Contacts of the helix formed by residues 75 - 82 (chain B) in PDB entry 1OFY
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 THR 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A GLY 5.9 0.4 - - - +
243A SER 4.9 2.1 + - - +
246A THR* 3.7 28.4 - - + +
63B HIS* 4.1 1.8 - - - -
64B THR 3.3 6.3 - - - -
65B VAL 3.4 22.9 - - - +
66B GLU 3.6 18.2 - - - +
67B GLY* 4.3 1.1 - - - -
73B TYR 3.2 6.9 + - - +
74B ILE* 1.3 76.3 - - - +
76B LEU* 1.3 55.1 + - - +
77B ASP* 3.6 11.1 + - - +
78B ARG* 3.1 22.4 + - - +
79B ALA* 2.8 33.6 + - - +
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Residues in contact with LEU 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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16B MET* 5.9 2.2 - - + -
17B PHE 3.8 13.0 - - - +
18B PRO* 3.9 10.3 - - + -
19B VAL 4.0 4.7 - - - +
59B CYS* 5.3 0.9 - - + -
60B SER* 4.1 15.9 - - - +
63B HIS* 3.3 27.3 + - + +
64B THR 2.8 17.0 + - - +
65B VAL* 3.9 15.5 - - + +
75B THR* 1.3 70.8 - - - +
77B ASP* 1.3 63.4 + - - +
79B ALA* 3.2 0.9 + - - +
80B MET* 2.9 50.9 + - + +
1297B HEC 3.6 41.3 - - + +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A SER 3.3 25.4 - - - +
244A CYS* 3.9 6.6 - - - +
253A ASN* 5.2 2.3 + - - -
256A ARG* 2.7 28.5 + - - -
65B VAL* 5.3 0.8 + - - +
75B THR* 3.6 7.3 + - - +
76B LEU* 1.3 79.4 - - - +
78B ARG* 1.3 63.2 + - - +
81B HIS* 2.8 46.4 + - + +
1297B HEC 4.8 11.7 - - + +
1302B GOL 2.8 33.0 + - - -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASP* 5.4 3.4 - - - +
252A ALA* 3.6 25.5 + - - +
253A ASN* 4.7 16.0 + - - +
74B ILE* 3.6 26.4 - - + +
75B THR* 3.1 18.7 + - - +
77B ASP* 1.3 81.5 - - - +
79B ALA* 1.3 60.3 + - - +
81B HIS* 5.4 0.2 - - - -
82B ALA* 2.8 60.3 + - + +
83B THR 3.8 0.4 - - - +
84B ASN* 2.8 61.0 + - - +
1294B HEC 2.6 29.7 + - + +
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Residues in contact with ALA 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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63B HIS* 3.6 32.5 - - + +
74B ILE* 4.1 1.5 - - - +
75B THR 2.8 17.1 + - - +
76B LEU 3.2 3.3 + - - +
78B ARG* 1.3 79.2 - - - +
80B MET* 1.3 78.5 + - + +
96B SER* 3.2 24.8 - - - -
1294B HEC 3.6 22.0 - - + +
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Residues in contact with MET 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 MET* 4.1 13.2 - - - -
59B CYS* 3.9 17.0 - - + -
76B LEU* 2.9 24.9 + - + +
79B ALA* 1.3 91.6 - - + +
81B HIS* 1.3 64.6 + - - +
96B SER* 3.8 0.9 - - - -
97B CYS* 3.1 39.9 + - - +
98B VAL* 3.4 4.0 + - - +
1294B HEC 3.4 30.5 - - + -
1295B HEC 4.3 1.6 - - - -
1297B HEC 3.5 63.0 - - + +
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Residues in contact with HIS 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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77B ASP* 2.8 37.5 + - - +
78B ARG* 5.2 0.2 - - - -
80B MET* 1.3 80.0 - - + +
82B ALA* 1.3 68.3 + - - +
83B THR* 3.4 7.8 + - - +
96B SER* 3.8 1.3 - - - -
98B VAL* 3.6 20.9 - - + +
1297B HEC 1.9 105.1 + + + -
1302B GOL 3.4 24.3 + - - +
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Residues in contact with ALA 82 (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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78B ARG* 2.8 56.3 + - + +
81B HIS* 1.3 77.2 - - - +
83B THR* 1.3 59.4 + - - +
85B ILE* 3.9 18.6 - - + -
96B SER* 2.4 28.8 + - - -
99B SER* 3.4 9.5 + - - -
1294B HEC 4.3 5.2 - - + +
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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