Contacts of the helix formed by residues 379 - 384 (chain A) 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 MET 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ILE* 4.1 18.6 - - + +
148A TYR* 3.5 40.9 - - + +
149A THR 2.7 12.9 + - - +
150A ARG* 3.7 51.6 - - + +
219A GLY* 5.0 3.1 - - - -
377A ILE 3.7 1.6 + - - -
378A ALA* 1.3 70.9 - - - +
380A GLU* 1.3 67.8 + - - +
382A ASN* 3.0 23.6 + - - +
383A GLN* 3.2 13.9 + - - +
458A LEU* 3.6 34.3 - - + +
460A LEU* 3.9 8.1 - - + -
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ARG* 3.2 17.2 - - - +
151A ILE* 2.7 36.6 + - - +
152A LEU 3.1 5.9 + - - -
378A ALA* 3.6 8.5 - - - +
379A MET* 1.3 81.2 - - + +
381A PHE* 1.3 61.0 + - - +
383A GLN* 3.3 5.3 + - - -
384A LEU* 3.1 21.4 + - - +
460A LEU* 4.6 9.2 - - + -
466A TYR* 2.6 44.8 + - + +
503A PHE* 3.4 25.4 - - + -
529A PHE* 4.3 11.9 - - + -
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Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 4.0 15.3 - + - -
210A PHE* 3.2 29.6 - + - -
377A ILE* 4.4 15.3 - - + -
378A ALA* 2.9 20.1 + - + +
380A GLU* 1.3 78.1 - - - +
382A ASN* 1.3 61.7 + - - +
384A LEU* 4.1 13.2 - - + -
385A TYR* 3.3 49.5 + + - +
526A GLY 4.3 4.5 - - - -
529A PHE* 3.2 55.8 - + + -
530A 0AH 4.1 17.7 - - - -
533A GLY* 6.5 0.4 - - - -
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Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 4.0 11.7 + - + -
210A PHE* 3.2 43.0 - - + +
212A THR* 4.8 1.3 - - - -
378A ALA 3.0 7.6 + - - +
379A MET* 3.0 15.7 + - - +
381A PHE* 1.3 75.6 - - - +
383A GLN* 1.3 62.2 + - - +
385A TYR* 3.2 11.3 + - - +
386A HIS* 2.8 39.9 + - - -
454A GLU* 4.4 12.8 - - - +
601A HEM 2.9 31.3 + - - +
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A MET 3.5 13.2 - - - +
380A GLU 3.5 6.5 - - - +
382A ASN* 1.3 77.6 + - - +
384A LEU* 1.3 53.2 + - - +
386A HIS* 2.7 45.7 + - - +
451A VAL* 3.8 32.9 + - - +
454A GLU* 4.2 18.8 + - - +
455A SER* 3.4 27.3 - - - +
458A LEU* 5.0 5.1 - - + +
460A LEU* 3.8 24.8 - - + +
503A PHE* 4.0 12.0 - - + -
504A TYR* 3.9 22.8 + - + +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A GLU 3.1 12.2 + - - +
381A PHE* 3.9 15.7 - - + +
383A GLN* 1.3 79.5 - - - +
385A TYR* 1.3 64.5 + - + +
386A HIS 3.2 3.2 + - - -
387A TRP* 3.0 29.9 + - + +
503A PHE* 4.3 3.5 - - + -
504A TYR* 5.2 3.3 - - - -
507A LEU* 4.0 24.0 - - + +
508A LEU* 6.0 0.2 - - - +
522A MET* 3.8 26.5 - - - +
525A MET* 3.7 16.8 - - + +
526A GLY* 3.5 40.2 - - - +
529A PHE* 4.2 12.8 - - + -
530A 0AH 5.0 2.0 - - + -
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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