Contacts of the helix formed by residues 67 - 82 (chain M) 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 67 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35I THR* 5.1 3.1 - - - +
61M ALA* 5.9 2.1 - - - +
63M LYS* 4.2 22.7 + - - +
65M THR* 3.7 18.6 + - - -
66M VAL* 1.3 78.8 - - - +
68M ALA* 1.3 64.8 + - - +
69M ASP* 3.2 18.1 - - + +
70M ASP* 3.3 22.9 + - + +
71M VAL* 3.4 12.6 + - - +
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Residues in contact with ALA 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I THR* 5.1 8.9 - - + +
38I LEU* 6.2 3.1 - - + -
67M ASP* 1.3 72.7 - - - +
69M ASP* 1.3 59.3 + - - +
71M VAL* 3.1 12.3 + - - +
72M ARG* 2.9 46.7 + - + +
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Residues in contact with ASP 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M ASP* 3.2 12.9 - - + +
68M ALA* 1.3 76.0 - - - +
70M ASP* 1.3 58.8 + - - +
72M ARG* 3.2 12.0 + - - +
73M LEU* 2.9 32.9 + - - +
104R ARG* 4.7 8.8 + - - -
105R HIS* 4.5 16.8 - - - +
107R LYS* 3.5 29.1 + - - -
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Residues in contact with ASP 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ASP 3.7 2.1 - - - +
54M ALA* 2.8 41.4 + - - +
57M TYR* 3.2 27.3 - - + +
58M SER* 3.6 6.6 + - - -
66M VAL* 3.3 16.4 - - + +
67M ASP* 3.3 24.7 + - + +
68M ALA 3.2 0.2 - - - -
69M ASP* 1.3 76.3 + - - +
71M VAL* 1.3 65.1 + - - +
73M LEU* 3.3 8.9 - - - +
74M ALA* 3.0 23.6 + - - +
105R HIS* 6.3 0.7 - - - -
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Residues in contact with VAL 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I THR* 5.0 13.7 - - - +
38I LEU* 5.5 2.2 - - + -
39I LEU* 3.7 32.3 - - + +
42I GLU* 3.5 32.5 - - - +
50M ILE* 6.0 1.3 - - + -
54M ALA* 6.2 0.9 - - + -
66M VAL* 4.5 11.0 - - + -
67M ASP 3.5 13.9 - - - +
68M ALA* 3.1 12.7 + - - +
70M ASP* 1.3 75.4 - - - +
72M ARG* 1.3 66.0 + - - +
74M ALA* 3.4 5.5 + - - +
75M ILE* 2.9 33.3 + - + +
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Residues in contact with ARG 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G LYS* 3.1 38.4 - - - +
38I LEU* 4.5 22.0 - - - +
42I GLU* 3.9 18.9 + - - -
68M ALA* 2.9 39.7 + - + +
69M ASP* 3.2 16.8 + - - +
71M VAL* 1.3 86.0 - - - +
73M LEU* 1.3 59.0 + - - +
75M ILE* 3.2 17.0 - - - +
76M GLN* 2.9 34.3 + - + +
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Residues in contact with LEU 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M TYR* 3.6 54.3 - - + +
69M ASP* 2.9 21.7 + - - +
70M ASP* 3.3 29.4 - - - +
72M ARG* 1.3 75.2 - - - +
74M ALA* 1.3 61.0 + - - +
76M GLN* 3.7 8.5 - - + +
77M CYS* 2.9 36.1 + - - -
101R GLN* 4.5 26.7 - - + +
102R LEU* 4.5 9.2 - - + -
104R ARG* 6.0 3.6 - - - +
105R HIS* 4.7 14.6 - - + -
122R ARG* 5.1 0.9 - - - +
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Residues in contact with ALA 74 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 4.8 15.5 - - + +
53M ASP* 4.1 28.7 - - + +
54M ALA* 5.4 0.4 - - + +
57M TYR* 5.2 3.8 - - + -
70M ASP* 3.0 22.8 + - - +
71M VAL* 3.7 6.7 - - - +
73M LEU* 1.3 80.8 - - + +
75M ILE* 1.3 58.5 + - + +
77M CYS* 3.3 4.9 + - - +
78M ARG* 3.0 36.4 + - - +
