Contacts of the helix formed by residues 264 - 268 (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 PRO 264 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1783 LEU* 5.2 0.2 - - + -
1803 LEU* 3.7 18.8 - - + -
2603 THR 3.7 7.0 - - - +
2613 LEU 4.7 0.9 - - - +
2623 PHE 3.6 6.7 - - - +
2633 GLN* 1.3 84.2 - - - +
2653 SER* 1.4 57.0 + - - +
2663 PHE 3.2 3.6 - - - -
2673 ILE* 3.0 22.7 + - + +
2693 MET* 2.9 43.5 + - + +
2713 SER* 3.5 26.5 - - - +
2723 ALA* 3.6 15.5 - - - +
2733 GLY* 4.0 9.2 - - - +
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Residues in contact with SER 265 (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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2633 GLN* 3.6 19.6 - - - +
2643 PRO* 1.4 73.7 - - - +
2663 PHE* 1.4 62.3 + - - +
2673 ILE 3.0 5.9 + - - -
2683 GLY* 3.4 10.3 + - - +
2693 MET 3.3 13.1 + - - +
2703 GLU* 5.4 4.7 - - - -
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Residues in contact with PHE 266 (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* 3.1 36.5 - + + +
1913 LYS* 5.0 3.6 + - - -
2273 MET* 5.6 4.9 - - + -
2563 ARG* 3.3 28.3 - - + -
2593 GLU* 3.6 38.8 - - + -
2603 THR* 3.9 16.2 - - + -
2633 GLN* 3.6 37.0 - - + +
2653 SER* 1.4 78.0 - - - +
2673 ILE* 1.3 63.0 + - - +
2683 GLY 3.7 0.4 - - - -
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Residues in contact with ILE 267 (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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1732 HIS* 4.6 10.0 - - - +
1803 LEU* 3.8 26.0 - - + -
1843 ASP* 5.0 15.3 - - + +
1853 LEU* 5.7 0.4 - - + -
1883 TYR* 3.5 31.2 - - + -
2603 THR* 3.6 24.0 - - + -
2643 PRO 3.0 15.7 + - - +
2663 PHE* 1.3 86.7 - - - +
2683 GLY* 1.3 63.9 + - - +
2693 MET* 3.0 28.1 + - + +
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Residues in contact with GLY 268 (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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1732 HIS* 4.1 32.7 + - - +
2653 SER* 3.4 12.1 + - - -
2663 PHE 3.7 0.6 - - - -
2673 ILE* 1.3 76.7 - - - +
2693 MET* 1.3 62.5 + - - +
2703 GLU* 3.9 9.1 + - - +
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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