Contacts of the helix formed by residues 478 - 484 (chain F) in PDB entry 1O01
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 GLY 478 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F TYR* 3.3 11.9 - - - -
132F TYR* 2.9 26.1 + - - -
461F ALA 2.6 19.2 + - - -
462F GLN 3.2 24.4 - - - -
464F PRO* 4.5 3.8 - - - -
477F LEU* 1.3 75.0 - - - +
479F GLU* 1.3 63.0 + - - +
480F TYR 3.2 0.4 - - - -
481F GLY 3.3 2.1 + - - -
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Residues in contact with GLU 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 3.6 26.2 + - + -
131F TYR* 3.5 4.0 + - - -
135F TRP* 3.5 39.2 - - + +
139F TYR* 4.1 23.2 - - + -
462F GLN 4.5 1.0 + - - -
478F GLY* 1.3 70.0 - - - -
480F TYR* 1.3 67.4 + - + +
482F LEU* 3.1 21.6 + - - +
483F GLN* 4.0 4.3 + - - +
140H HIS* 3.3 29.9 + - + -
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Residues in contact with TYR 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E LYS* 3.6 32.4 - - + +
144E ILE* 5.1 1.3 - - + -
154E THR* 2.8 23.5 + - + -
156E HIS* 2.6 37.3 + + - -
488E VAL* 3.7 27.1 - - + -
462F GLN 6.0 0.2 - - - -
464F PRO* 3.5 44.6 - - + -
475F ARG* 3.8 19.3 + - + +
478F GLY 3.2 0.2 - - - -
479F GLU* 1.3 82.6 - - + +
481F GLY* 1.3 60.5 + - - +
482F LEU 3.1 1.7 + - - -
483F GLN* 3.2 47.9 + - - +
484F ALA* 4.5 1.2 + - - +
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Residues in contact with GLY 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F TYR* 3.7 10.8 - - - -
181F PRO* 3.5 11.5 - - - +
475F ARG 3.6 15.5 - - - +
476F GLU* 4.2 1.6 - - - -
477F LEU 3.1 22.7 + - - -
478F GLY 3.3 0.4 + - - -
479F GLU 3.1 1.4 - - - -
480F TYR* 1.3 76.6 - - - +
482F LEU* 1.3 58.5 + - - +
483F GLN 3.5 0.2 - - - -
484F ALA* 4.6 2.8 + - - +
485F TYR* 3.3 26.2 - - - -
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Residues in contact with LEU 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F TYR* 3.7 32.5 - - + -
135F TRP* 3.6 38.1 - - + +
139F TYR* 3.5 42.6 - - + -
181F PRO* 4.0 10.8 - - + +
184F ALA* 4.6 2.7 - - + -
185F THR* 3.8 19.9 - - + +
479F GLU* 3.1 12.9 + - - +
481F GLY* 1.3 78.5 - - - +
483F GLN* 1.3 64.7 + - - +
484F ALA 3.4 1.1 - - - -
485F TYR* 3.1 17.9 + - - +
486F THR* 3.2 14.9 + - - -
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Residues in contact with GLN 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TYR* 4.9 4.9 + - - -
483E GLN* 3.9 38.6 - - - +
139F TYR* 3.3 21.7 + - - +
479F GLU* 4.6 2.5 - - + +
480F TYR* 3.2 44.7 + - - +
482F LEU* 1.3 77.7 - - - +
484F ALA* 1.3 62.3 + - - +
485F TYR 3.2 0.9 + - - -
486F THR* 3.3 20.7 + - - +
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Residues in contact with ALA 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F VAL* 4.0 6.8 - - - +
240F LYS* 3.6 31.7 - - - +
264F ARG* 5.3 2.7 - - + +
266F THR* 3.5 33.0 - - + +
475F ARG 5.7 4.7 - - - +
480F TYR 4.5 2.2 + - - +
481F GLY 4.6 1.7 + - - +
482F LEU 3.4 0.8 - - - -
483F GLN* 1.3 77.6 - - - +
485F TYR* 1.3 65.7 + - + +
486F THR 3.3 3.3 + - - +
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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