H ASP* 3.4 12.0 - - - +
73H TYR* 2.9 45.4 + - - -
141N ARG* 4.4 20.0 - - - -
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Residues in contact with ASP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489F PHE* 5.1 7.8 - - - -
54H ALA* 4.8 5.4 - - + +
57H PHE* 4.8 7.7 - - + -
58H MET* 3.3 47.5 - - + +
65H LYS 3.8 0.5 - - - +
66H LEU* 3.6 7.7 - - + -
67H THR* 2.8 40.8 + - - +
68H THR 3.2 1.0 - - - -
69H SER* 1.3 81.9 + - - +
71H ILE* 1.3 62.1 + - + +
73H TYR* 3.4 8.4 + - - +
74H ALA* 2.9 24.8 + - - +
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Residues in contact with ILE 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ILE* 4.1 23.6 - - + -
51H ALA* 6.4 1.1 - - - -
54H ALA* 4.0 16.2 - - + -
66H LEU* 4.9 14.6 - - + -
67H THR 3.8 4.7 + - - +
68H THR 3.4 6.1 + - - +
70H ASP* 1.3 75.5 - - + +
72H ASP* 1.3 60.4 + - - +
74H ALA* 3.0 6.2 + - + -
75H LEU* 2.9 36.1 + - + +
35L VAL* 3.8 20.9 - - + -
39L MET* 3.6 47.1 - - + -
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Residues in contact with ASP 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 3.9 23.7 + - - -
68H THR* 3.0 30.9 + - - +
69H SER* 3.4 13.5 - - - +
70H ASP 3.2 0.2 - - - -
71H ILE* 1.3 78.0 - - - +
73H TYR* 1.3 61.8 + - + +
75H LEU* 3.3 33.7 + - - +
76H LYS* 4.8 2.3 - - - +
42L PHE* 6.0 0.9 - - - -
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Residues in contact with TYR 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C GLN* 5.5 2.8 + - - -
74C ARG* 4.3 13.6 + - - -
489F PHE* 4.1 18.1 + + + +
543F SER 3.7 22.4 + - - -
544F GLY* 4.1 0.9 - - - -
545F PRO* 3.6 30.9 - - + +
547F TYR* 5.8 0.2 - - - +
563F GLU* 3.0 34.9 - - - +
57H PHE* 4.4 2.6 - - + -
69H SER* 2.9 40.1 + - - +
70H ASP* 3.9 7.2 - - - +
72H ASP* 1.3 76.0 - - + +
74H ALA* 1.3 59.2 + - - +
75H LEU 3.2 2.9 - - - -
76H LYS* 3.3 41.7 + - - +
141N ARG* 4.3 22.7 + - - +
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Residues in contact with ALA 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ILE* 4.5 18.0 - - + +
53H ASP* 5.0 3.9 - - + +
54H ALA* 4.2 13.9 - - + +
57H PHE* 3.8 26.2 - - + -
70H ASP 2.9 15.2 + - - +
71H ILE* 3.0 15.9 + - - +
73H TYR* 1.3 74.7 - - - +
75H LEU* 1.3 56.0 + - - +
76H LYS 3.2 7.2 + - - -
77H LEU* 3.9 21.5 - - - +
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Residues in contact with LEU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ARG* 6.1 0.9 - - - +
50H ILE* 4.7 23.6 - - + -
71H ILE* 2.9 22.7 + - + +
72H ASP* 3.5 26.0 - - - +
73H TYR 3.2 1.8 - - - -
74H ALA* 1.3 75.9 - - - +
76H LYS* 1.3 56.3 + - - +
77H LEU* 3.2 11.0 + - - +
42L PHE* 6.3 6.1 - - + -
46L TYR* 3.9 30.3 - - + +
82L SER* 5.6 1.5 + - - +
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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