Contacts of the strand formed by residues 376 - 381 (chain A) in PDB entry 1PJS
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 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A ALA* 3.7 7.2 - - - -
352A SER* 3.3 22.2 + - - +
354A ARG* 3.0 26.9 + - - +
370A ASN 3.1 20.1 + - - -
371A LEU* 3.2 19.0 + - - +
373A ALA 2.9 28.0 + - - +
374A GLU* 2.8 22.4 - - - +
375A LYS 1.4 82.8 - - - +
377A THR* 1.3 62.1 + - - +
378A LEU* 3.6 12.4 + - + +
403A MET* 4.8 2.6 - - - +
441A VAL 4.5 2.9 - - - +
442A GLY* 4.6 2.8 - - - -
354B ARG* 4.2 5.9 + - - -
367B ASP* 5.6 1.0 - - - +
370B ASN* 3.5 11.3 - - - +
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Residues in contact with THR 377 (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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344A LEU* 2.9 46.1 + - + +
350A ALA* 3.5 12.5 - - - +
352A SER 3.0 7.9 + - - +
353A VAL* 4.1 8.4 - - + +
354A ARG* 2.9 27.2 + - - +
376A GLN* 1.3 73.6 - - - +
378A LEU* 1.3 73.3 + - - +
379A VAL* 4.7 1.1 - - + -
440A ILE* 4.4 5.4 - - + -
441A VAL 3.7 9.0 - - - +
442A GLY* 4.8 2.3 - - - -
443A ARG 5.5 0.5 + - - -
444A VAL* 3.9 24.8 - - + +
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Residues in contact with LEU 378 (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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354A ARG* 3.6 28.3 - - + -
356A VAL* 5.8 0.2 - - + -
371A LEU* 3.0 49.1 - - + +
376A GLN* 3.6 17.3 - - + +
377A THR* 1.3 77.9 - - - +
379A VAL* 1.3 66.5 + - - +
380A PHE* 3.7 21.8 - - + -
394A LEU* 4.4 7.9 - - + -
399A MET* 4.9 2.9 - - - -
439A ILE 3.6 0.4 - - - +
440A ILE* 3.3 6.8 - - - +
441A VAL* 2.7 60.3 + - + +
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Residues in contact with VAL 379 (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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333A ALA* 3.6 27.6 - - + -
344A LEU* 3.8 29.2 - - + -
353A VAL* 4.8 5.6 - - + -
354A ARG 2.9 16.6 + - - +
355A LEU* 3.5 4.2 - - + -
356A VAL* 2.7 33.2 + - - +
377A THR* 4.7 3.4 - - + -
378A LEU* 1.3 79.0 - - - +
380A PHE* 1.3 57.3 + - - +
381A TYR* 3.8 7.5 + - + -
438A LEU* 3.1 29.6 - - + -
439A ILE 3.4 2.9 - - - +
440A ILE* 4.8 9.2 - - + -
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Residues in contact with PHE 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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356A VAL* 3.7 27.1 - - + -
357A THR 4.8 7.0 - - - -
358A GLY* 5.9 1.3 - - - -
366A LEU* 4.6 8.3 - - + -
368A TRP* 4.8 3.1 - + - -
371A LEU* 3.6 23.6 - - + -
378A LEU* 3.7 27.6 - - + -
379A VAL* 1.3 75.2 - - - +
381A TYR* 1.3 64.3 + - - +
382A MET 4.0 0.3 + - - -
383A GLY* 4.8 7.2 + - - +
390A ILE* 3.5 44.9 - - + -
394A LEU* 4.9 0.2 - - + -
437A ALA 4.4 0.9 - - - +
438A LEU* 2.9 22.6 - - - +
439A ILE* 2.8 46.9 + - + +
441A VAL* 4.2 10.3 - - + -
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Residues in contact with TYR 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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306A ILE* 4.5 2.0 - - + -
307A PHE* 3.7 24.2 - + + -
331A THR* 2.5 25.1 + - - -
332A ALA* 3.7 6.5 - - + -
333A ALA* 3.0 23.2 + - - +
355A LEU* 3.4 24.6 - - + +
356A VAL 2.9 17.0 + - - +
357A THR* 3.7 1.0 - - - -
358A GLY 3.2 16.1 + - - -
379A VAL* 3.8 23.6 - - + -
380A PHE* 1.3 78.3 - - - +
382A MET* 1.3 79.0 + - + +
383A GLY* 3.4 0.7 + - - -
438A LEU* 4.3 2.7 - - + -
501A SAH 3.1 62.8 - - + +
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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