Contacts of the helix formed by residues 67 - 83 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H THR* 5.0 3.8 - - - +
63L LYS* 4.1 24.0 + - - +
65L THR* 3.6 19.8 + - - -
66L VAL* 1.3 82.4 - - - +
68L ALA* 1.3 65.4 + - - +
69L ASP* 3.3 13.0 - - + +
70L ASP* 3.3 22.4 - - + +
71L VAL* 3.6 7.4 + - - +
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Residues in contact with ALA 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H THR* 5.1 9.2 - - + +
38H LEU* 5.9 3.8 - - + -
67L ASP* 1.3 72.3 - - - +
69L ASP* 1.3 60.5 + - - +
71L VAL* 3.1 11.9 + - - +
72L ARG* 2.9 44.1 + - + +
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Residues in contact with ASP 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L ASP* 3.3 8.1 - - + +
68L ALA* 1.3 75.3 - - - +
70L ASP* 1.3 60.2 + - - +
72L ARG* 3.9 14.1 - - - +
73L LEU* 2.9 37.7 + - - +
104Q ARG* 4.4 17.0 + - - +
105Q HIS* 4.5 16.8 - - - +
107Q LYS* 3.4 27.9 + - - +
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Residues in contact with ASP 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L ASP 3.8 1.7 - - - +
54L ALA* 3.0 38.9 + - - +
57L TYR* 3.3 30.1 - - + +
58L SER* 3.9 4.5 + - - -
66L VAL* 3.4 17.9 - - + +
67L ASP* 3.3 25.2 + - + +
69L ASP* 1.3 77.6 - - - +
71L VAL* 1.3 56.4 + - - +
73L LEU* 3.3 9.2 - - - +
74L ALA* 3.0 29.7 + - - +
105Q HIS* 6.0 2.2 - - + +
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Residues in contact with VAL 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H THR* 5.0 12.6 - - - +
38H LEU* 5.3 4.5 - - + -
39H LEU* 3.8 34.8 - - + +
42H GLU* 3.5 31.2 - - - +
50L ILE* 6.2 0.7 - - + -
54L ALA* 6.2 1.3 - - + -
66L VAL* 4.7 10.8 - - + -
67L ASP 3.6 12.1 + - - +
68L ALA* 3.1 12.0 + - - +
70L ASP* 1.3 75.3 - - - +
72L ARG* 1.3 65.6 + - - +
74L ALA* 3.7 4.9 - - - +
75L ILE* 2.9 32.2 + - + +
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Residues in contact with ARG 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F LYS* 3.1 37.1 - - - +
38H LEU* 4.0 26.7 - - - +
42H GLU* 3.9 18.0 + - - -
68L ALA* 2.9 36.7 + - + +
69L ASP* 3.5 20.6 - - - +
70L ASP 3.2 0.4 - - - -
71L VAL* 1.3 85.6 - - - +
73L LEU* 1.3 59.6 + - - +
75L ILE* 3.2 15.2 - - - +
76L GLN* 3.0 32.5 + - + +
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Residues in contact with LEU 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L TYR* 3.6 47.3 - - + -
69L ASP* 2.9 35.6 + - - +
70L ASP* 3.3 23.3 - - - +
72L ARG* 1.3 74.4 - - - +
74L ALA* 1.3 61.3 + - - +
76L GLN* 3.6 8.2 - - + +
77L CYS* 2.9 37.0 + - - -
101Q GLN* 4.2 27.8 - - + +
102Q LEU* 4.5 8.7 - - + -
104Q ARG* 5.5 9.2 - - - +
105Q HIS* 4.3 15.5 - - + -
122Q ARG* 5.2 0.9 - - - +
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Residues in contact with ALA 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L ILE* 5.0 13.5 - - + +
53L ASP* 4.4 25.1 - - + +
54L ALA* 5.5 0.4 - - + +
57L TYR* 5.3 5.6 - - + -
70L ASP* 3.0 24.6 + - - +
71L VAL* 3.7 6.5 - - - +
73L LEU* 1.3 79.7 - - + +
75L ILE* 1.3 59.2 + - + +
77L CYS* 3.4 4.6 + - - +
78L ARG* 2.9 35.8 + - + +
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Residues in contact with ILE 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287F LYS* 6.4 1.6 - - + -
289F GLU* 3.0 32.9 - - - +
39H LEU* 5.4 2.9 - - + -
42H GLU* 3.3 48.7 - - + +
