Contacts of the helix formed by residues 54 - 64 (chain A) in PDB entry 2A0M
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 LYS 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY 3.0 13.8 + - - +
53A LYS* 1.3 97.3 - - + +
55A GLY* 1.3 63.7 + - - +
56A PRO* 3.4 2.0 - - - -
57A ALA* 3.3 14.2 + - + +
58A ALA* 3.1 18.7 + - - +
284A PRO* 3.5 20.0 - - + +
285A LEU* 4.4 28.8 - - + +
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Residues in contact with GLY 55 (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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52A ALA 2.9 13.5 + - - -
54A LYS* 1.3 77.8 - - - +
56A PRO* 1.3 68.6 - - - +
58A ALA* 3.3 1.7 + - - +
59A PHE* 2.9 25.3 + - - +
118A ILE* 4.6 0.2 - - - -
119A GLY 3.6 10.1 - - - -
282A LEU* 3.7 23.4 - - - +
284A PRO* 3.8 8.5 - - - +
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Residues in contact with PRO 56 (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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36A GLY* 4.4 0.4 - - - -
37A PHE 4.0 1.6 - - - +
38A PRO* 3.9 25.8 - - + -
52A ALA 3.8 1.8 - - - +
53A LYS 3.6 13.2 - - - +
54A LYS 3.7 0.2 - - - -
55A GLY* 1.3 89.8 - - - +
57A ALA* 1.3 56.5 + - - +
59A PHE* 3.4 1.4 + - - +
60A ARG* 2.9 54.3 + - - +
88A ASP* 4.1 7.2 - - - +
118A ILE* 3.5 37.9 - - + +
119A GLY 3.3 11.9 - - - +
120A GLY 3.8 0.2 - - - +
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Residues in contact with ALA 57 (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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53A LYS 5.3 0.6 + - - +
54A LYS* 3.3 16.3 + - + +
56A PRO* 1.3 78.0 - - - +
58A ALA* 1.3 63.3 + - - +
60A ARG* 3.4 10.5 + - - +
61A PHE* 3.0 23.6 + - - +
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Residues in contact with ALA 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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54A LYS 3.1 6.0 + - - +
55A GLY 3.7 4.3 - - - +
57A ALA* 1.3 75.9 - - - +
59A PHE* 1.3 63.5 + - - +
61A PHE* 3.2 16.4 + - - +
62A PHE* 3.4 19.3 + - + -
282A LEU* 4.6 1.1 - - + -
284A PRO* 3.5 33.7 - - + -
288A GLU 5.1 2.2 - - - +
292A PRO* 3.7 21.8 - - + -
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Residues in contact with PHE 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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34A ILE* 4.6 8.1 - - + -
55A GLY 2.9 17.1 + - - +
56A PRO 3.6 3.4 - - - +
58A ALA* 1.3 73.4 - - - +
60A ARG* 1.3 66.1 + - + +
62A PHE 3.3 1.2 + - - -
63A LEU* 2.8 50.6 + - + +
116A PHE* 3.6 32.3 - + - -
118A ILE* 3.7 36.3 - - + -
279A MET* 4.3 0.7 - - - -
282A LEU* 4.4 6.8 - - + +
292A PRO* 4.9 1.8 - - - -
295A ALA* 3.7 31.0 - - + -
296A VAL* 3.2 28.9 - - + +
299A PHE* 3.7 22.9 - + + -
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Residues in contact with ARG 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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34A ILE* 4.7 5.3 - - + +
35A ILE 4.7 0.8 - - - -
36A GLY* 3.8 9.4 - - - +
56A PRO* 2.9 35.3 + - - +
57A ALA* 3.8 8.5 - - - +
59A PHE* 1.3 76.6 - - + +
61A PHE* 1.3 65.6 + - - +
63A LEU* 3.2 16.5 + - + +
64A GLN* 3.2 37.5 + - + +
85A ASP* 2.7 42.6 + - - +
87A GLY* 3.3 18.6 + - - -
88A ASP* 2.8 34.7 + - - -
118A ILE* 5.1 4.0 - - + +
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Residues in contact with PHE 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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57A ALA 3.0 13.7 + - - +
58A ALA* 3.2 13.6 + - - +
60A ARG* 1.3 79.1 - - - +
62A PHE* 1.3 93.0 + + + +
64A GLN* 3.5 12.2 + - - +
65A ARG* 2.9 72.4 + - - -
289A TYR* 5.6 2.9 - + - -
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Residues in contact with PHE 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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58A ALA* 3.4 15.6 + - - -
59A PHE 3.3 2.0 + - - -
61A PHE* 1.3 101.3 - + + +
63A LEU* 1.3 64.7 + - - +
64A GLN 3.1 1.8 - - - -
65A ARG* 2.9 21.1 + - - +
66A LEU* 3.0 30.9 + - + +
288A GLU 4.1 8.7 - - - -
289A TYR* 3.8 44.4 - + - -
292A PRO* 3.7 18.4 - - + +
293A ARG* 3.6 41.1 - - + -
296A VAL* 3.8 18.4 - - + -
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Residues in contact with LEU 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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18A LEU* 3.9 40.7 - - + +
19A LEU* 4.0 6.2 + - - -
22A PHE* 3.8 29.2 - - + -
34A ILE* 3.8 14.4 - - + -
59A PHE* 2.8 33.4 + - + +
60A ARG* 3.4 19.5 - - + +
62A PHE* 1.3 78.2 - - - +
64A GLN* 1.3 61.1 + - + +
65A ARG 3.3 1.0 + - - -
66A LEU 4.3 1.7 + - - -
85A ASP* 4.9 5.6 - - - +
296A VAL* 3.7 9.8 - - + +
299A PHE* 4.1 21.5 - - + -
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Residues in contact with GLN 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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17A ARG* 6.0 0.6 - - - +
19A LEU* 3.6 44.1 - - + +
60A ARG* 3.2 26.2 + - + +
61A PHE* 3.7 14.3 - - - +
62A PHE 3.1 0.8 - - - -
63A LEU* 1.3 77.8 - - + +
65A ARG* 1.3 74.0 + - + +
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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