Contacts of the helix formed by residues 57 - 66 (chain A) in PDB entry 1EL0
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 GLY 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A THR 3.3 2.2 - - - -
56A VAL* 1.3 81.6 - - - +
58A TRP* 1.3 61.8 + - - +
59A VAL 3.0 4.3 + - - +
60A GLN* 3.2 29.0 + - - +
61A ARG* 3.3 22.6 + - - -
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Residues in contact with TRP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 2.7 49.8 + - + -
17A GLU* 3.9 10.4 - - - +
18A GLN 3.9 13.2 - - - +
19A GLU* 5.6 4.3 - - - -
20A ILE* 3.6 22.2 - - + +
25A ILE* 3.8 4.7 - - + -
42A PHE* 3.1 50.5 - + - -
52A ALA* 3.9 8.7 - - + -
56A VAL* 3.0 29.8 - - + +
57A GLY* 1.3 72.5 - - - +
59A VAL* 1.3 63.6 - - + +
61A ARG* 3.1 26.5 - - - +
62A HIS* 2.7 41.0 + + + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.6 21.1 - - + -
40A LEU* 3.2 30.7 - - + -
42A PHE* 3.5 10.8 - - + -
54A ASP 3.1 24.9 - - - +
56A VAL* 3.0 27.1 - - + -
57A GLY 3.0 0.4 - - - -
58A TRP* 1.3 92.1 - - + +
60A GLN* 1.3 58.0 + - - +
62A HIS* 3.0 2.8 + - - +
63A ARG* 2.6 40.4 + - + +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP 3.6 21.4 + - - -
55A THR* 3.5 38.2 - - - +
57A GLY* 3.2 19.5 + - - +
59A VAL* 1.3 81.5 - - - +
61A ARG* 1.3 52.6 + - - +
63A ARG* 3.0 22.5 + - - +
64A LYS* 2.6 39.5 + - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.7 5.4 - - + +
57A GLY* 3.3 28.6 + - - -
58A TRP* 3.1 29.0 - - - +
60A GLN* 1.3 79.7 - - - +
62A HIS* 1.3 72.8 + - + +
64A LYS* 3.9 7.5 - - - +
65A MET* 3.5 25.8 + - - +
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE 2.9 29.0 + - - -
21A PRO* 3.4 5.7 - - + -
22A LEU* 3.1 44.2 - - + +
25A ILE* 3.1 29.9 - - + +
28A TYR* 5.4 0.4 - - - -
42A PHE* 3.9 17.7 - + + -
58A TRP* 2.7 29.3 + + + +
59A VAL 3.0 7.7 + - - +
61A ARG* 1.3 89.9 - - + +
63A ARG* 1.3 53.5 + - - +
65A MET 3.5 0.3 + - - -
66A LEU* 2.8 43.2 + - + +
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.0 51.0 + - + +
59A VAL 2.6 32.0 + - - +
60A GLN* 3.0 33.0 + - - +
62A HIS* 1.3 69.8 - - - +
64A LYS* 1.3 102.7 + - - +
65A MET 3.2 1.8 - - - -
66A LEU 2.5 24.1 - - - +
67A ARG* 4.7 0.3 - - - -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN 2.6 23.8 + - - +
61A ARG* 3.9 10.1 - - - +
62A HIS 3.3 0.2 - - - -
63A ARG* 1.3 99.3 - - - +
65A MET* 1.3 75.4 + - + +
66A LEU 4.4 0.2 - - - +
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 5.4 5.6 - - + -
61A ARG 3.5 16.1 + - - +
62A HIS* 3.5 1.0 + - - -
63A ARG 3.2 0.2 - - - -
64A LYS* 1.3 93.9 - - + +
66A LEU* 1.3 79.5 + - + +
67A ARG* 5.6 0.3 - - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.3 28.7 - - + -
26A LEU* 2.7 34.3 - - - +
27A CYS* 4.2 11.2 - - + -
28A TYR* 4.7 3.8 - - + +
62A HIS* 2.8 27.0 + - + +
63A ARG* 2.5 29.9 - - - +
64A LYS 4.2 0.3 - - - +
65A MET* 1.3 87.1 - - + +
67A ARG* 1.3 65.5 + - + +
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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