Contacts of the helix formed by residues 71 - 85 (chain E) 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 THR 71 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E ALA* 4.3 1.6 - - - -
70E ILE* 1.3 83.3 - - - +
72E ARG* 1.3 58.8 + - - +
73E SER* 3.6 9.8 + - - -
74E ARG* 3.2 23.8 + - - +
75E LEU* 2.9 24.6 + - - +
160E PRO* 3.4 23.1 - - + +
163E ARG* 3.8 37.0 - - + +
28F ASP* 5.0 0.9 - - - +
14H T 4.3 13.3 + - + +
15H C 5.9 0.4 - - - +
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Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E MET* 5.8 4.0 - - + +
62E THR* 3.9 23.4 + - - +
65E ALA* 4.3 9.6 - - + +
70E ILE 4.1 0.6 + - - -
71E THR* 1.3 72.6 - - - +
73E SER* 1.3 56.7 + - - +
75E LEU* 3.3 9.3 + - - +
76E SER* 2.8 33.1 + - - -
160E PRO 4.3 2.0 + - - -
161E TRP* 2.9 25.7 + - - +
162E LEU* 3.7 16.0 + - - +
163E ARG 3.0 27.7 + - - +
3G A 6.1 0.2 - - - +
4G G 3.9 20.5 + - - +
5G A 3.2 36.5 + - + +
6G T 3.8 13.6 + - + -
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Residues in contact with SER 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E THR* 3.7 10.1 - - - -
72E ARG* 1.3 77.2 - - - +
74E ARG* 1.3 67.3 + - - +
76E SER* 3.1 4.6 + - - -
77E HIS* 3.1 26.9 + - - -
6G T 3.9 11.4 + - - +
7G T 2.7 14.5 + - - +
14H T 4.3 4.5 - - - -
15H C 2.6 38.7 + - - -
16H A 3.0 8.4 + - - -
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 3.5 24.6 - - - +
44E TYR* 5.8 0.4 - - + -
69E LYS 5.6 0.2 + - - -
70E ILE* 3.7 39.6 - - + +
71E THR* 3.2 18.6 + - - +
73E SER* 1.3 78.8 - - - +
75E LEU* 1.3 57.9 + - - +
77E HIS* 3.4 4.0 + - - +
78E ALA* 2.9 28.5 + - + +
24F THR* 5.1 7.9 - - - +
13H C 2.7 62.4 + - + +
14H T 3.5 40.4 + - + +
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Residues in contact with LEU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 3.8 25.8 - - + -
61E MET* 2.9 51.1 - - + +
64E LEU* 3.8 16.4 - - + -
65E ALA* 3.5 17.9 - - + +
70E ILE* 4.0 10.3 - - + +
71E THR 2.9 14.5 + - - +
72E ARG* 3.5 10.3 - - - +
73E SER 3.1 0.2 - - - -
74E ARG* 1.3 74.2 - - - +
76E SER* 1.3 60.1 + - - +
78E ALA* 3.2 2.0 + - - +
79E VAL* 2.8 46.6 + - + +
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Residues in contact with SER 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E MET* 4.7 2.0 - - - -
72E ARG 2.8 19.7 + - - -
73E SER 3.1 7.6 + - - -
75E LEU* 1.3 73.3 - - - +
77E HIS* 1.3 64.9 + - - +
79E VAL* 3.2 0.9 + - - -
80E ALA* 2.9 23.3 + - - +
90E ARG* 3.9 8.1 + - - +
5G A 3.9 0.3 - - - +
6G T 2.6 51.7 + - - +
7G T 3.8 20.2 - - - -
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Residues in contact with HIS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E TYR* 4.7 2.9 + - - +
73E SER 3.1 18.4 + - - -
74E ARG* 3.7 7.2 - - - +
76E SER* 1.3 77.9 - - - +
78E ALA* 1.3 64.0 + - - +
80E ALA* 3.2 10.0 + - - +
81E ARG* 3.2 21.1 + - - +
7G T 3.7 18.2 - + + +
8G G 2.9 44.7 + - - -
9G A 3.9 2.4 + - - -
12H T 6.3 1.1 - - + -
13H C 4.5 16.6 - + + +
14H T 3.1 28.6 + - + -
