Contacts of the helix formed by residues 56 - 67 (chain A) in PDB entry 2OFY
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 ALA 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ILE* 5.3 0.2 - - - +
54A THR 3.4 4.1 + - - +
55A PRO* 1.3 73.3 - - - +
57A PHE* 1.3 67.6 + - - +
58A PHE* 4.4 2.9 - - + +
59A THR* 3.2 23.3 + - - +
60A ILE* 3.1 22.9 + - - +
54B THR* 4.5 20.9 - - - +
55B PRO 3.7 8.5 - - - +
56B ALA* 4.4 1.3 - - - +
57B PHE 3.7 0.4 - - - -
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Residues in contact with PHE 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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56A ALA* 1.3 71.7 - - - +
58A PHE* 1.3 97.6 + + + +
60A ILE* 3.3 1.9 + - - +
61A ALA* 2.9 28.7 + - + +
71A LEU* 4.3 11.4 - - + -
17B LEU* 4.9 1.6 - - + -
55B PRO* 2.8 21.2 + - + +
57B PHE* 3.1 35.7 - + - +
60B ILE* 3.7 29.6 - - + -
71B LEU* 3.8 24.0 - - + -
74B VAL* 4.0 22.2 - - + -
75B ALA* 4.2 26.2 - - + -
78B VAL* 4.3 2.2 - - + -
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Residues in contact with PHE 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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56A ALA* 3.2 3.4 - - + +
57A PHE* 1.3 96.9 - + + +
59A THR* 1.3 56.9 + - - +
61A ALA* 3.5 7.5 + - + +
62A ALA* 3.0 28.4 + - - +
13B ARG* 3.2 60.8 + - + +
14B GLY* 5.1 1.8 - - - -
17B LEU* 4.0 16.4 - - + -
53B ALA 5.9 0.7 - - - -
54B THR* 5.8 1.8 - - - -
55B PRO* 4.1 20.4 - - + -
78B VAL* 2.9 53.6 - - + -
79B THR* 4.4 2.9 - - + -
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Residues in contact with THR 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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39A ILE* 3.9 31.0 - - + +
43A THR* 4.5 5.4 - - + -
47A ILE* 3.7 29.4 - - + -
56A ALA* 3.2 24.6 + - - +
58A PHE* 1.3 75.4 - - - +
60A ILE* 1.3 67.2 + - - +
62A ALA* 3.1 6.7 + - - +
63A VAL* 3.0 23.1 + - + +
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Residues in contact with ILE 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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17A LEU* 3.8 25.6 - - + -
21A LEU* 4.0 11.8 - - + +
47A ILE* 3.8 37.2 - - + -
55A PRO* 4.0 14.1 - - + -
56A ALA 3.1 15.8 + - - +
59A THR* 1.3 74.9 - - + +
61A ALA* 1.3 58.5 + - - +
63A VAL* 3.3 4.6 + - + +
64A ALA* 2.8 30.8 + - + +
71A LEU* 4.1 7.2 - - + -
74A VAL* 5.3 0.7 - - + -
57B PHE* 3.7 49.1 - - + -
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Residues in contact with ALA 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 PHE* 2.9 22.7 + - + +
58A PHE* 3.6 13.0 - - + +
60A ILE* 1.3 77.7 - - - +
62A ALA* 1.3 61.8 + - - +
64A ALA* 3.9 0.9 - - - +
65A ARG* 3.0 25.4 + - - +
71A LEU* 3.9 29.4 - - + +
75B ALA* 4.3 15.0 - - + -
79B THR* 6.5 0.7 - - + -
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Residues in contact with ALA 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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37A ALA* 3.6 26.2 - - + +
39A ILE* 5.8 1.3 - - + -
58A PHE 3.0 17.6 + - - +
59A THR* 3.1 6.5 + - - +
61A ALA* 1.3 77.8 - - - +
63A VAL* 1.3 61.5 + - - +
65A ARG* 2.9 42.4 + - - +
66A VAL* 3.2 8.7 + - - +
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Residues in contact with VAL 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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21A LEU* 4.2 16.8 - - + -
33A VAL* 4.2 11.2 - - + -
37A ALA* 3.9 13.9 - - + -
39A ILE* 3.8 28.3 - - + -
44A LEU* 4.3 16.8 - - + -
47A ILE* 5.1 3.8 - - + -
59A THR* 3.0 23.2 + - + +
60A ILE* 3.9 5.6 - - - +
62A ALA* 1.3 74.3 - - - +
64A ALA* 1.3 67.1 + - - +
66A VAL* 3.1 5.6 + - - +
67A LEU* 3.0 43.6 + - + +
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Residues in contact with ALA 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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21A LEU* 4.9 3.5 - - + +
60A ILE* 2.8 19.2 + - + +
61A ALA 3.9 2.2 - - - +
63A VAL* 1.3 77.7 - - - +
65A ARG* 1.3 61.7 + - - +
67A LEU* 3.1 2.7 + - - -
68A ASP 3.0 4.2 + - - -
69A LEU* 2.9 61.1 + - + +
71A LEU* 3.5 26.9 - - + +
74A VAL* 5.4 0.7 - - + -
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Residues in contact with ARG 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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36A ASP* 3.1 28.4 + - - +
37A ALA* 3.8 16.0 + - - +
61A ALA 3.0 16.4 + - - +
62A ALA* 2.9 33.0 + - - +
64A ALA* 1.3 77.3 - - - +
66A VAL* 1.3 76.0 + - - +
68A ASP* 3.1 19.3 + - - +
69A LEU 4.9 1.6 - - - -
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Residues in contact with VAL 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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28A MSE 4.5 18.7 - - + +
33A VAL* 4.1 24.7 - - + +
36A ASP* 3.5 54.7 - - + +
37A ALA* 3.5 6.1 - - + +
62A ALA 3.2 15.1 + - - +
63A VAL* 3.1 9.5 + - - +
65A ARG* 1.3 85.8 - - - +
67A LEU* 1.3 58.3 + - - +
68A ASP* 3.5 4.9 + - - +
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Residues in contact with LEU 67 (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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21A LEU* 3.8 32.1 - - + +
24A ALA* 4.0 20.0 - - + +
25A ARG* 3.7 26.0 - - + +
28A MSE 3.9 21.0 - - + +
33A VAL* 3.9 20.6 - - + -
63A VAL* 3.0 36.1 + - + +
64A ALA 3.1 3.8 + - - +
66A VAL* 1.3 75.2 - - - +
68A ASP* 1.3 68.4 + - - +
69A LEU* 3.2 10.5 + - + +
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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