Contacts of the helix formed by residues 59 - 69 (chain E) in PDB entry 4LSZ
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 HIS 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E ALA 3.3 21.8 - - - -
23E ARG 3.2 18.7 + - - -
24E ALA 3.7 4.8 - - - -
25E GLY* 3.4 23.6 + - - -
27E ASP* 5.9 0.7 - - - +
54E ALA* 3.0 13.7 + - + +
57E ASN* 3.5 31.7 + - + +
58E GLY* 1.3 73.4 + - - +
60E LEU* 1.3 58.7 + - - +
61E GLU* 3.4 6.7 - - - -
62E ILE* 3.2 20.2 + - + +
63E VAL* 2.9 29.8 + - - +
95E ILE* 3.6 3.1 - - - +
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Residues in contact with LEU 60 (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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58E GLY 3.1 8.3 + - - +
59E HIS* 1.3 73.6 - - - +
61E GLU* 1.3 74.3 + - - +
63E VAL* 3.3 2.7 + - + +
64E GLU* 3.0 51.8 + - + +
94E GLU* 3.6 44.2 - - + +
95E ILE* 3.9 26.7 - - + -
98E ALA* 4.6 2.5 - - + -
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Residues in contact with GLU 61 (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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27E ASP* 3.0 27.8 - - + +
58E GLY 4.8 1.2 - - - +
59E HIS* 4.0 4.0 - - - -
60E LEU* 1.3 95.4 + - - +
62E ILE* 1.3 59.7 + - - +
64E GLU* 3.4 9.1 + - - +
65E VAL* 3.0 29.9 + - - +
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Residues in contact with ILE 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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21E ALA 4.1 2.7 - - - +
22E ALA* 4.1 6.7 - - + +
25E GLY* 3.5 40.8 - - - +
26E GLN 3.8 6.3 - - - +
27E ASP* 3.9 21.1 - - + +
30E VAL* 3.8 31.0 - - + -
54E ALA* 3.6 18.8 - - + -
59E HIS* 3.2 15.6 + - + +
61E GLU* 1.3 76.5 - - - +
63E VAL* 1.3 65.6 + - - +
65E VAL* 3.1 9.2 - - + +
66E LEU* 3.0 34.9 + - + +
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Residues in contact with VAL 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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51E LEU* 4.1 16.7 - - + +
54E ALA* 3.9 5.4 - - + -
55E ALA* 3.7 36.1 - - + +
59E HIS 2.9 17.8 + - - +
60E LEU* 3.4 10.5 - - - +
62E ILE* 1.3 75.8 - - - +
64E GLU* 1.3 59.7 + - - +
66E LEU* 3.4 3.0 + - - +
67E LEU* 3.0 47.0 + - + +
95E ILE* 3.9 21.1 - - + -
98E ALA* 4.3 13.0 - - + -
99E LEU* 4.6 4.0 - - + -
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Residues in contact with GLU 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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60E LEU* 3.0 35.6 + - + +
61E GLU* 3.9 7.8 - - - +
62E ILE 3.2 0.4 - - - -
63E VAL* 1.3 74.3 - - - +
65E VAL* 1.3 64.6 + - - +
67E LEU* 3.3 6.5 + - + +
68E LYS* 3.0 46.1 + - - +
98E ALA* 4.1 26.9 - - + +
102E TYR* 5.3 4.0 - - + -
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Residues in contact with VAL 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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27E ASP 5.8 0.4 - - - +
30E VAL* 3.8 23.3 - - + -
31E ARG* 4.2 27.4 - - + -
34E MET* 5.0 2.7 - - + -
61E GLU 3.0 18.7 + - - +
62E ILE* 3.1 24.7 - - + +
64E GLU* 1.3 75.7 - - - +
66E LEU* 1.3 61.7 - - - +
68E LYS* 3.3 8.9 + - + +
69E HIS* 3.2 43.5 + - + +
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Residues in contact with LEU 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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18E LEU* 4.6 9.2 - - + -
22E ALA* 4.7 0.2 - - + -
30E VAL* 4.6 15.5 - - + -
34E MET* 4.6 6.7 - - + -
40E VAL* 3.7 21.1 - - + +
50E PRO* 3.5 24.7 - - + +
51E LEU* 3.5 38.8 - - + +
54E ALA* 4.3 2.2 - - + -
62E ILE* 3.0 34.4 + - + +
63E VAL 3.6 3.8 - - - +
65E VAL* 1.3 77.3 - - + +
67E LEU* 1.3 63.5 + - - +
69E HIS* 3.1 14.8 + - - +
71E ALA* 3.2 27.3 + - + +
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Residues in contact with LEU 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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51E LEU* 4.0 26.5 - - + -
63E VAL* 3.0 39.0 + - + +
64E GLU* 3.6 7.2 - - - +
65E VAL 3.3 0.2 - - - -
66E LEU* 1.3 77.1 - - - +
68E LYS* 1.3 61.1 + - - +
70E ASP* 3.1 15.2 + - - +
71E ALA 4.0 8.7 + - - +
73E VAL* 4.1 13.5 - - + -
98E ALA* 3.7 33.4 - - + +
99E LEU* 4.1 4.0 - - + +
102E TYR* 3.4 50.2 - - + -
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Residues in contact with LYS 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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64E GLU* 3.0 37.8 + - - +
65E VAL* 3.8 8.3 - - + +
66E LEU 3.3 0.2 - - - -
67E LEU* 1.3 75.7 - - - +
69E HIS* 1.3 66.2 + - + +
70E ASP* 3.2 8.9 + - - +
102E TYR* 3.4 26.6 + - - +
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Residues in contact with HIS 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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31E ARG* 6.2 0.4 - - - -
34E MET* 3.3 56.7 + - + +
35E ALA* 5.1 1.8 - - - -
40E VAL* 3.4 14.5 - - + +
65E VAL* 3.2 24.8 + - + +
66E LEU 3.1 8.5 + - - +
68E LYS* 1.3 87.9 - - + +
70E ASP* 1.3 70.6 + - - +
71E ALA 3.4 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