Contacts of the helix formed by residues 478 - 484 (chain B) in PDB entry 1O04
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B TYR* 3.3 15.5 - - - -
132B TYR* 2.7 30.7 + - - -
461B ALA 2.7 15.2 + - - -
462B GLN 3.3 24.1 - - - -
464B PRO* 4.7 3.8 - - - -
477B LEU* 1.3 71.6 - - - +
479B GLU* 1.3 65.5 + - - -
480B TYR* 3.1 1.1 - - - -
481B GLY 3.3 1.7 + - - -
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Residues in contact with GLU 479 (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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142A LYS* 3.6 24.9 + - - -
131B TYR* 3.5 4.6 + - - -
135B TRP* 3.5 39.3 - - + +
139B TYR* 4.0 25.3 - - + -
462B GLN 4.6 1.0 + - - -
478B GLY* 1.3 73.8 - - - -
480B TYR* 1.3 65.3 + - + +
482B LEU* 3.0 22.0 + - - +
483B GLN* 4.1 3.8 + - - +
140D HIS* 3.2 33.2 + - + +
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Residues in contact with TYR 480 (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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142A LYS* 3.6 36.5 - - + +
144A ILE* 5.0 1.6 - - + -
154A THR* 2.9 23.1 + - + -
156A HIS* 2.7 35.2 + + - -
488A VAL* 3.7 25.8 - - + -
462B GLN 5.7 0.2 - - - -
464B PRO* 3.4 40.2 - - + -
475B ARG* 3.9 18.6 + - + +
477B LEU 4.0 5.2 - - - +
479B GLU* 1.3 82.9 - - - +
481B GLY* 1.3 60.0 + - - +
483B GLN* 3.1 49.0 + - - +
484B ALA 4.6 1.0 + - - -
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Residues in contact with GLY 481 (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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132B TYR* 3.6 10.3 - - - -
181B PRO* 3.4 12.7 - - - +
475B ARG 3.6 16.5 + - - +
476B GLU* 4.2 1.3 - - - -
477B LEU 3.0 23.3 + - - -
478B GLY 3.3 0.2 + - - -
479B GLU 3.1 1.2 - - - -
480B TYR* 1.3 75.3 - - - +
482B LEU* 1.3 58.7 + - - +
483B GLN 3.4 0.2 - - - -
484B ALA* 4.5 2.7 + - - +
485B TYR* 3.3 26.0 - - - -
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Residues in contact with LEU 482 (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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132B TYR* 3.6 33.0 - - + -
135B TRP* 3.6 38.1 - - + +
139B TYR* 3.5 42.4 - - + -
181B PRO* 4.0 11.4 - - + -
184B ALA* 4.5 2.9 - - + -
185B THR* 3.8 21.5 - - + +
479B GLU* 3.0 14.2 + - - +
481B GLY* 1.3 77.6 - - - +
483B GLN* 1.3 64.1 + - - +
484B ALA 3.3 1.1 - - - -
485B TYR* 3.1 12.1 + - - +
486B THR* 3.1 19.5 + - - -
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Residues in contact with GLN 483 (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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139A TYR* 5.0 3.8 + - - -
483A GLN* 3.6 38.6 - - - +
488A VAL* 6.0 0.5 - - - +
139B TYR* 3.3 21.5 + - - +
479B GLU* 4.5 2.3 - - - +
480B TYR* 3.1 44.4 + - - +
482B LEU* 1.3 77.1 - - - +
484B ALA* 1.3 62.2 + - - +
485B TYR 3.2 1.2 + - - -
486B THR* 3.3 22.2 + - - +
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Residues in contact with ALA 484 (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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159B VAL* 3.9 6.1 - - - +
240B LYS* 3.6 31.8 - - - +
264B ARG* 5.4 3.0 - - + +
266B THR* 3.6 31.4 - - + +
475B ARG 5.8 3.8 - - - +
480B TYR 4.6 1.6 + - - +
481B GLY 4.5 2.9 + - - +
482B LEU 3.3 0.4 - - - -
483B GLN* 1.3 78.4 - - + +
485B TYR* 1.3 65.9 + - + +
486B THR 3.4 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