Contacts of the strand formed by residues 382 - 388 (chain A) in PDB entry 6PAU
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 ILE 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A TRP* 3.8 29.2 - - + +
374A TRP 3.5 17.0 - - - +
375A PHE 4.2 3.6 - - - +
376A LEU 3.5 10.5 - - - +
377A PRO* 3.4 4.0 - - - +
378A ARG* 2.9 55.2 + - + +
381A ILE* 1.3 80.1 - - + +
383A ASP* 1.3 78.3 + - - +
384A THR* 4.1 12.6 - - - +
399A SER* 4.4 0.9 - - - -
400A PHE 3.6 15.0 - - - +
401A TYR* 4.3 0.9 - - + -
422A PHE* 3.7 29.4 - - + -
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Residues in contact with ASP 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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377A PRO* 4.9 6.7 - - - +
378A ARG 5.6 0.9 - - - -
379A GLU* 5.8 2.8 - - - -
380A HIS 5.2 5.8 + - - -
382A ILE* 1.3 80.0 + - - +
384A THR* 1.3 64.4 + - - +
385A PHE* 4.1 12.6 - - + -
399A SER* 3.1 5.2 - - - -
400A PHE* 2.9 66.5 + - + +
402A THR* 4.4 11.4 + - - -
445A LYS* 3.3 31.3 + - - +
447A PHE* 5.0 1.9 - - - -
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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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340A PRO* 3.5 5.5 - - - +
341A MET* 2.8 48.1 + - + +
349A VAL* 5.6 0.4 - - + -
375A PHE* 2.6 39.8 + - + +
377A PRO* 4.1 8.6 - - - +
382A ILE* 4.1 2.5 + - - +
383A ASP* 1.3 76.3 + - - +
385A PHE* 1.3 70.3 + - - +
386A VAL* 4.5 2.7 - - + -
397A PHE* 4.1 19.7 - - + -
398A LEU 3.3 10.5 - - - +
399A SER* 3.6 8.3 - - - -
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Residues in contact with PHE 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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338A LEU* 3.9 20.6 - - + +
339A ARG* 3.4 11.0 - - - +
340A PRO* 3.6 37.5 - - + -
383A ASP* 4.1 24.0 - - + -
384A THR* 1.3 79.9 - - - +
386A VAL* 1.3 61.9 + - - +
397A PHE* 3.0 4.7 - - - +
398A LEU* 2.8 52.6 + - + +
400A PHE* 4.8 2.2 - + - -
441A LEU* 3.7 37.7 - - + -
445A LYS* 4.0 22.0 - - - -
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Residues in contact with VAL 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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337A GLY 3.2 2.4 - - - +
338A LEU* 3.3 3.7 - - - +
339A ARG* 2.8 74.3 + - + +
340A PRO 4.3 0.7 - - - +
341A MET* 3.8 26.5 - - + -
345A ASP* 3.8 3.8 - - - +
349A VAL* 4.1 14.6 - - + -
352A LEU* 6.3 0.2 - - + -
384A THR* 4.5 1.6 - - + -
385A PHE* 1.3 76.8 - - - +
387A VAL* 1.3 64.5 + - - +
388A GLU 4.7 0.9 - - - +
394A LEU* 4.0 18.2 - - + -
396A ASP 3.4 7.4 - - - +
397A PHE* 3.8 13.0 - - + -
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Residues in contact with VAL 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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335A THR* 3.9 13.9 - - + -
336A SER 3.5 23.1 - - - +
337A GLY 3.5 2.7 - - - -
338A LEU* 3.6 24.0 - - + -
386A VAL* 1.3 71.5 - - - +
388A GLU* 1.3 62.8 + - - +
389A SER* 5.5 1.1 - - - -
394A LEU* 3.4 4.7 - - - -
395A THR* 2.9 38.6 + - - +
396A ASP* 2.8 40.2 + - + +
429A THR* 3.9 8.3 - - - +
434A LEU* 4.2 7.6 - - + -
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Residues in contact with GLU 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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336A SER 4.4 1.9 - - - +
337A GLY* 3.0 31.1 + - - +
339A ARG* 2.8 35.7 + - - +
344A LYS* 4.9 7.7 + - - -
386A VAL 3.9 1.0 - - - -
387A VAL* 1.3 71.4 - - - +
389A SER* 1.3 73.6 + - - +
390A PRO* 4.8 1.6 - - - +
392A GLY* 3.7 29.5 - - - +
393A LYS 3.6 3.4 - - - -
394A LEU* 4.0 10.8 - - + -
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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