Contacts of the helix formed by residues 382 - 394 (chain A) in PDB entry 1PS9
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 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLY 3.3 4.8 + - - -
381A ALA* 1.3 80.9 - - - +
383A PRO* 1.3 71.2 - - - +
384A ALA 3.0 4.3 + - - -
385A GLY 3.1 1.5 + - - +
386A LEU* 2.8 27.4 + - - +
409A GLY 3.9 0.2 - - - -
410A GLY 3.9 8.5 - - - -
462A ALA 5.1 0.4 + - - -
701A FAD 3.4 26.3 + - - -
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Residues in contact with PRO 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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382A GLY* 1.3 81.7 - - - +
384A ALA* 1.3 55.9 + - - +
386A LEU* 4.0 10.7 - - + +
387A ALA* 3.0 31.5 + - - +
409A GLY 3.8 12.1 - - - +
412A PHE* 4.4 23.1 - - + -
431A TYR* 4.5 3.9 + - + -
657A ALA* 4.7 1.8 - - + +
660A ALA* 4.4 3.8 - - + -
661A ILE* 3.6 30.9 - - + +
701A FAD 3.4 44.2 - - - +
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Residues in contact with ALA 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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383A PRO* 1.3 76.0 - - - +
385A GLY* 1.3 67.1 + - - +
387A ALA* 3.8 1.9 - - - +
388A PHE* 3.2 17.5 + - - +
462A ALA* 4.2 12.3 - - + -
646A ILE* 3.6 15.5 - - + +
647A GLY* 3.9 20.6 - - - +
660A ALA* 3.8 19.0 - - + +
664A GLY* 3.9 1.9 - - - -
701A FAD 2.9 27.8 + - - +
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Residues in contact with GLY 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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378A VAL* 3.7 17.7 - - - +
380A GLY 3.4 21.9 + - - -
382A GLY 3.1 4.6 + - - +
384A ALA* 1.3 79.6 - - - +
386A LEU* 1.3 52.8 + - - +
388A PHE* 3.1 3.5 + - - +
389A ALA* 2.7 37.9 + - - +
401A LEU* 4.3 1.6 - - - -
462A ALA* 3.6 8.2 - - - +
646A ILE* 4.5 1.3 - - - -
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Residues in contact with LEU 386 (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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381A ALA 3.2 20.8 - - - +
382A GLY 2.8 25.1 + - - +
383A PRO* 4.0 4.0 - - + +
385A GLY* 1.3 71.9 - - - +
387A ALA* 1.3 62.9 + - - +
389A ALA* 3.7 3.1 - - - +
390A ILE* 3.1 30.4 + - - +
401A LEU* 3.6 26.0 - - + -
408A ILE* 4.1 16.6 - - + -
409A GLY* 4.2 9.2 - - - +
412A PHE* 6.4 0.4 - - + -
428A LEU* 4.7 4.7 - - + -
431A TYR* 3.6 44.2 - - + -
435A ILE* 3.9 19.7 - - + -
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Residues in contact with ALA 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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383A PRO 3.0 21.0 + - - +
384A ALA 3.8 3.1 - - - +
386A LEU* 1.3 77.4 - - - +
388A PHE* 1.3 62.3 + - - +
390A ILE* 3.9 0.4 - - - +
391A ASN* 2.8 33.3 + - - +
431A TYR* 3.9 12.9 - - - +
661A ILE* 3.7 25.8 - - + +
664A GLY 4.4 2.0 - - - -
665A THR* 3.7 20.2 - - - +
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Residues in contact with PHE 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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376A LEU* 3.7 26.0 - - + -
378A VAL* 3.5 26.0 - - + -
384A ALA 3.2 10.5 + - - +
385A GLY* 3.1 6.8 + - - +
387A ALA* 1.3 80.0 - - - +
389A ALA* 1.3 52.5 + - - +
391A ASN 3.3 0.7 + - - -
392A ALA* 2.8 47.3 + - + +
399A VAL* 5.2 0.9 - - + -
460A ILE* 3.5 36.1 - - + -
646A ILE* 4.0 6.1 - - + -
664A GLY* 3.4 18.1 - - - +
667A LEU* 3.5 24.7 - - + -
668A ALA* 3.2 42.9 - - + +
671A ILE* 4.0 6.7 - - + -
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Residues in contact with ALA 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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378A VAL* 4.6 0.9 - - + -
385A GLY 2.7 22.6 + - - +
386A LEU* 3.7 3.6 - - - +
388A PHE* 1.3 75.9 - - - +
390A ILE* 1.3 61.0 + - + +
392A ALA 3.3 0.2 + - - -
393A ALA* 3.0 30.8 + - - +
399A VAL* 3.7 28.8 - - + +
401A LEU* 4.3 23.3 - - + -
440A VAL* 4.0 9.4 - - + -
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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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386A LEU* 3.1 15.6 + - - +
387A ALA 3.9 4.5 - - - +
389A ALA* 1.3 77.4 - - + +
391A ASN* 1.3 67.4 + - - +
394A ALA* 3.1 29.5 + - - +
430A TYR* 4.3 13.5 - - - +
431A TYR* 3.5 34.1 - - + +
434A MET* 3.8 40.4 - - + +
435A ILE* 4.0 17.9 - - + +
438A THR* 3.5 22.6 - - + +
440A VAL* 4.2 2.0 - - + -
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Residues in contact with ASN 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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358A ARG* 5.4 2.4 - - - -
367A ILE* 4.7 9.2 - - - +
387A ALA* 2.8 25.6 + - - +
388A PHE 3.3 1.0 + - - -
389A ALA 3.2 0.4 - - - -
390A ILE* 1.3 87.9 - - - +
392A ALA* 1.3 60.1 + - - +
394A ALA* 3.8 5.6 + - - +
395A ARG* 3.0 29.5 + - - +
665A THR* 3.7 29.2 + - - +
668A ALA* 3.4 18.6 - - + -
669A LEU* 4.2 16.5 - - + +
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Residues in contact with ALA 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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376A LEU* 4.2 9.0 - - + -
388A PHE* 2.8 39.1 + - + +
389A ALA 3.9 2.7 - - - +
391A ASN* 1.3 77.2 - - - +
393A ALA* 1.3 59.9 + - - +
395A ARG* 3.1 26.6 + - - +
397A HIS* 3.2 25.3 + - + +
399A VAL* 4.0 12.3 - - + -
668A ALA* 3.8 6.0 - - + +
671A ILE* 4.8 0.2 - - + -
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Residues in contact with ALA 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 ALA 3.0 17.6 + - - +
392A ALA* 1.3 73.3 - - - +
394A ALA* 1.3 60.2 + - - +
395A ARG 3.0 5.2 - - - -
396A GLY* 3.3 11.6 + - - -
397A HIS 3.4 15.1 - - - +
399A VAL* 3.8 9.2 - - + +
438A THR* 3.7 26.1 - - - +
439A GLY 5.0 0.7 - - - -
440A VAL* 3.6 24.5 - - + +
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Residues in contact with ALA 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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367A ILE* 5.3 7.2 - - + +
390A ILE 3.1 20.7 + - - +
391A ASN* 4.1 7.4 - - - +
392A ALA 3.2 0.4 - - - -
393A ALA* 1.3 76.9 - - - +
395A ARG* 1.3 60.6 + - + +
396A GLY 3.4 0.2 - - - -
438A THR* 3.8 16.1 - - + +
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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