Contacts of the helix formed by residues 67 - 75 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489G PHE* 6.4 2.5 - - + -
58I MET* 5.0 4.3 - - + -
63I ARG* 6.0 4.7 - - - +
65I LYS* 4.5 8.1 - - + +
66I LEU* 1.3 73.4 - - - +
68I THR* 1.3 64.7 + - - +
69I SER* 2.3 33.8 + - - +
70I ASP* 2.3 47.1 + - - +
71I ILE* 3.6 7.3 - - - +
32M GLU* 5.8 2.2 - - - -
35M VAL* 3.5 15.0 - - - +
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Residues in contact with THR 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I THR* 1.3 74.5 - - - +
69I SER* 1.3 62.3 + - - +
71I ILE* 3.2 7.8 + - - +
72I ASP* 2.9 38.1 + - - +
32M GLU* 6.0 0.2 - - - +
34M ARG* 4.7 4.5 - - + -
35M VAL* 3.4 34.1 - - + +
38M GLN* 3.4 28.0 - - + +
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Residues in contact with SER 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489G PHE* 4.9 14.5 - - - -
67I THR* 2.3 30.2 + - - +
68I THR* 1.3 78.6 + - - +
70I ASP* 1.3 62.3 + - - +
72I ASP* 3.2 14.8 + - - +
73I TYR* 2.9 49.6 + - - -
141O ARG* 6.1 3.1 - - - -
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Residues in contact with ASP 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489G PHE* 5.7 3.3 - - - -
54I ALA* 4.8 6.3 - - + -
57I PHE* 4.3 10.9 - - + -
58I MET* 3.3 38.6 - - + +
66I LEU* 3.2 10.9 - - + -
67I THR* 2.3 47.8 + - - +
68I THR 3.2 0.2 - - - -
69I SER* 1.3 79.8 + - - +
71I ILE* 1.3 61.2 + - + +
73I TYR* 3.1 12.8 + - - +
74I ALA* 2.9 23.7 + - - +
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Residues in contact with ILE 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ILE* 4.5 18.2 - - + -
54I ALA* 4.0 15.9 - - + -
66I LEU* 5.3 8.3 - - + -
67I THR 3.6 5.6 - - - +
68I THR* 3.2 6.6 + - - +
70I ASP* 1.3 75.3 - - + +
72I ASP* 1.3 62.2 + - - +
74I ALA* 2.9 8.5 + - + +
75I LEU* 2.9 34.8 + - + +
35M VAL* 3.7 30.1 - - + -
39M MET* 3.6 39.9 - - + -
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Residues in contact with ASP 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I THR* 2.9 27.5 + - - +
69I SER* 3.3 17.2 - - - +
71I ILE* 1.3 76.6 - - - +
73I TYR* 1.3 67.1 + - + +
75I LEU* 3.2 31.0 + - - +
76I LYS* 4.8 2.6 - - - +
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Residues in contact with TYR 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489G PHE* 4.3 19.3 + + + +
543G SER 4.7 10.4 + - - -
545G PRO* 3.7 33.8 - - + +
563G GLU* 3.1 39.5 - - - +
57I PHE* 3.2 19.5 - + + -
69I SER* 2.9 36.4 + - - -
70I ASP* 3.1 7.2 + - - +
72I ASP* 1.3 80.5 - - + +
74I ALA* 1.3 62.0 + - - +
75I LEU 3.3 0.3 + - - -
76I LYS* 3.6 25.6 + - - +
141O ARG* 4.0 23.8 + - - -
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ILE* 4.4 18.5 - - + +
53I ASP* 5.0 4.6 - - + +
54I ALA* 4.2 14.8 - - + +
57I PHE* 3.6 22.4 - - + -
70I ASP 2.9 13.2 + - - +
71I ILE* 2.9 15.8 + - - +
73I TYR* 1.3 78.9 - - - +
75I LEU* 1.3 57.0 + - - +
76I LYS 3.2 6.1 + - - -
77I LEU* 3.7 23.2 - - - +
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I ILE* 5.1 17.3 - - + -
71I ILE* 2.9 21.7 + - + +
72I ASP* 3.6 22.2 - - - +
73I TYR 3.1 1.8 - - - -
74I ALA* 1.3 76.3 - - - +
76I LYS* 1.3 57.5 + - - +
77I LEU* 3.2 12.3 + - + +
42M PHE* 6.2 4.9 - - + -
46M TYR* 4.1 27.8 - - + +
82M SER* 5.3 9.0 - - - +
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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