Contacts of the helix formed by residues 39 - 47 (chain E) in PDB entry 6P59
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 SER 39 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E ALA 3.2 4.1 + - - -
37E LEU 3.1 11.6 - - - +
38E THR* 1.3 79.4 - - - +
40E GLY* 1.3 58.1 + - - +
41E THR 3.3 0.2 + - - -
42E ILE* 3.1 38.1 + - - +
43E LYS* 3.0 22.0 + - - +
77E PHE* 4.1 11.8 - - - -
110E LEU* 2.4 40.9 + - - +
112E CYS* 3.9 7.4 - - - -
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Residues in contact with GLY 40 (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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38E THR 3.3 2.5 + - - -
39E SER* 1.3 71.0 - - - +
41E THR* 1.3 62.4 + - - +
43E LYS* 3.3 16.8 + - - +
44E ALA* 3.2 23.6 + - - +
110E LEU 3.1 6.1 + - - -
111E ASP* 3.1 26.5 + - - -
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Residues in contact with THR 41 (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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39E SER* 3.7 1.6 - - - -
40E GLY* 1.3 75.0 - - - +
42E ILE* 1.3 66.2 + - - +
43E LYS 3.4 0.5 + - - -
44E ALA* 3.5 12.0 + - - +
45E MET* 3.6 33.7 + - + +
62E PHE* 4.8 3.6 - - + -
109E PHE* 3.0 31.6 + - + +
110E LEU* 3.2 26.0 + - + -
111E ASP* 4.0 4.5 + - - +
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Residues in contact with ILE 42 (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 LEU* 4.0 25.8 - - + -
36E ALA* 3.5 28.7 - - + +
39E SER* 3.1 21.1 + - - +
41E THR* 1.3 75.9 - - - +
43E LYS* 1.3 63.5 + - - +
45E MET* 3.1 17.4 + - - +
46E LEU* 3.2 36.2 + - + +
60E VAL* 5.3 4.5 - - + -
62E PHE* 3.6 37.5 - - + -
70E LEU* 6.2 0.2 - - + -
77E PHE* 4.3 9.0 - - + -
110E LEU* 4.1 5.8 - - + -
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Residues in contact with LYS 43 (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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37E LEU* 3.8 40.2 + - + +
39E SER 3.0 18.8 + - - +
40E GLY* 3.6 14.7 - - - +
41E THR 3.2 0.6 - - - -
42E ILE* 1.3 78.3 - - - +
44E ALA* 1.3 57.1 + - - +
47E SER* 2.8 42.6 + - - +
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Residues in contact with ALA 44 (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 GLY 3.2 15.3 + - - +
41E THR* 3.9 6.7 - - - +
42E ILE 3.3 0.2 - - - -
43E LYS* 1.3 76.5 - - - +
45E MET* 1.3 59.1 + - + +
47E SER 3.8 6.3 - - - +
54E GLU* 3.8 16.1 - - - +
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Residues in contact with MET 45 (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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41E THR* 3.6 34.3 - - + +
42E ILE* 3.1 10.4 + - - +
44E ALA* 1.3 79.6 - - + +
46E LEU* 1.3 64.8 + - + +
47E SER 3.8 0.2 - - - -
54E GLU* 3.5 13.6 - - - +
57E THR* 3.1 19.2 + - - +
60E VAL* 3.9 35.7 - - + -
62E PHE* 4.3 10.1 - - + -
109E PHE* 6.2 1.1 - - + -
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Residues in contact with LEU 46 (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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19E VAL* 3.8 31.6 - - + -
21E LEU* 6.0 0.2 - - + -
33E ARG* 2.7 38.1 + - + +
36E ALA* 4.7 1.8 - - + -
37E LEU* 4.2 12.3 - - + -
42E ILE* 3.2 36.1 + - + +
43E LYS 3.1 1.6 + - - -
45E MET* 1.3 86.7 - - + +
47E SER* 1.3 59.4 + - - +
54E GLU 3.2 12.8 - - - +
55E ASN* 3.5 7.6 - - - +
57E THR* 3.5 35.2 - - - +
58E ASN* 4.9 1.1 - - - +
59E GLU 5.2 0.4 - - - +
60E VAL* 4.3 16.8 - - + -
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Residues in contact with SER 47 (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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33E ARG* 6.1 0.2 - - - -
37E LEU* 4.6 11.2 - - - -
43E LYS* 2.8 32.6 + - - +
44E ALA* 3.8 12.6 - - - +
46E LEU* 1.3 80.0 - - - +
48E GLY* 1.3 60.6 + - - +
54E GLU* 3.7 8.0 - - - +
55E ASN* 4.0 8.3 + - - -
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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