Contacts of the helix formed by residues 486 - 495 (chain B) in PDB entry 1PTH
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 GLU 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B ARG* 6.1 2.9 - - - +
438B ARG* 5.6 5.2 - - - +
484B GLU* 3.3 10.7 + - + +
485B LYS* 1.3 76.0 - - - +
487B MET* 1.3 62.7 + - + +
489B ALA* 2.8 28.2 + - - +
490B GLU* 3.3 4.0 + - - +
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Residues in contact with MET 487 (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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180B ARG* 5.8 0.4 - - - +
181B PHE* 3.5 37.5 - - + +
436B GLY 4.7 13.5 - - - +
437B GLY* 5.6 1.8 - - - -
438B ARG* 3.6 34.5 - - + +
482B THR* 4.7 10.8 - - + +
484B GLU* 2.6 35.8 + - + +
486B GLU* 1.3 75.1 - - - +
488B ALA* 1.3 55.7 + - - +
490B GLU* 3.0 6.7 + - - +
491B LEU* 2.8 36.2 + - + +
509B LEU* 4.5 18.2 - - - +
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Residues in contact with ALA 488 (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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478B PHE* 3.1 37.7 - - - +
479B GLN* 3.5 9.3 + - - +
482B THR* 3.4 22.9 - - + -
484B GLU* 2.7 37.8 + - - +
485B LYS 3.9 3.8 - - - +
487B MET* 1.3 72.9 - - - +
489B ALA* 1.3 58.3 + - - +
491B LEU* 3.7 1.5 + - - -
492B GLU* 3.1 17.0 + - - +
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Residues in contact with ALA 489 (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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479B GLN* 4.3 7.2 - - - +
485B LYS 3.1 13.9 + - - +
486B GLU* 2.8 14.5 + - - +
488B ALA* 1.3 76.8 - - - +
490B GLU* 1.3 62.3 + - - +
492B GLU* 3.3 8.5 - - - +
493B GLU* 3.2 22.0 + - - +
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Residues in contact with GLU 490 (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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176B PHE* 3.5 19.6 - - - -
180B ARG* 2.5 49.0 + - - -
181B PHE* 3.7 15.2 - - + -
486B GLU 3.3 2.7 + - - +
487B MET* 3.0 11.9 + - - +
489B ALA* 1.3 76.1 - - - +
491B LEU* 1.3 65.9 + - - +
492B GLU 3.0 1.8 - - - -
493B GLU* 2.9 27.7 + - + +
494B LEU* 2.8 30.7 + - + +
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Residues in contact with LEU 491 (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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177B LEU* 4.6 2.7 - - + -
181B PHE* 3.5 30.7 - - + -
478B PHE* 3.1 31.9 - - + -
481B LEU* 4.6 8.3 - - + -
482B THR* 4.2 20.4 - - + -
487B MET* 2.8 23.0 + - + +
488B ALA 3.9 0.4 - - - +
490B GLU* 1.3 75.6 - - - +
492B GLU* 1.3 57.4 + - - +
494B LEU* 3.0 5.7 + - - -
495B TYR* 2.7 51.5 + - + +
501B LEU* 5.4 2.7 - - + -
509B LEU* 3.6 31.9 - - + -
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Residues in contact with GLU 492 (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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477B SER* 5.1 1.6 - - - -
478B PHE* 3.6 24.9 + - + -
479B GLN* 2.9 29.2 + - - +
488B ALA 3.1 13.2 + - - +
489B ALA* 3.3 13.0 - - - +
491B LEU* 1.3 77.5 - - - +
493B GLU* 1.3 60.0 + - - +
496B GLY* 2.9 34.3 + - - +
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Residues in contact with GLU 493 (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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168B LYS* 3.4 23.9 + - - -
489B ALA 3.2 8.7 + - - +
490B GLU* 2.9 39.3 + - + +
492B GLU* 1.3 78.5 - - - +
494B LEU* 1.3 65.5 + - + +
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Residues in contact with LEU 494 (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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168B LYS* 3.7 13.9 - - - +
170B GLN 5.2 0.3 - - - +
172B PRO* 3.8 35.2 - - + +
176B PHE* 3.5 36.3 - - + -
177B LEU* 4.0 8.7 - - + -
181B PHE* 3.7 28.5 - - + -
490B GLU* 2.8 24.8 + - + +
491B LEU* 3.4 6.5 - - - +
493B GLU* 1.3 83.4 - - + +
495B TYR* 1.3 63.7 + - + +
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Residues in contact with TYR 495 (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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167B GLY* 3.7 3.8 - - - -
168B LYS* 3.4 27.0 + - - +
171B LEU* 5.1 5.2 - - + -
172B PRO* 3.6 24.9 - - + -
177B LEU* 2.8 32.3 - - + +
478B PHE* 3.5 31.6 - + + -
491B LEU* 2.7 25.3 + - + -
494B LEU* 1.3 77.0 - - + +
496B GLY* 1.3 57.5 + - - +
497B ASP 3.3 9.8 + - - +
500B ALA* 3.5 19.3 - - + +
501B LEU* 3.8 20.2 - - + -
502B GLU* 2.8 44.5 + - + +
505B PRO* 3.8 10.6 - - + +
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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