Contacts of the strand formed by residues 368 - 375 (chain A) in PDB entry 6MBZ
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A PRO 3.9 0.4 + - - -
367A PRO* 1.3 73.4 - - - +
369A VAL* 1.3 59.8 + - - +
370A LYS 4.4 0.3 + - - -
400A CYS* 6.3 2.9 - - - -
401A CYS 3.5 11.7 - - - +
402A VAL* 3.9 9.5 - - + +
445A GLU 4.2 0.5 - - - +
446A SER* 2.9 19.7 + - - -
447A GLN* 4.4 2.6 + - - +
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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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332A PHE* 4.0 21.8 - - + -
352A VAL* 5.2 0.9 - - + -
368A GLN* 1.3 75.6 - - - +
370A LYS* 1.3 62.9 + - - +
400A CYS* 3.9 1.3 - - - +
401A CYS* 2.8 38.6 + - - +
403A MET* 4.3 10.8 - - + -
414A ALA* 3.4 31.9 - - + -
416A PHE* 3.4 18.5 - - + -
444A PHE* 4.2 11.0 - - + -
445A GLU 3.4 19.5 - - - +
446A SER* 4.0 8.5 - - - +
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Residues in contact with LYS 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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368A GLN 4.4 0.2 + - - -
369A VAL* 1.3 76.3 - - - +
371A ALA* 1.3 61.8 + - - +
372A THR* 5.5 0.9 - - + -
400A CYS* 4.1 16.6 - - + -
443A LEU 3.6 1.7 - - - +
444A PHE* 3.5 1.0 - - - -
445A GLU* 2.9 47.0 + - + +
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Residues in contact with ALA 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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369A VAL 4.3 0.8 + - - -
370A LYS* 1.3 74.6 - - - +
372A THR* 1.3 63.0 + - - +
397A LEU* 4.1 11.1 - - - +
399A ASN 3.9 18.4 + - - +
400A CYS* 5.4 0.2 - - - +
416A PHE* 4.5 8.6 - - + -
419A MET* 3.7 22.7 - - + -
442A ILE* 4.3 2.9 - - + -
443A LEU 3.2 5.6 - - - +
444A PHE* 3.5 33.0 - - + -
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Residues in contact with THR 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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370A LYS* 5.5 0.9 - - + -
371A ALA* 1.3 77.8 - - - +
373A ILE* 1.3 67.9 + - - +
374A ILE* 4.2 8.0 - - + +
392A TYR 4.0 14.6 + - - +
395A GLU 4.8 5.9 + - - -
397A LEU* 4.6 8.4 - - - +
442A ILE* 4.6 4.0 - - - +
443A LEU* 2.8 55.7 + - + +
445A GLU* 4.0 9.2 - - - +
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Residues in contact with ILE 373 (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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342A LEU* 5.5 1.1 - - + -
372A THR* 1.3 77.8 + - - +
374A ILE* 1.3 66.8 + - - +
392A TYR 4.1 1.2 + - - -
393A SER 4.1 1.6 + - - -
394A GLY* 3.2 39.4 + - - +
395A GLU 4.3 5.3 - - - +
397A LEU* 4.5 13.8 - - + +
421A LEU* 3.8 36.1 - - + -
424A ILE* 4.2 13.0 - - + -
440A PHE* 4.0 24.9 - - + -
441A THR 3.5 12.6 - - - +
442A ILE* 4.4 11.7 - - + +
466A VAL* 4.6 7.0 - - + -
468A VAL* 4.2 6.5 - - + -
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Residues in contact with ILE 374 (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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372A THR* 4.2 18.4 - - + +
373A ILE* 1.3 80.7 - - - +
375A SER* 1.3 68.8 + - - +
378A GLN* 3.8 12.8 - - + -
379A ALA* 3.9 24.5 - - + +
382A LEU* 4.4 9.4 - - + -
392A TYR 4.3 14.4 - - - +
393A SER* 3.9 7.9 - - - +
440A PHE* 3.5 7.6 - - - +
441A THR* 2.9 46.4 + - + +
443A LEU* 4.0 26.9 - - + -
462A LEU* 4.3 1.6 - - + -
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Residues in contact with SER 375 (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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374A ILE* 1.3 81.6 - - - +
376A GLU* 1.3 60.0 + - - +
377A GLN* 3.3 8.1 + - - +
378A GLN* 3.0 21.5 + - - +
379A ALA* 3.0 23.7 + - - +
393A SER* 3.3 24.2 - - - -
438A GLU* 5.5 5.2 - - - -
439A LYS 4.4 1.1 - - - -
440A PHE* 3.6 21.4 - - - -
441A THR* 4.6 0.2 - - - +
496A PHE* 5.0 0.2 - - - -
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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