Contacts of the helix formed by residues 70 - 81 (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 SER 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASP* 2.9 23.8 + - - -
68B ASP 4.4 0.6 + - - -
69B LEU* 1.3 72.2 - - - +
71B LEU* 1.3 62.6 + - - +
72B ASP* 3.3 4.0 + - - +
73B ASP* 3.1 39.0 + - - +
74B VAL* 3.0 23.7 + - - +
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Residues in contact with LEU 71 (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* 3.8 25.0 - - + -
71A LEU* 3.6 28.5 - - + +
72A ASP* 2.8 17.0 + - - +
75A ALA* 3.8 29.8 - - + -
57B PHE* 4.2 9.0 - - + -
60B ILE* 4.0 7.9 - - + -
61B ALA* 3.9 23.6 - - + -
64B ALA* 3.7 25.8 - - + -
69B LEU 3.5 2.0 + - - +
70B SER* 1.3 71.7 - - - +
72B ASP* 1.3 56.3 + - - +
74B VAL* 3.3 7.6 + - + +
75B ALA* 2.9 30.3 + - - +
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Residues in contact with ASP 72 (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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69A LEU 4.5 1.4 - - - +
70A SER* 2.5 33.6 + - - -
71A LEU* 2.8 29.5 + - - +
72A ASP* 3.2 11.5 + - - +
70B SER* 3.2 4.0 - - - +
71B LEU* 1.3 77.1 - - - +
73B ASP* 1.3 66.1 + - - +
75B ALA* 3.3 6.0 + - - +
76B ALA* 3.1 23.2 + - - +
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Residues in contact with ASP 73 (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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20B LEU* 5.0 2.0 - - + -
69B LEU* 6.2 0.2 - - + -
70B SER* 3.1 32.2 + - - +
72B ASP* 1.3 78.7 - - - +
74B VAL* 1.3 63.4 + - + +
76B ALA* 3.3 6.1 + - - +
77B VAL* 3.3 30.2 + - + +
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Residues in contact with VAL 74 (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* 4.0 15.3 - - + -
17B LEU* 3.7 28.9 - - + -
20B LEU* 3.8 22.7 - - + -
21B LEU* 4.9 3.6 - - + -
60B ILE* 4.3 8.3 - - + -
64B ALA* 4.9 1.8 - - + -
69B LEU* 4.1 24.7 - - + -
70B SER 3.0 16.3 + - - +
71B LEU* 3.5 15.5 - - + +
73B ASP* 1.3 75.0 - - + +
75B ALA* 1.3 63.6 + - - +
77B VAL* 3.1 4.0 + - - +
78B VAL* 3.0 23.8 + - + +
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Residues in contact with ALA 75 (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* 4.2 8.9 - - + -
61A ALA* 4.3 11.0 - - + -
71A LEU* 3.9 20.4 - - + -
71B LEU 2.9 19.7 + - - +
72B ASP* 3.7 5.8 - - - +
74B VAL* 1.3 74.0 - - - +
76B ALA* 1.3 53.2 - - - +
78B VAL* 2.7 23.5 - - + +
79B THR* 2.6 27.7 + - + +
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Residues in contact with ALA 76 (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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72B ASP 3.1 12.9 + - - +
73B ASP* 3.6 11.7 - - - +
74B VAL 3.3 0.2 - - - -
75B ALA* 1.3 76.8 - - - +
77B VAL* 1.3 65.0 + - + +
79B THR* 4.0 3.6 - - - -
80B PHE* 3.1 41.9 + - + +
81B GLY 4.3 0.2 - - - +
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Residues in contact with VAL 77 (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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16B ARG* 3.3 10.7 + - + +
20B LEU* 3.7 38.6 - - + -
73B ASP* 3.3 16.2 - - + +
74B VAL 3.1 3.0 + - - -
76B ALA* 1.3 81.9 - - + +
78B VAL* 1.3 63.0 + - - +
79B THR 3.3 0.4 - - - -
81B GLY* 2.8 44.8 + - - +
82B PRO* 4.1 16.8 - - + -
83B VAL* 5.7 2.5 - - + +
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Residues in contact with VAL 78 (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* 4.3 0.9 - - + -
58A PHE* 2.9 38.8 - - + -
13B ARG* 3.3 13.1 - - - +
16B ARG* 2.7 34.1 + - - +
17B LEU* 3.6 47.3 - - + -
20B LEU* 5.6 0.7 - - + -
74B VAL* 3.0 17.4 + - + +
75B ALA* 2.7 33.7 - - - +
77B VAL* 1.3 79.0 - - + +
79B THR* 1.3 55.9 + - + +
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Residues in contact with THR 79 (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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58A PHE* 4.4 2.0 - - + -
9B GLU* 5.6 3.0 - - - +
13B ARG* 3.4 32.8 - - - +
16B ARG* 3.3 10.6 + - - +
75B ALA* 2.6 23.9 + - - +
76B ALA* 4.0 0.2 - - - -
78B VAL* 1.3 85.3 - - + +
80B PHE* 1.3 86.6 + - - +
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Residues in contact with PHE 80 (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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16B ARG* 4.0 6.3 + - - -
76B ALA* 3.1 32.6 + - + +
79B THR* 1.3 100.3 - - - +
81B GLY* 1.3 62.3 + - - +
82B PRO 4.7 1.6 - - - +
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Residues in contact with GLY 81 (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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16B ARG* 3.0 25.4 - - - +
76B ALA 4.3 0.2 - - - +
77B VAL* 2.8 25.7 + - - +
80B PHE* 1.3 84.6 - - - +
82B PRO* 1.4 78.7 - - - +
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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