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Residues in contact with ILE 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G LYS* 6.4 1.6 - - + -
289G GLU* 3.1 28.0 - - - +
39I LEU* 5.3 2.7 - - + -
42I GLU* 3.3 48.7 - - + +
46I ARG* 3.3 13.7 + - - +
50M ILE* 5.5 9.9 - - + -
71M VAL* 2.9 21.9 + - + +
72M ARG* 3.2 29.4 - - - +
74M ALA* 1.3 76.0 - - + +
76M GLN* 1.3 60.9 + - - +
78M ARG* 4.8 0.9 - - - -
79M ALA* 2.8 32.7 + - - +
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Residues in contact with GLN 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G GLU* 2.9 30.8 - - - +
292G LYS* 4.0 20.0 + - - +
72M ARG* 2.9 28.6 + - + +
73M LEU* 3.7 8.3 - - - +
74M ALA 3.3 0.2 - - - -
75M ILE* 1.3 79.6 - - - +
77M CYS* 1.3 56.8 + - - +
79M ALA* 3.8 2.6 - - - +
80M ASP* 2.9 38.1 + - - +
101R GLN* 4.6 24.5 - - - +
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Residues in contact with CYS 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M TYR* 4.2 4.3 - - + -
73M LEU* 2.9 28.4 + - - +
74M ALA* 3.7 5.4 - - - +
76M GLN* 1.3 76.7 - - - +
78M ARG* 1.3 61.4 + - + +
80M ASP* 3.1 11.6 + - - +
81M GLN* 2.9 37.4 + - - +
101R GLN* 4.2 15.7 - - - -
122R ARG* 2.8 41.7 - - - +
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Residues in contact with ARG 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ARG* 3.3 29.5 + - - +
46M TYR* 3.0 37.6 + - - +
49M THR* 2.4 37.2 + - - +
50M ILE* 3.2 24.3 - - - +
53M ASP* 3.3 19.3 - - - +
74M ALA* 3.0 18.2 + - - +
75M ILE* 4.8 0.2 - - - -
77M CYS* 1.3 80.4 - - + +
79M ALA* 1.3 58.2 + - - +
81M GLN* 3.4 25.4 + - - +
82M SER* 2.9 27.2 + - - -
83M PHE 4.3 0.7 + - - -
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Residues in contact with ALA 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G GLU* 3.8 22.9 - - + +
292G LYS* 6.0 4.7 - - + +
46I ARG* 3.0 11.4 - - - +
75M ILE 2.8 21.2 + - - +
76M GLN* 3.8 4.0 - - - +
78M ARG* 1.3 73.9 - - - +
80M ASP* 1.3 65.5 + - - +
81M GLN 3.2 0.4 - - - -
83M PHE* 3.2 42.9 + - + +
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Residues in contact with ASP 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G LYS* 4.5 14.6 + - - +
76M GLN* 2.9 25.5 + - - +
77M CYS* 3.1 12.0 + - - +
79M ALA* 1.3 80.1 - - - +
81M GLN* 1.3 62.2 + - + +
83M PHE 4.9 0.7 + - - -
84M THR* 6.2 0.3 - - - -
97R THR* 6.0 0.9 - - - +
101R GLN* 4.7 12.6 + - - +
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Residues in contact with GLN 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I LEU 4.6 4.7 - - - -
77M CYS* 2.9 25.4 + - - +
78M ARG* 3.1 34.8 + - + +
80M ASP* 1.3 81.6 - - + +
82M SER* 1.3 64.7 + - - +
83M PHE 3.6 1.1 + - - -
84M THR* 5.3 2.9 + - - -
122R ARG* 5.6 11.7 - - - +
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Residues in contact with SER 82 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ARG* 5.8 4.3 - - - -
50I ILE* 5.8 3.6 - - - +
75I LEU* 5.3 8.3 - - - +
77I LEU* 3.2 41.1 + - - +
78M ARG 2.9 13.6 + - - -
81M GLN* 1.3 76.6 - - - +
83M PHE* 1.3 61.4 + - - +
84M THR 3.8 2.2 - - - -
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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