Contacts of the strand formed by residues 366 - 372 (chain A) in PDB entry 3APO
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 ARG 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A HIS 5.7 0.2 - - - +
365A HIS* 1.3 73.5 + - - +
367A TRP* 1.3 70.5 + - - +
394A GLU* 2.9 47.9 + - - -
395A HIS* 3.7 20.4 + - + +
396A ILE* 3.5 12.5 - - + +
397A GLN* 3.0 22.3 + - - +
423A PHE 3.2 11.0 - - - +
424A LYS* 4.3 15.3 - - - +
425A GLY* 5.2 0.4 - - - -
451A VAL* 3.8 40.4 + - + +
452A ASN* 3.9 10.7 + - - -
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Residues in contact with TRP 367 (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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351A GLU* 5.4 3.1 - - - -
353A LEU* 5.5 0.7 - - + -
358A LEU* 6.1 0.2 - - + -
361A ARG* 2.9 64.4 + - + -
362A LEU* 3.7 26.5 - - + -
365A HIS* 3.1 44.1 - + + +
366A ARG* 1.3 76.6 - - - +
368A LEU* 1.3 60.4 + - - +
369A VAL* 3.8 10.2 + - + -
396A ILE* 4.0 4.5 - - - -
397A GLN* 3.2 59.5 - - + -
399A VAL* 4.1 25.4 - - + -
421A ALA 3.8 0.5 - - - +
422A VAL* 3.2 2.9 - - - -
423A PHE* 2.8 38.7 + - - +
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Residues in contact with LEU 368 (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 TRP* 1.3 71.9 - - - +
369A VAL* 1.3 60.4 + - - +
387A LEU* 3.7 28.0 - - + -
391A LEU* 3.6 25.6 - - + -
396A ILE* 3.7 12.0 - - + +
397A GLN 2.8 11.2 + - - +
398A VAL* 3.5 13.5 - - + +
399A VAL* 2.9 27.3 + - - +
420A LEU* 3.5 31.2 - - + -
421A ALA 3.4 9.2 - - - +
422A VAL* 4.0 15.9 - - + +
443A ILE* 4.0 10.1 - - + -
446A PHE* 4.4 8.5 - - + -
447A ALA* 4.4 6.7 - - + -
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Residues in contact with VAL 369 (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 LEU* 4.3 12.3 - - + -
362A LEU* 4.4 0.2 - - + -
367A TRP* 3.9 10.8 - - + -
368A LEU* 1.3 78.2 - - - +
370A PHE* 1.3 62.8 + - - +
371A PHE* 3.5 35.7 + - + -
399A VAL* 3.5 22.7 - - + +
401A PHE* 4.1 18.2 - - + -
419A SER 3.5 1.2 - - - +
420A LEU* 3.4 7.1 - - - -
421A ALA 2.6 39.7 + - - +
423A PHE* 3.8 24.5 - - + -
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Residues in contact with PHE 370 (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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350A PHE* 3.5 31.6 - + + -
368A LEU* 4.7 0.2 - - + -
369A VAL* 1.3 68.6 - - - +
371A PHE* 1.3 60.3 + - - +
372A HIS* 3.7 4.0 + - + +
380A ASN* 3.8 21.8 - - - -
384A LEU* 3.9 24.0 - - + -
387A LEU* 3.6 27.4 - - + -
398A VAL* 3.9 9.0 - - + -
399A VAL 2.9 19.1 + - - -
400A ARG* 3.2 15.1 - - + +
401A PHE 2.7 31.6 + - - +
419A SER 3.7 4.3 - - - -
420A LEU* 3.6 37.5 - - + -
438A LYS* 5.4 2.0 - - + -
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Residues in contact with PHE 371 (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 LEU* 4.5 10.5 - - + -
369A VAL* 3.7 26.5 - - + -
370A PHE* 1.3 72.7 - - - +
372A HIS* 1.3 61.2 + - - +
401A PHE* 3.5 27.4 - + + -
403A CYS* 3.9 9.9 - - - -
409A ILE* 4.6 0.9 - - + -
410A CYS* 3.7 23.8 - - - -
413A LEU* 4.0 21.5 - - + -
415A VAL* 3.9 24.7 - - + -
418A PRO* 3.2 7.2 - - - +
419A SER* 2.7 43.9 + - - +
421A ALA* 3.8 26.9 - - + -
423A PHE* 4.0 14.1 - + - -
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Residues in contact with HIS 372 (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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352A LEU* 4.1 1.8 - - + +
370A PHE* 3.7 10.0 + - + +
371A PHE* 1.3 75.6 - - - +
373A PHE* 1.3 69.9 + - - +
374A GLY 3.8 25.6 - - - -
400A ARG* 3.3 44.6 + - + +
401A PHE 3.0 25.2 + - - +
402A ASP* 3.6 15.2 + - - +
403A CYS* 2.8 28.9 + - - +
418A PRO* 4.4 9.9 - - + -
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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