Contacts of the strand formed by residues 361 - 371 (chain A) in PDB entry 6BHG
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 THR 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A GLU* 3.3 2.5 - - - -
358A TRP 2.9 28.9 + - - -
359A GLU* 3.3 3.8 + - - -
360A GLY* 1.3 80.3 + - - +
362A TRP* 1.3 74.9 + - - +
363A TRP* 3.1 45.0 - - + -
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Residues in contact with TRP 362 (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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355A LYS* 4.1 32.9 + - + +
356A THR 3.7 4.7 - - - -
357A GLU* 3.5 35.7 - - + +
360A GLY 4.6 5.8 + - - -
361A THR* 1.3 84.4 - - - +
363A TRP* 1.3 61.1 + - - +
364A LYS 4.3 0.2 + - - -
393A THR 3.4 22.0 - - - -
394A ARG 3.3 18.8 - - - -
396A GLU* 3.9 21.8 - - + -
399A PHE* 3.7 36.8 - + + -
16B PRO* 4.2 5.4 - - + -
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Residues in contact with TRP 363 (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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355A LYS* 3.2 7.3 - - - -
356A THR 2.9 39.5 + - - +
358A TRP* 2.9 48.5 + + + +
359A GLU* 5.8 0.7 - - + -
361A THR* 3.1 48.1 + - + -
362A TRP* 1.3 72.7 - - - +
364A LYS* 1.3 67.3 + - - +
365A SER* 3.3 1.0 + - - -
379A PHE* 3.7 19.7 - + + -
381A ASP* 3.6 34.1 - - + +
382A ASP* 4.3 6.5 - - - -
514A UNX 3.7 4.9 - - - -
524A UNX 3.3 22.9 - - - -
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Residues in contact with LYS 364 (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 ILE 4.1 2.9 - - - -
355A LYS* 4.4 22.8 - - + +
362A TRP 4.3 0.4 + - - -
363A TRP* 1.3 74.1 - - - +
365A SER* 1.3 58.3 + - - +
379A PHE* 3.9 2.1 - - - -
380A LEU* 3.1 37.3 + - + +
381A ASP* 4.5 6.4 + - - +
514A UNX 2.9 22.0 - - - -
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Residues in contact with SER 365 (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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353A LEU* 3.4 11.8 - - - +
354A ILE* 2.7 48.0 + - - +
356A THR* 2.8 24.5 + - - -
363A TRP 3.9 4.3 - - - -
364A LYS* 1.3 76.6 - - - +
366A ARG* 1.3 60.5 + - - +
377A ILE* 3.5 15.2 - - - +
378A LEU 3.1 15.7 - - - -
379A PHE* 4.3 4.3 - - - -
380A LEU* 3.9 6.1 - - - +
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Residues in contact with ARG 366 (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 GLY* 4.0 14.1 - - - +
352A GLN 3.4 10.8 - - - +
353A LEU* 3.8 12.8 - - + -
365A SER* 1.3 75.7 - - - +
367A VAL* 1.3 70.1 + - - +
368A GLU* 2.7 36.0 + - - +
377A ILE* 3.5 5.6 - - - -
378A LEU* 2.8 56.3 + - + +
380A LEU* 4.3 15.7 - - + +
521A UNX 3.2 28.8 - - - -
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Residues in contact with VAL 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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348A LEU* 4.1 22.7 - - + -
349A LYS 3.3 30.1 - - - +
350A SER* 4.0 3.4 - - - +
351A GLY* 2.7 30.0 + - - -
352A GLN* 2.8 26.0 + - + +
354A ILE* 4.6 6.7 - - + -
366A ARG* 1.3 70.1 - - - +
368A GLU* 1.3 63.0 + - - +
369A GLU 4.0 6.7 - - - +
370A VAL* 4.3 6.3 - - + -
375A VAL* 3.5 22.0 - - + -
376A ARG 3.8 3.4 - - - -
377A ILE* 4.0 17.5 - - + -
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Residues in contact with GLU 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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350A SER* 3.4 16.1 + - - -
366A ARG* 2.7 51.5 + - - +
367A VAL* 1.3 75.1 - - - +
369A GLU* 1.3 62.2 + - - +
376A ARG* 2.8 51.8 + - - +
378A LEU* 3.5 32.7 - - + +
385A CYS* 4.3 3.2 - - - -
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Residues in contact with GLU 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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350A SER* 5.0 5.2 - - - -
367A VAL* 3.6 2.8 - - - +
368A GLU* 1.3 81.5 - - - +
370A VAL* 1.3 72.6 + - - +
371A ASP* 4.9 4.7 - - - +
375A VAL* 3.4 7.2 - - - +
376A ARG* 2.8 64.9 + - + +
387A TRP* 3.6 21.5 - - + -
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Residues in contact with VAL 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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348A LEU* 3.5 29.4 - - + +
349A LYS* 4.9 0.2 - - - -
350A SER* 4.9 6.7 - - - +
367A VAL* 4.3 10.5 - - + -
369A GLU* 1.3 85.8 - - - +
371A ASP* 1.3 65.9 + - - +
372A GLY 4.0 13.9 - - - +
374A LEU 3.7 9.4 - - - +
375A VAL* 4.4 7.2 - - + -
390A ARG* 4.2 12.8 - - - +
537A UNX 3.8 13.0 - - - -
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Residues in contact with ASP 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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288A LYS 5.2 2.4 - - - +
290A LYS* 5.1 5.9 - - - +
292A ARG* 3.1 39.8 + - - -
304A TYR* 3.4 14.4 - - - -
369A GLU* 4.9 3.8 - - - +
370A VAL* 1.3 75.6 - - - +
372A GLY* 1.3 67.7 + - - +
373A SER 3.1 0.5 + - - -
374A LEU* 2.9 24.4 + - + +
387A TRP* 3.6 28.6 - - + -
537A UNX 3.7 1.8 - - - -
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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