46H ARG* 3.5 20.2 + - - +
50L ILE* 5.6 10.1 - - + -
71L VAL* 2.9 21.7 + - + +
72L ARG* 3.2 25.6 - - - +
74L ALA* 1.3 76.4 - - + +
76L GLN* 1.3 61.6 + - + +
78L ARG* 4.7 0.7 - - - -
79L ALA* 2.8 25.6 + - - +
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Residues in contact with GLN 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F GLU* 2.9 31.6 - - - +
292F LYS* 3.8 21.9 + - - +
72L ARG* 3.0 24.0 + - + +
73L LEU* 3.6 9.4 - - - +
74L ALA 3.3 0.4 - - - -
75L ILE* 1.3 76.9 - - + +
77L CYS* 1.3 57.7 + - - +
79L ALA* 3.4 2.9 + - - +
80L ASP* 3.0 37.4 + - - +
101Q GLN* 4.6 22.6 - - - +
104Q ARG* 5.9 4.7 - - - +
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Residues in contact with CYS 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L TYR* 4.3 3.1 - - + +
73L LEU* 2.9 25.0 + - - +
74L ALA* 3.9 5.2 - - - +
76L GLN* 1.3 75.9 - - - +
78L ARG* 1.3 62.1 + - + +
80L ASP* 3.0 12.1 + - - +
81L GLN* 2.9 35.7 + - - +
101Q GLN* 3.8 17.7 - - - -
102Q LEU* 5.2 0.4 - - - -
122Q ARG* 2.7 45.3 - - - +
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Residues in contact with ARG 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ARG* 3.7 29.3 + - - +
46L TYR* 3.2 44.8 + - - +
49L THR* 2.4 32.7 + - - +
50L ILE* 3.4 20.6 - - - +
53L ASP* 3.6 22.0 - - - +
74L ALA* 2.9 21.1 + - - +
75L ILE* 4.7 0.2 - - - -
77L CYS* 1.3 76.0 - - + +
79L ALA* 1.3 61.8 + - - +
81L GLN* 3.7 27.3 + - - +
82L SER* 3.5 21.6 + - - -
83L PHE* 4.3 2.8 + - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F GLU* 3.9 21.1 - - + +
292F LYS* 6.1 4.3 - - + -
46H ARG* 3.6 6.4 - - - +
75L ILE 2.8 21.4 + - - +
76L GLN* 3.8 4.7 - - - +
78L ARG* 1.3 73.3 - - - +
80L ASP* 1.3 65.7 + - - +
81L GLN 3.3 0.7 - - - -
83L PHE* 3.3 47.1 + - + +
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Residues in contact with ASP 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292F LYS* 4.8 11.4 + - - +
76L GLN* 3.0 23.7 + - - +
77L CYS* 3.0 13.2 + - - +
79L ALA* 1.3 79.9 - - - +
81L GLN* 1.3 61.9 + - + +
83L PHE 4.9 0.4 - - - -
84L THR* 5.8 2.6 + - - -
97Q THR* 5.9 1.9 - - - +
101Q GLN* 4.6 14.2 + - - +
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Residues in contact with GLN 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H LEU 4.6 4.2 - - - -
77L CYS* 2.9 23.9 + - + +
78L ARG* 3.6 32.4 + - - +
79L ALA 3.3 0.6 - - - -
80L ASP* 1.3 81.4 - - + +
82L SER* 1.3 64.0 + - - +
83L PHE 3.6 1.9 + - - -
84L THR* 5.0 5.2 + - - -
122Q ARG* 5.4 12.7 - - - +
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H LEU* 5.6 1.7 + - - +
77H LEU* 3.3 40.1 + - - +
78L ARG* 3.5 10.2 + - - -
81L GLN* 1.3 80.3 - - - +
83L PHE* 1.3 61.4 + - - +
84L THR 3.7 2.2 - - - -
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Residues in contact with PHE 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289F GLU* 3.2 32.1 - - + -
290F HIS* 5.1 2.0 - - - -
292F LYS* 5.4 4.4 - - + +
293F GLY* 3.6 27.0 - - - -
46H ARG* 5.4 16.8 - - + +
49H GLU* 3.2 35.2 - - + -
77H LEU* 5.0 7.2 - - + -
78L ARG 4.4 1.1 - - - +
79L ALA* 3.3 43.9 + - + +
80L ASP 5.8 0.2 - - - -
81L GLN 3.6 2.0 - - - -
82L SER* 1.3 80.2 - - - +
84L THR* 1.3 65.4 + - - +
85L SER* 4.0 2.9 + - - -
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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