Contacts of the strand formed by residues 486 - 493 (chain A) in PDB entry 6CNB
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 LEU 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A LEU* 3.1 11.0 - - - +
474A PHE 2.9 23.8 + - - -
483A LEU* 4.0 19.1 - - + -
484A SER 3.1 27.2 + - - +
485A ILE* 1.3 89.4 - - - +
487A SER* 1.3 62.2 + - - +
488A HIS* 3.9 6.1 - - + +
504A VAL* 5.3 4.9 - - + -
507A PRO* 5.0 11.7 - - + -
508A TYR* 3.6 29.6 - - + +
535A MET* 3.7 14.8 - - - +
536A GLY 5.0 2.7 - - - +
537A VAL* 3.7 29.6 - - + -
540A ASN* 5.8 2.0 - - + +
551A ILE* 6.0 1.8 - - + -
1073B TYR* 4.0 5.4 - - - +
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Residues in contact with SER 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 4.9 0.2 - - - +
471A VAL* 4.5 2.2 - - - -
472A VAL 3.5 6.5 - - - -
473A LEU* 3.9 15.9 - - - -
486A LEU* 1.3 79.9 - - - +
488A HIS* 1.3 63.0 + - - +
531A ALA* 3.2 31.0 + - - -
532A ILE* 3.3 11.2 - - - +
535A MET* 3.5 6.5 + - - -
536A GLY* 3.0 21.4 + - - -
537A VAL* 3.5 22.0 + - - +
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 3.4 23.1 - - - +
391A GLU 3.6 17.8 + - - -
392A VAL* 3.2 30.0 - - + +
471A VAL* 3.7 2.3 - - - -
472A VAL* 2.9 34.0 + - + +
474A PHE* 3.5 17.6 - - + +
486A LEU* 3.9 6.6 - - + +
487A SER* 1.3 77.1 - - - +
489A TYR* 1.3 63.8 + - - +
490A ALA 3.3 1.3 + - - +
500A LEU* 5.9 0.2 - - - +
504A VAL* 4.7 15.9 - - + -
508A TYR* 3.0 25.7 + - - -
532A ILE* 4.7 2.5 - - - -
537A VAL* 3.3 30.6 - - + +
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Residues in contact with TYR 489 (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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390A ASP* 2.8 25.0 + - - +
391A GLU* 3.0 36.3 - - + +
468A ASP* 5.5 2.0 - - - +
469A GLY* 3.9 26.0 - - - -
470A ASP 4.0 2.5 - - - -
471A VAL* 3.9 16.2 - - + -
488A HIS* 1.3 69.6 - - - +
490A ALA* 1.3 62.9 + - - +
532A ILE* 3.3 35.4 - - + +
538A LYS* 4.3 17.5 + - - -
119F ARG* 5.0 10.5 - - - -
122F MET* 5.5 7.1 - - - +
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Residues in contact with ALA 490 (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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391A GLU* 5.3 0.2 - - - -
392A VAL* 3.7 13.9 - - + +
394A VAL* 4.2 11.4 - - + -
466A LEU* 4.7 8.5 - - + -
467A GLU 3.3 7.0 - - - +
468A ASP* 3.3 4.7 - - - +
469A GLY 3.0 25.5 + - - -
470A ASP 2.9 21.0 + - - +
472A VAL* 3.7 23.1 - - + -
488A HIS 3.3 2.4 + - - -
489A TYR* 1.3 73.5 - - - +
491A LYS* 1.3 59.3 + - - +
492A ILE* 5.2 0.7 - - + -
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Residues in contact with LYS 491 (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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387A LEU* 4.1 29.8 - - + -
391A GLU* 4.7 15.0 - - + -
392A VAL 3.4 6.0 + - - +
393A ALA* 3.1 9.3 - - + +
394A VAL 2.9 22.7 + - - -
468A ASP* 3.1 38.3 + - + +
489A TYR 3.7 1.0 + - - -
490A ALA* 1.3 75.4 - - - +
492A ILE* 1.3 73.6 + - - +
493A ARG* 3.7 32.1 - - + +
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Residues in contact with ILE 492 (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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394A VAL* 3.6 27.8 - - + +
396A ASP* 3.6 25.8 - - + -
399A ALA* 4.0 15.7 - - + -
427A HIS* 3.4 36.3 - - + +
466A LEU* 4.1 13.9 - - + +
467A GLU* 4.3 20.2 - - - +
468A ASP* 4.9 3.0 - - - +
490A ALA* 5.2 0.7 - - + -
491A LYS* 1.3 80.8 - - - +
493A ARG* 1.3 76.1 + - - +
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Residues in contact with ARG 493 (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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387A LEU* 6.0 1.2 - - - +
393A ALA* 4.3 13.5 - - + -
394A VAL 3.3 6.5 + - - +
395A PRO* 3.9 0.2 - - - +
396A ASP* 3.1 28.7 + - - +
491A LYS* 3.7 31.3 + - + +
492A ILE* 1.3 83.2 + - - +
494A PRO* 1.3 74.7 - - + +
499A ARG* 3.1 23.1 - - - +
94K PRO* 6.2 0.4 - - - +
95K HIS* 2.8 44.8 + - + +
97K SER* 3.7 7.8 - - - +
98K GLU* 2.6 43.4 + - - +
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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