Contacts of the helix formed by residues 383 - 394 (chain A) in PDB entry 2YPT
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 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A TRP* 3.5 45.5 - - + +
119A GLU* 3.7 9.6 - - + +
373A PHE* 3.3 17.2 - - + -
378A PHE* 4.0 15.3 - - + -
381A SER* 3.4 21.5 - - - +
382A GLN* 1.4 82.7 - - - +
384A THR* 1.4 59.2 + - - +
386A ILE* 3.7 18.2 - - + +
387A GLY* 3.0 22.5 + - - -
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Residues in contact with THR 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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119A GLU* 3.1 22.6 + - - -
186A LEU* 3.8 20.6 - - + +
189A ILE* 3.7 40.4 - - + -
190A LYS* 3.6 18.3 - - + +
363A PHE* 4.6 2.4 - - + -
367A ILE* 4.9 11.5 - - + +
382A GLN 3.8 1.7 + - - -
383A PRO* 1.4 68.1 - - - +
385A LEU* 1.4 60.4 + - - +
387A GLY* 3.1 4.1 + - - -
388A LEU* 3.0 28.0 + - + +
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Residues in contact with LEU 385 (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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102A TRP* 4.2 5.2 - - + -
119A GLU* 4.3 1.6 + - - -
123A SER* 3.5 43.7 - - - +
126A PHE* 3.7 26.9 - - + -
127A LEU* 3.8 28.0 - - + -
182A SER* 5.1 4.7 - - - +
185A LEU* 6.4 0.7 - - + -
186A LEU* 3.6 28.6 - - + +
383A PRO 3.6 0.4 - - - -
384A THR* 1.4 76.5 - - - +
386A ILE* 1.3 57.7 + - - +
388A LEU* 3.3 16.4 + - + +
389A LEU* 3.1 31.7 + - + +
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.9 4.5 - - + -
102A TRP* 3.7 16.8 - - + -
126A PHE* 3.7 34.3 - - + -
373A PHE* 4.2 7.2 - - + -
378A PHE* 3.6 53.8 - - + -
383A PRO* 3.7 23.9 - - + +
384A THR 3.3 0.4 - - - -
385A LEU* 1.3 72.7 - - - +
387A GLY* 1.3 55.1 + - - +
389A LEU* 3.1 13.3 + - + +
390A ILE* 2.8 49.5 + - + +
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Residues in contact with GLY 387 (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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363A PHE* 3.5 12.0 - - - -
367A ILE* 5.4 1.6 - - - -
372A LEU* 5.8 0.2 - - - -
373A PHE* 3.7 24.7 - - - -
383A PRO 3.0 10.7 + - - -
384A THR* 3.1 5.8 + - - -
386A ILE* 1.3 76.5 - - - +
388A LEU* 1.3 54.6 + - - +
390A ILE* 4.8 2.9 - - - -
391A ILE* 3.1 39.2 + - - +
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Residues in contact with LEU 388 (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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185A LEU* 4.2 18.6 - - + -
186A LEU* 4.4 9.2 - - + -
189A ILE* 4.1 22.7 - - + -
360A PHE* 4.5 8.7 - - + -
363A PHE* 3.6 20.2 - - + -
384A THR 3.0 20.2 + - - +
385A LEU* 3.4 22.0 - - + +
387A GLY* 1.3 75.0 - - - +
389A LEU* 1.3 58.3 + - + +
392A PHE* 3.0 59.0 + - + +
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Residues in contact with LEU 389 (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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98A ILE* 5.2 4.9 - - + -
126A PHE* 4.0 17.0 - - + -
127A LEU* 6.0 3.4 - - + -
385A LEU* 3.1 28.7 + - + +
386A ILE* 3.1 29.1 + - + +
388A LEU* 1.3 74.7 - - + +
390A ILE* 1.3 61.7 + - + +
393A GLN* 3.0 41.2 + - + +
394A PHE* 3.7 10.0 - - + -
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Residues in contact with ILE 390 (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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372A LEU* 3.8 28.3 - - + +
373A PHE* 4.1 16.4 - - + -
376A PHE* 3.6 52.0 - - + -
378A PHE* 4.3 3.8 - - + -
386A ILE* 2.8 41.5 + - + +
387A GLY* 4.3 3.6 - - - +
389A LEU* 1.3 72.5 - - + +
391A ILE* 1.3 57.9 + - - +
394A PHE* 3.0 22.8 + - + +
395A ILE* 3.0 33.4 + - + -
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Residues in contact with ILE 391 (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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363A PHE* 3.7 31.0 - - + +
366A LEU* 3.8 22.0 - - + +
367A ILE* 3.8 29.8 - - + +
372A LEU* 3.9 23.3 - - + -
373A PHE* 5.4 0.2 - - + -
387A GLY* 3.1 22.0 + - - +
390A ILE* 1.3 74.4 - - - +
392A PHE* 1.3 58.5 + - - +
395A ILE* 3.4 10.3 + - + -
396A PHE* 2.9 64.8 + - + -
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Residues in contact with PHE 392 (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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356A SER* 5.9 1.1 - - - -
359A CYS* 3.6 30.3 - - + -
360A PHE* 4.1 30.3 - + - -
363A PHE* 3.5 44.2 - + + -
388A LEU* 3.0 42.7 + - + +
391A ILE* 1.3 76.2 - - - +
393A GLN* 1.3 56.7 + - + +
396A PHE* 3.6 16.2 - + - +
400A ASN* 3.0 26.9 + - - -
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Residues in contact with GLN 393 (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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389A LEU* 3.0 26.8 + - + +
392A PHE* 1.3 77.7 - - + +
394A PHE* 1.4 76.4 + - + +
397A SER* 2.9 15.3 + - - -
400A ASN* 4.8 2.6 + - - +
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Residues in contact with PHE 394 (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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23A VAL* 3.7 38.7 - - + +
27A SER* 5.3 4.3 - - - -
93A LEU* 3.8 32.8 - - + -
98A ILE* 4.8 11.4 - - + -
376A PHE* 3.7 25.4 - + + -
389A LEU* 3.7 22.4 - - + -
390A ILE* 3.0 22.2 + - + +
392A PHE 3.6 0.2 - - - -
393A GLN* 1.4 90.9 - - + +
395A ILE* 1.3 65.2 + - - +
396A PHE 3.4 1.3 - - - -
397A SER* 3.0 21.6 + - - -
398A PRO* 4.4 1.7 - - - +
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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