Contacts of the helix formed by residues 61 - 69 (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 MET 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E ARG* 1.3 70.4 - - - +
62E THR* 1.3 60.2 + - - +
64E LEU* 3.0 4.3 + - - -
65E ALA 2.9 24.9 + - - -
72E ARG* 5.8 4.3 - - + -
75E LEU* 2.9 41.2 - - + +
76E SER* 4.7 0.4 - - - -
79E VAL* 3.9 25.4 - - + -
90E ARG* 5.3 1.8 - - - -
100E GLN* 3.2 29.7 + - + +
101E PHE 4.4 1.8 - - - +
102E ALA* 3.9 23.8 - - - -
5G A 3.6 25.0 + - - +
6G T 3.3 29.8 - - - +
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Residues in contact with THR 62 (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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60E ARG* 3.4 0.8 - - - -
61E MET* 1.3 77.3 - - - +
63E GLU* 1.3 58.0 + - - +
65E ALA* 3.2 7.6 + - - +
66E LYS* 2.8 28.8 + - + +
72E ARG* 3.9 19.9 + - - +
161E TRP* 4.0 32.3 - - + +
162E LEU* 5.2 4.7 - - + -
4G G 4.2 7.3 + - - +
5G A 2.6 23.6 + - - -
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Residues in contact with GLU 63 (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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59E LEU* 4.3 18.6 - - + +
60E ARG* 3.0 31.7 + - + +
62E THR* 1.3 78.2 - - - +
64E LEU* 1.3 63.9 + - - +
66E LYS* 3.2 8.8 + - + +
67E TYR* 3.1 48.4 + - + -
101E PHE* 5.9 0.5 - - - -
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Residues in contact with LEU 64 (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* 4.1 30.1 - - + +
50E LYS* 4.3 11.0 - - + -
51E LEU* 3.9 28.0 - - + -
59E LEU* 4.1 23.5 - - + +
60E ARG 2.9 11.4 + - - +
61E MET* 3.3 9.6 - - - +
63E GLU* 1.3 79.0 - - - +
65E ALA* 1.3 62.5 + - - +
67E TYR* 3.2 1.9 + - + +
68E ALA* 3.0 24.5 + - + +
75E LEU* 3.8 26.7 - - + -
79E VAL* 4.8 2.9 - - + -
102E ALA* 3.9 19.7 - - + -
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Residues in contact with ALA 65 (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 2.9 11.8 + - - +
62E THR* 3.5 11.2 - - - +
64E LEU* 1.3 77.1 - - - +
66E LYS* 1.3 51.1 + - - +
68E ALA 3.3 0.3 + - - -
69E LYS* 2.7 31.5 + - - -
70E ILE* 3.2 37.4 + - + +
71E THR 4.3 0.2 - - - -
72E ARG* 4.3 13.9 - - + +
75E LEU* 3.5 13.6 - - + +
161E TRP* 3.9 9.6 - - + -
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Residues in contact with LYS 66 (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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62E THR* 2.8 20.7 + - + +
63E GLU* 3.2 8.9 + - + +
65E ALA* 1.3 72.7 - - - +
67E TYR* 1.3 61.3 + - + +
69E LYS* 3.0 38.4 + - - +
161E TRP* 3.6 46.5 - - + +
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Residues in contact with TYR 67 (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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50E LYS* 3.6 49.1 + - + -
59E LEU* 3.7 23.6 - - + +
63E GLU* 3.1 44.1 + - + -
64E LEU* 3.7 4.7 - - + +
66E LYS* 1.3 78.1 - - + +
68E ALA* 1.3 62.8 + - - +
69E LYS* 3.4 18.6 + - - +
21F GLU* 4.4 10.3 - - - +
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Residues in contact with ALA 68 (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* 5.4 3.8 - - + +
46E GLY 6.3 0.4 - - - -
47E LEU* 3.7 26.5 - - + -
64E LEU* 3.0 16.7 + - + +
65E ALA 3.8 3.1 - - - +
67E TYR* 1.3 74.8 - - - +
69E LYS* 1.3 70.3 + - - +
70E ILE* 3.6 23.7 - - + +
20F ILE* 5.9 1.9 - - - +
24F THR* 3.9 9.2 + - - +
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Residues in contact with LYS 69 (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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65E ALA 2.7 13.2 + - - -
66E LYS* 3.0 26.0 + - - +
67E TYR* 3.2 14.4 - - - +
68E ALA* 1.3 79.0 - - - +
70E ILE* 1.3 56.7 + - - +
74E ARG* 5.6 0.2 + - - -
151E GLN* 2.9 36.6 + - - +
160E PRO* 3.7 17.1 - - - +
161E TRP* 3.8 15.2 - - + -
21F GLU* 3.6 44.2 + - + -
24F THR* 3.8 23.1 - - + +
25F LEU* 4.0 20.8 - - + +
28F ASP* 5.3 2.3 - - - +
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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