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Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E TYR* 3.4 42.5 + - + -
47E LEU* 4.0 17.9 - - + -
70E ILE* 5.8 0.9 - - + -
74E ARG* 2.9 20.7 + - + +
75E LEU* 3.6 5.2 - - - +
77E HIS* 1.3 75.7 - - - +
79E VAL* 1.3 57.5 + - - +
81E ARG* 3.2 4.7 + - - +
82E LEU* 2.9 32.8 + - - +
13H C 4.8 1.1 + - - +
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Residues in contact with VAL 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LEU* 5.0 0.7 - - + -
61E MET* 3.9 17.0 - - + -
64E LEU* 4.8 2.9 - - + -
75E LEU* 2.8 43.0 + - + +
76E SER 3.9 2.9 - - - +
78E ALA* 1.3 69.4 - - - +
80E ALA* 1.3 60.0 + - - +
81E ARG 3.1 1.3 - - - -
82E LEU* 3.7 14.1 - - + +
83E GLU* 2.8 28.9 + - + +
88E VAL* 3.7 25.1 - - + -
90E ARG* 3.7 29.4 - - + +
102E ALA* 4.8 10.1 - - + -
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Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E SER 2.9 13.5 + - - +
77E HIS* 3.2 13.4 + - - +
79E VAL* 1.3 76.1 - - - +
81E ARG* 1.3 57.8 + - - +
83E GLU* 3.7 5.8 - - - +
84E LYS* 3.0 32.5 + - - +
90E ARG* 4.4 14.9 - - - +
7G T 5.0 9.4 - - - +
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Residues in contact with ARG 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 3.9 4.4 - - - +
39E GLY 3.1 26.7 + - - -
40E MET* 3.8 13.5 - - - +
44E TYR* 3.7 25.3 - - + +
77E HIS 3.2 9.2 + - - +
78E ALA 3.5 8.5 - - - +
79E VAL 3.1 0.4 - - - -
80E ALA* 1.3 81.7 - - - +
82E LEU* 1.3 62.3 + - - +
84E LYS* 3.4 8.5 + - + +
85E ASN* 3.1 47.3 + - - +
87E TRP* 3.7 15.2 - - - -
11H A 4.7 0.6 + - - -
12H T 2.7 44.8 + - - +
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET* 4.4 6.3 - - - -
44E TYR* 3.9 31.6 - - + -
47E LEU* 4.2 26.2 - - + -
48E LEU* 4.1 21.3 - - + -
78E ALA 2.9 22.9 + - - +
79E VAL* 3.4 7.6 + - + +
80E ALA 3.4 0.2 - - - -
81E ARG* 1.3 79.3 - - - +
83E GLU* 1.3 60.5 + - - +
85E ASN* 3.1 6.3 + - - +
86E GLY 3.0 21.1 + - - -
87E TRP* 3.0 35.9 + - + -
88E VAL* 4.0 20.9 - - + +
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Residues in contact with GLU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E VAL* 2.8 19.3 + - + +
80E ALA* 3.7 5.4 - - - +
82E LEU* 1.3 74.5 - - - +
84E LYS* 1.3 65.8 + - - +
86E GLY* 3.0 14.2 + - - -
88E VAL* 3.3 23.4 + - - +
89E ARG* 4.0 3.5 - - + +
90E ARG* 3.0 60.9 + - - +
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Residues in contact with LYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ALA 3.0 21.3 + - - +
81E ARG* 3.5 9.4 - - + +
82E LEU 3.3 0.2 - - - -
83E GLU* 1.3 78.6 - - - +
85E ASN* 1.3 60.5 + - - +
86E GLY* 3.2 1.2 + - - -
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Residues in contact with ASN 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E ARG* 3.1 37.1 + - - +
82E LEU* 3.1 24.5 + - - +
84E LYS* 1.3 76.7 - - - +
86E GLY* 1.3 59.4 + - - +
87E TRP* 3.1 51.2 + - + -
107E GLU* 5.9 0.7 - - - +
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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