Contacts of the helix formed by residues 56 - 68 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 4.7 17.9 - - + -
55A PRO 3.5 10.8 - - - +
56A ALA* 4.4 1.3 - - - +
57A PHE* 3.7 0.9 - - - -
52B ILE* 5.0 2.2 - - - +
54B THR 3.6 2.9 + - - -
55B PRO* 1.3 74.2 - - - +
57B PHE* 1.3 65.4 + - - +
58B PHE* 4.3 3.4 - - + +
59B THR* 3.5 26.2 - - - +
60B ILE* 3.1 22.9 + - - +
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Residues in contact with PHE 57 (chain B).
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* 4.1 18.6 - - + -
55A PRO* 2.8 21.9 + - + +
57A PHE* 3.1 35.6 - + - +
60A ILE* 3.7 37.7 - - + -
71A LEU* 3.9 18.2 - - + -
74A VAL* 4.3 15.7 - - + -
75A ALA* 4.7 4.3 - - + -
56B ALA* 1.3 72.0 - - - +
58B PHE* 1.4 92.8 + + + +
60B ILE* 3.3 2.1 + - - +
61B ALA* 2.8 32.4 + - + +
71B LEU* 4.2 25.8 - - + -
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU 5.6 1.3 - - - -
13A ARG* 3.4 55.6 - - + +
14A GLY* 3.9 7.0 - - - -
17A LEU* 3.8 30.5 - - + -
55A PRO* 4.7 15.9 + - + -
74A VAL* 6.3 0.2 - - + -
75A ALA* 5.9 0.4 - - - -
78A VAL* 4.2 18.6 - - + -
80A PHE* 3.8 25.9 - + + -
56B ALA* 3.3 4.0 - - + +
57B PHE* 1.4 93.5 - + + +
59B THR* 1.3 59.7 + - - +
61B ALA* 3.8 2.2 - - - +
62B ALA* 3.0 29.3 + - - +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ILE* 4.1 23.6 - - + +
43B THR* 4.1 16.2 - - + +
47B ILE* 3.3 32.8 - - + -
56B ALA* 3.2 28.4 + - - +
58B PHE* 1.3 75.9 - - - +
60B ILE* 1.3 66.9 + - - +
62B ALA* 3.3 5.0 + - - +
63B VAL* 3.1 24.0 + - + +
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Residues in contact with ILE 60 (chain B).
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* 3.7 40.8 - - + -
17B LEU* 4.0 14.4 - - + -
21B LEU* 4.0 13.4 - - + +
47B ILE* 3.9 33.0 - - + -
55B PRO* 3.9 24.9 - - + -
56B ALA 3.1 13.1 + - - +
57B PHE 3.8 0.9 - - - +
59B THR* 1.3 76.8 - - - +
61B ALA* 1.3 51.8 + - - +
63B VAL* 3.3 4.5 + - + +
64B ALA* 2.8 37.0 + - + +
71B LEU* 4.0 7.6 - - + -
74B VAL* 4.3 12.6 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 4.4 7.4 - - + +
80A PHE* 3.6 23.2 - - + -
57B PHE* 2.8 25.7 + - + +
58B PHE* 3.8 5.6 - - - +
60B ILE* 1.3 76.0 - - - +
62B ALA* 1.3 57.0 + - - +
64B ALA* 3.4 2.3 + - - +
65B ARG* 2.9 29.5 + - - +
71B LEU* 3.9 31.1 - - + +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.6 27.4 - - + +
37B ALA* 3.4 32.1 - - + +
39B ILE* 5.2 2.5 - - + -
58B PHE 3.0 18.8 + - - +
59B THR* 3.7 5.6 - - - +
60B ILE 3.3 0.2 - - - -
61B ALA* 1.3 74.9 - - - +
63B VAL* 1.3 65.0 + - - +
65B ARG* 3.2 3.6 + - - +
66B VAL* 3.2 27.4 + - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.3 21.5 - - + -
33B VAL* 4.4 6.1 - - + -
37B ALA* 4.3 10.1 - - + -
39B ILE* 3.6 30.1 - - + -
44B LEU* 3.9 21.8 - - + -
47B ILE* 5.4 1.6 - - + -
59B THR* 3.1 18.8 + - + +
60B ILE* 3.9 2.9 - - - +
62B ALA* 1.3 72.1 - - - +
64B ALA* 1.3 67.2 + - - +
66B VAL* 3.2 4.9 + - - +
67B LEU* 2.9 47.8 + - + +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 5.1 2.4 - - + +
60B ILE* 2.8 23.8 + - + +
61B ALA 3.6 4.5 - - - +
63B VAL* 1.3 73.1 - - - +
65B ARG* 1.3 62.9 + - - +
67B LEU 3.2 0.7 + - - -
68B ASP 2.9 19.6 + - - -
69B LEU* 3.0 43.5 + - + +
71B LEU* 3.7 23.3 - - + -
74B VAL* 4.9 4.0 - - + -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ALA* 2.7 39.2 + - - +
76A ALA* 3.8 8.3 + - - +
78A VAL 2.4 26.4 + - - -
79A THR* 3.7 7.9 - - - +
80A PHE* 3.4 32.4 - - + +
61B ALA 2.9 13.9 + - - +
62B ALA 3.4 9.9 - - - +
63B VAL 3.2 0.2 - - - -
64B ALA* 1.3 80.3 - - - +
66B VAL* 1.3 64.6 + - + +
68B ASP* 3.3 10.3 + - - +
69B LEU 5.2 0.9 - - - -
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 6.3 0.7 - - + -
28B MSE 5.0 15.3 - - + +
33B VAL* 4.2 30.5 - - + +
36B ASP* 3.6 31.2 - - + +
37B ALA* 3.6 27.8 - - + +
62B ALA 3.2 13.9 + - - +
63B VAL 3.7 6.7 - - - +
65B ARG* 1.3 80.3 - - + +
67B LEU* 1.3 61.6 + - + +
68B ASP* 3.3 2.6 + - - +
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.6 29.4 - - + +
24B ALA* 3.9 14.0 - - + +
25B ARG* 3.7 27.4 - - + +
28B MSE 4.1 14.8 - - - -
33B VAL* 3.9 26.9 - - + -
48B GLU* 5.9 0.4 - - - +
63B VAL* 2.9 40.5 + - + +
64B ALA 4.1 1.8 - - - +
66B VAL* 1.3 78.4 - - - +
68B ASP* 1.3 69.7 + - - +
69B LEU* 3.3 18.2 + - + +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ALA 2.9 4.7 + - - -
65B ARG* 3.3 11.1 + - - +
66B VAL 3.3 2.6 - - - +
67B LEU* 1.3 81.4 - - - +
69B LEU* 1.3 63.9 + - - +
70B SER 4.4 0.3 + - - -
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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