Contacts of the strand formed by residues 429 - 436 (chain A) in PDB entry 1BWC
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 LYS 429 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A TYR* 4.7 9.6 + - - -
423A CYS* 3.2 3.7 - - - -
424A ALA* 2.8 40.5 + - + +
427A GLU* 3.4 19.4 - - - +
428A GLU* 1.3 74.6 - - - +
430A VAL* 1.3 66.4 - - - +
431A VAL* 3.3 29.1 + - + +
451A VAL 5.9 0.4 - - - +
454A GLY* 4.1 26.1 - - - +
455A ALA 3.8 10.1 - - - +
456A THR* 4.0 8.1 - - + -
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Residues in contact with VAL 430 (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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421A MET* 4.0 26.2 - - + -
422A VAL 3.7 3.6 - - - -
423A CYS* 4.4 2.0 - - - -
428A GLU 4.3 0.4 - - - +
429A LYS* 1.3 75.5 - - - +
431A VAL* 1.3 61.8 + - - +
432A GLY 3.8 19.5 - - - +
433A ILE* 4.0 19.1 - - + -
451A VAL* 4.0 29.7 - - + +
455A ALA* 2.8 24.0 + - + +
456A THR 3.8 2.7 - - - -
457A LYS* 3.8 19.7 - - - +
460A PHE* 3.9 17.9 - - + -
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Residues in contact with VAL 431 (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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366A ASN* 4.5 5.0 + - - +
381A GLY* 3.4 7.7 - - - -
382A LEU* 2.8 43.7 + - + +
387A ALA* 4.3 6.7 - - + -
391A TYR* 3.8 21.8 - - + +
422A VAL* 3.0 31.1 + - + +
423A CYS 4.6 0.2 - - - -
424A ALA* 3.8 26.2 - - + +
429A LYS* 3.3 20.3 + - + +
430A VAL* 1.3 75.6 - - - +
432A GLY* 1.3 58.6 + - - +
451A VAL* 5.0 5.8 - - - -
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Residues in contact with GLY 432 (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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380A VAL* 3.5 9.0 - - - -
382A LEU 3.5 18.4 - - - -
421A MET* 3.5 2.3 - - - -
422A VAL* 2.8 34.6 + - - +
430A VAL* 3.5 4.3 - - - +
431A VAL* 1.3 81.1 - - - +
433A ILE* 1.3 68.7 + - - +
434A HIS* 4.2 3.4 - - - -
451A VAL* 5.4 0.9 - - - +
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Residues in contact with ILE 433 (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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379A THR* 3.4 2.0 - - - -
380A VAL* 2.9 42.1 + - + +
420A LYS 3.4 9.6 - - - +
421A MET* 5.1 2.9 - - + -
430A VAL* 4.0 8.3 - - + -
432A GLY* 1.3 77.9 - - - +
434A HIS* 1.3 74.2 + - - +
435A MET* 4.5 11.2 - - + -
444A LEU* 4.8 7.0 - - + -
447A PHE* 3.9 24.0 - - + +
451A VAL* 3.5 27.4 - - + -
460A PHE* 3.9 18.6 - - + -
474A LEU* 4.0 29.2 - - + -
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Residues in contact with HIS 434 (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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227A ASP* 3.8 24.2 + - + +
229A MET* 3.6 3.5 - - + +
230A ILE* 3.9 20.8 - - + +
378A GLY 3.5 4.9 - - - -
379A THR* 2.8 26.6 + - - +
380A VAL 4.3 4.9 - - - -
381A GLY 4.4 3.4 - - - -
382A LEU 2.8 36.7 + - - -
383A THR* 3.6 13.9 - - + -
419A MET* 3.4 0.7 - - - -
420A LYS* 2.7 46.5 + - + +
422A VAL* 3.9 20.1 - - + +
432A GLY* 4.1 1.2 - - - -
433A ILE* 1.3 81.5 + - - +
435A MET* 1.3 61.7 + - - +
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Residues in contact with MET 435 (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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230A ILE* 3.7 7.4 - - - +
377A ILE* 3.3 7.6 - - - +
378A GLY* 2.8 39.2 + - - +
418A VAL 3.1 12.8 - - - +
419A MET* 3.9 13.7 - - + -
433A ILE* 4.5 5.2 - - + -
434A HIS* 1.3 76.5 - - - +
436A GLN* 1.3 61.7 - - - +
440A CYS* 3.7 27.1 - - + +
443A MET* 3.5 46.9 - - + +
444A LEU* 3.9 27.1 - - + -
447A PHE* 4.9 0.7 - - + -
474A LEU* 4.0 22.9 - - + -
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Residues in contact with GLN 436 (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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230A ILE* 4.1 7.8 - - + +
233A ASN* 3.1 29.9 + - - +
234A CYS* 3.5 33.8 + - - +
237A GLU* 4.6 3.4 - - - +
373A SER* 3.6 12.7 + - - -
374A HIS 4.3 2.8 + - - -
375A PRO* 3.0 43.3 + - + +
376A PRO 3.3 7.2 - - - +
377A ILE* 3.5 14.4 - - + +
416A LYS 3.8 1.8 - - - +
417A CYS* 3.3 3.1 - - - -
418A VAL* 3.0 35.5 + - + +
435A MET* 1.3 74.6 - - - +
437A GLY* 1.3 58.6 + - - +
440A CYS* 3.8 3.6 - - - -
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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