Contacts of the helix formed by residues 56 - 68 (chain E) in PDB entry 2X6L
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 GLU 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E TYR* 5.9 0.2 - - - +
16E THR 4.5 13.8 - - - +
17E ALA* 5.5 2.8 - - - +
53E ASP* 2.9 38.6 + - - +
55E SER* 1.3 81.4 - - - +
57E SER* 1.3 65.2 + - - +
58E TRP* 3.3 32.1 + - + +
59E VAL* 3.2 9.9 + - + +
60E GLN* 3.1 23.6 + - - +
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Residues in contact with SER 57 (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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55E SER 3.9 1.6 + - - -
56E GLU* 1.3 71.2 - - - +
58E TRP* 1.3 65.0 + - - +
60E GLN* 3.1 12.2 + - - +
61E GLU* 2.8 50.1 + - - +
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Residues in contact with TRP 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E THR* 4.1 13.6 + - + -
18E ARG 3.5 18.0 + - - -
19E LYS* 3.5 49.1 - - + +
20E LEU* 3.7 23.8 - - + -
42E PHE* 3.6 25.8 - + - -
52E ALA* 4.3 3.8 - - + -
56E GLU* 3.3 30.7 + - + -
57E SER* 1.3 83.4 + - - +
59E VAL* 1.3 68.7 + - + +
61E GLU* 3.2 11.7 + - - +
62E TYR* 2.8 80.7 + + + -
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Residues in contact with VAL 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E VAL* 3.9 33.9 - - + -
42E PHE* 3.7 11.8 - - + -
52E ALA* 3.5 18.6 - - + -
53E ASP 3.5 23.1 - - - +
54E PRO* 4.2 7.2 - - + -
56E GLU* 3.4 12.1 - - + +
57E SER 3.2 0.6 - - - -
58E TRP* 1.3 108.3 - - + +
60E GLN* 1.3 63.7 + - - +
62E TYR* 3.4 2.1 + - - +
63E VAL* 3.1 23.3 + - + +
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Residues in contact with GLN 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PRO* 3.1 23.7 + - + +
55E SER* 3.8 14.3 + - - +
56E GLU 3.1 13.8 + - - +
57E SER* 3.1 9.9 + - - +
59E VAL* 1.3 75.0 - - + +
61E GLU* 1.3 63.1 + - + +
63E VAL* 3.3 6.6 + - - +
64E TYR* 2.9 45.2 + - + -
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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
----------------------------------------------------------
19E LYS* 5.0 6.6 + - - -
57E SER* 2.8 36.6 + - - +
58E TRP* 3.6 11.9 - - - +
60E GLN* 1.3 78.9 - - + +
62E TYR* 1.3 67.3 + - + +
64E TYR* 3.3 8.0 + - - +
65E ASP* 2.9 25.3 + - - +
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Residues in contact with TYR 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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19E LYS* 3.7 22.1 - - - -
20E LEU 2.6 30.2 + - - -
22E ARG* 3.0 48.7 + - + +
25E VAL* 4.2 20.4 - - + -
42E PHE* 3.5 20.2 - + + -
58E TRP* 2.8 53.2 + + + +
61E GLU* 1.3 77.5 - - + +
63E VAL* 1.3 63.7 + - - +
65E ASP* 3.2 6.0 + - + +
66E LEU* 3.0 31.2 + - + +
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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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28E TYR* 3.7 39.2 - - + +
30E GLU* 5.5 2.9 - - - +
40E VAL* 4.1 31.0 - - + -
42E PHE* 4.2 4.3 - - + -
59E VAL 3.1 16.7 + - - +
60E GLN* 3.6 8.3 - - - +
62E TYR* 1.3 75.2 - - - +
64E TYR* 1.3 74.0 + - + +
66E LEU* 3.1 10.6 + - - +
67E GLU* 2.9 24.6 + - + +
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Residues in contact with TYR 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 GLN* 2.9 44.2 + - + +
61E GLU* 3.6 7.2 - - - +
63E VAL* 1.3 83.3 - - + +
65E ASP* 1.3 57.6 + - - +
67E GLU* 3.3 5.1 + - - +
68E LEU* 3.0 49.4 + - + +
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Residues in contact with ASP 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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22E ARG* 3.1 37.3 + - - +
61E GLU 2.9 17.0 + - - +
62E TYR* 3.7 5.2 - - + +
63E VAL 3.2 0.2 - - - -
64E TYR* 1.3 74.2 - - - +
66E LEU* 1.3 64.4 + - - +
68E LEU* 4.9 0.7 - - - -
69E ASN* 3.0 57.8 + - - +
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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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22E ARG* 3.6 27.4 - - - +
25E VAL* 3.9 22.0 - - + +
26E VAL* 3.9 26.7 - - - +
27E ASP* 4.2 8.3 - - - +
28E TYR* 4.0 26.9 - - + -
42E PHE* 4.2 7.0 - - + -
62E TYR* 3.0 23.6 + - + +
63E VAL 3.5 5.6 - - - +
65E ASP* 1.3 79.8 - - - +
67E GLU* 1.3 65.4 + - - +
69E ASN 4.0 9.0 + - - +
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Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR* 2.5 34.6 + - - +
63E VAL* 2.9 18.3 + - + +
64E TYR* 3.6 6.7 - - - +
66E LEU* 1.3 81.2 - - - +
68E LEU* 1.3 61.2 + - + +
69E ASN 3.6 3.3 + - - +
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Residues in contact with LEU 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 TYR* 3.0 38.8 + - + +
65E ASP* 4.9 0.2 - - - -
67E GLU* 1.3 78.7 - - + +
69E ASN* 1.3 83.0 + - - +
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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