Contacts of the helix formed by residues 252 - 257 (chain 3) in PDB entry 1O1F
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 ASN 252 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1963 ARG* 3.5 18.9 + - - -
2273 MET* 5.7 1.6 - - - -
2303 ALA* 3.3 42.7 + - + +
2333 SER* 5.0 2.2 + - - -
2363 LEU* 3.9 11.4 - - - +
2373 GLU* 4.0 10.0 + - - +
2513 GLY* 1.3 75.0 - - - +
2533 GLU* 1.4 58.8 + - - +
2543 ARG* 2.8 16.4 + - - +
2553 PHE* 3.1 37.6 + - + -
2563 ARG* 3.8 13.2 - - - +
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Residues in contact with GLU 253 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1893 LEU* 4.6 6.1 - - + +
1923 ILE* 3.6 28.2 - - + +
1933 LEU* 4.1 16.6 - - + -
1963 ARG* 3.3 39.9 + - - +
2503 ILE* 3.5 12.7 - - + -
2513 GLY 3.0 28.8 + - - -
2523 ASN* 1.4 69.6 + - - +
2543 ARG* 1.3 65.7 + - - +
2553 PHE 3.1 0.9 - - - -
2563 ARG* 3.0 44.8 + - - +
2573 CYS* 3.1 17.2 + - - +
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Residues in contact with ARG 254 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1893 LEU* 5.7 0.2 - - - -
2153 LYS 5.4 0.4 + - - -
2163 LEU* 2.9 33.6 + - + +
2173 CYS* 2.9 30.7 - - - +
2183 TYR* 3.1 59.1 + - + +
2363 LEU 3.1 20.9 + - - -
2383 LYS* 3.5 32.7 - - - +
2503 ILE* 3.6 23.9 - - + +
2513 GLY 3.1 27.4 - - - +
2523 ASN 3.5 1.1 - - - +
2533 GLU* 1.3 73.8 - - - +
2553 PHE* 1.4 61.1 + - + +
2583 PRO* 3.7 1.7 - - - +
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Residues in contact with PHE 255 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2183 TYR* 3.4 23.1 - - + +
2203 ALA* 4.4 3.1 - - + -
2233 PHE* 3.0 48.7 - + + -
2263 GLU* 3.4 54.7 - - + -
2273 MET* 3.3 34.8 - - + -
2303 ALA* 4.8 1.8 - - + -
2363 LEU* 4.5 9.4 - - + -
2513 GLY 5.1 1.1 - - - -
2523 ASN* 3.1 30.5 + - - -
2533 GLU 3.1 0.8 - - - -
2543 ARG* 1.4 79.1 - - + +
2563 ARG* 1.3 69.4 + - + +
2573 CYS 3.1 2.5 - - - -
2583 PRO* 3.6 1.5 - - - +
2593 GLU* 3.1 18.2 + - - +
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Residues in contact with ARG 256 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1883 TYR* 3.3 22.3 + - - +
1913 LYS* 5.9 0.2 - - - +
1923 ILE* 3.6 44.0 + - + +
1953 GLU* 3.7 13.5 + - - -
1963 ARG* 6.2 0.2 - - - +
2273 MET* 3.7 33.5 - - + +
2523 ASN* 3.8 9.0 - - - +
2533 GLU* 3.0 45.9 + - - +
2553 PHE* 1.3 84.2 - - + +
2573 CYS* 1.3 60.0 + - - +
2593 GLU* 4.0 7.4 - - - -
2603 THR* 3.4 2.4 + - - -
2663 PHE* 3.3 21.3 - - + -
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Residues in contact with CYS 257 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853 LEU* 3.2 40.5 - - - +
1883 TYR* 3.8 10.0 - - + -
1893 LEU* 3.8 17.0 - - + -
1923 ILE* 4.0 8.2 - - + +
2133 LYS* 4.2 17.5 - - - -
2173 CYS* 4.2 9.2 - - - -
2533 GLU 3.1 13.5 + - - +
2553 PHE 3.1 0.8 - - - -
2563 ARG* 1.3 75.1 - - - +
2583 PRO* 1.3 68.5 - - + +
2603 THR* 2.6 27.7 + - - -
3063 TYR* 5.1 0.4 - - - -
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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