Contacts of the strand formed by residues 398 - 403 (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 GLN 398 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LYS 3.0 13.0 + - - +
375A ASN* 2.5 37.4 + - - +
376A LEU* 2.8 30.0 + - - +
396A GLY 3.7 1.6 + - - +
397A HIS* 1.3 72.5 - - - +
399A VAL* 1.3 66.7 + - - +
400A THR* 5.0 4.7 - - - +
441A THR* 5.3 6.5 - - + +
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Residues in contact with VAL 399 (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* 3.8 8.7 - - + +
378A VAL* 3.8 27.6 - - + -
388A PHE* 5.2 0.4 - - + -
389A ALA* 3.7 36.8 - - + +
392A ALA* 4.0 11.9 - - + -
393A ALA* 3.8 19.4 - - + +
397A HIS* 3.7 6.4 + - + +
398A GLN* 1.3 81.2 - - - +
400A THR* 1.3 62.2 + - - +
401A LEU 4.0 0.7 - - - +
439A GLY 4.8 1.6 + - - +
440A VAL* 3.9 14.2 - - + +
441A THR* 2.7 36.6 + - - +
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Residues in contact with THR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASN* 4.7 2.1 + - - -
376A LEU 3.2 6.7 + - - -
378A VAL 3.1 22.1 + - - -
398A GLN* 5.0 4.3 - - - +
399A VAL* 1.3 75.5 - - - +
401A LEU* 1.3 59.2 - - - +
402A PHE* 3.4 40.3 - - + -
441A THR* 3.2 24.7 - - + +
443A LYS* 4.2 18.4 - - + +
456A PHE* 3.5 28.0 - - + -
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Residues in contact with LEU 401 (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* 3.5 26.5 - - + +
380A GLY 3.4 26.9 - - - +
381A ALA* 4.1 10.3 - - + -
385A GLY 4.3 6.5 - - - -
386A LEU* 3.6 30.5 - - + -
389A ALA* 4.3 15.5 - - + -
399A VAL* 4.0 1.6 - - + -
400A THR* 1.3 70.6 - - - +
402A PHE* 1.3 60.5 + - - +
435A ILE* 4.1 8.5 - - + -
440A VAL* 4.0 14.8 - - + +
441A THR 3.0 8.1 + - - +
442A LEU* 3.7 21.6 - - + +
443A LYS* 2.9 28.4 + - - +
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Residues in contact with PHE 402 (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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377A ALA* 4.4 5.8 - - + -
378A VAL 3.0 16.2 + - - +
379A VAL* 4.8 5.8 - - + -
380A GLY* 2.9 29.4 + - - -
381A ALA 3.7 0.2 + - - -
400A THR* 3.4 37.2 - - + -
401A LEU* 1.3 75.3 - - - +
403A ASP* 1.3 64.3 + - - +
443A LYS* 3.3 34.8 - - + +
446A HIS* 4.0 11.0 - + + +
448A VAL* 3.4 34.8 - - + -
453A LEU* 3.3 35.9 - - + -
456A PHE* 3.9 22.0 - + - -
701A FAD 4.9 1.1 - - - -
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Residues in contact with ASP 403 (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* 2.7 41.7 + - + +
401A LEU 5.5 0.2 - - - +
402A PHE* 1.3 77.3 - - - +
404A ALA* 1.3 59.4 + - - +
405A HIS* 2.8 30.8 + - - +
407A GLU 4.1 5.9 - - - +
410A GLY 4.9 0.5 + - - -
443A LYS 3.2 5.3 + - - -
444A LEU* 3.4 13.8 - - + -
445A ASN 2.8 25.5 + - - -
446A HIS 3.1 7.1 + - - -
701A FAD 2.7 43.9 + - - -
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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