Contacts of the helix formed by residues 61 - 69 (chain F) in PDB entry 3ZPL
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 MET 61 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ARG* 1.3 72.1 - - - +
62F THR* 1.3 58.2 - - - +
64F LEU* 3.0 4.7 + - - -
65F ALA* 2.9 25.5 + - - -
72F ARG* 5.8 4.7 - - + -
75F LEU* 2.9 39.8 - - + +
76F SER* 4.7 0.9 - - - -
79F VAL* 3.9 25.8 - - + -
90F ARG* 4.8 1.8 - - - +
100F GLN* 3.1 22.6 + - + +
101F PHE 4.4 2.9 - - - +
102F ALA* 3.9 23.1 - - - -
5H A 3.6 26.8 + - - +
6H T 3.2 36.3 - - - +
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Residues in contact with THR 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ARG* 3.3 1.1 - - - -
61F MET* 1.3 75.7 - - - +
63F GLU* 1.3 59.3 + - - +
65F ALA* 3.2 7.2 + - - +
66F LYS* 2.8 27.9 + - + +
72F ARG* 3.0 44.3 + - - +
161F TRP* 4.0 20.6 - - + +
162F LEU* 5.1 2.2 - - + -
4H G 3.9 5.9 - - - +
5H A 2.4 27.1 + - - -
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F LEU* 4.2 18.6 - - + +
60F ARG* 3.0 25.9 + - + +
62F THR* 1.3 79.4 - - - +
64F LEU* 1.3 62.9 + - - +
66F LYS* 3.1 8.7 + - - +
67F TYR* 3.1 50.5 + - + -
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 4.1 23.3 - - + +
50F LYS* 4.2 18.6 - - + -
51F LEU* 3.9 27.6 - - + -
59F LEU* 4.1 23.5 - - + +
60F ARG 2.9 10.9 + - - +
61F MET* 3.3 10.3 - - - +
63F GLU* 1.3 77.6 - - - +
65F ALA* 1.3 63.6 + - - +
67F TYR* 3.3 2.5 + - + +
68F ALA* 3.0 24.3 + - + +
75F LEU* 3.8 26.2 - - + -
79F VAL* 4.8 3.1 - - + -
102F ALA* 3.9 19.7 - - + -
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Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F MET 2.9 11.8 + - - +
62F THR* 3.5 11.9 - - - +
64F LEU* 1.3 78.2 - - - +
66F LYS* 1.3 51.5 + - - +
68F ALA 3.3 0.5 + - - -
69F LYS* 2.7 31.7 + - - -
70F ILE* 3.2 37.2 + - + +
72F ARG* 4.3 13.5 - - + +
75F LEU* 3.4 14.2 - - + +
161F TRP* 3.8 10.0 - - + -
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Residues in contact with LYS 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLU* 6.1 0.2 - - - -
62F THR* 2.8 20.4 + - + +
63F GLU* 3.1 9.6 + - - +
65F ALA* 1.3 72.2 - - - +
67F TYR* 1.3 65.2 + - + +
69F LYS* 3.5 9.9 + - - +
151F GLN* 5.0 2.9 - - - +
161F TRP* 3.7 43.1 - - + +
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Residues in contact with TYR 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ARG* 6.0 5.4 - - - -
21E GLU* 3.9 29.3 - - - +
50F LYS* 5.0 14.8 - - + -
59F LEU* 3.7 30.8 - - + +
63F GLU* 3.1 42.1 + - + -
64F LEU* 3.7 4.9 - - + +
66F LYS* 1.3 79.5 - - + +
68F ALA* 1.3 60.2 + - - +
69F LYS* 3.4 1.7 + - - +
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Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 5.9 2.3 - - - +
21E GLU* 5.8 0.7 - - - -
24E THR* 4.0 9.7 + - - +
43F VAL* 5.4 4.4 - - + +
46F GLY 6.3 0.7 - - - -
47F LEU* 3.7 26.9 - - + -
64F LEU* 3.0 17.1 + - + +
65F ALA 3.8 2.9 - - - +
67F TYR* 1.3 74.4 - - - +
69F LYS* 1.3 69.8 + - - +
70F ILE* 3.5 23.3 - - + +
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Residues in contact with LYS 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLU* 4.7 9.2 - - + +
24E THR* 3.9 20.4 - - + +
25E LEU* 3.8 32.2 - - + +
28E ASP* 5.3 2.6 - - - +
65F ALA 2.7 15.1 + - - -
66F LYS 3.5 7.6 + - - +
67F TYR 3.2 6.8 - - - +
68F ALA* 1.3 77.6 - - - +
70F ILE* 1.3 57.7 + - - +
151F GLN* 5.8 0.9 - - - +
160F PRO* 3.7 17.0 - - - +
161F TRP* 4.0 10.1 - - + -
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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