Contacts of the strand formed by residues 490 - 500 (chain D) in PDB entry 3CB4
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 GLU 490 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332D SER* 3.2 39.7 + - - +
333D ALA* 5.9 0.4 - - + -
486D LEU* 3.2 1.8 - - - -
487D ILE 3.1 29.1 + - - +
488D ASN* 3.0 15.9 + - + +
489D GLY* 1.3 76.7 - - - +
491D ARG* 1.3 61.8 + - - +
492D VAL* 3.1 13.0 + - + +
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Residues in contact with ARG 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D SER* 5.1 3.0 + - - -
482D ARG* 3.8 18.8 - - - +
484D ASP* 3.6 33.5 + - + +
485D VAL 4.0 3.4 - - - +
486D LEU* 3.9 18.6 - - + +
489D GLY 3.5 4.7 + - - +
490D GLU* 1.3 69.9 + - - +
492D VAL* 1.3 58.9 + - - +
493D ASP* 3.3 30.6 + - - +
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Residues in contact with VAL 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D SER* 3.9 27.4 - - - +
332D SER* 4.9 7.4 - - - +
333D ALA* 4.2 10.1 - - + +
334D LEU* 4.2 8.5 - - + -
485D VAL* 2.9 22.7 + - - +
486D LEU* 4.7 0.2 - - - -
487D ILE* 4.1 25.8 - - + +
490D GLU* 3.1 15.0 + - + +
491D ARG* 1.3 68.9 - - - +
493D ASP* 1.3 64.7 + - - +
494D ALA 4.3 0.7 - - - +
495D LEU* 3.4 44.4 + - + +
496D ALA* 3.8 5.0 + - - +
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Residues in contact with ASP 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D GLU* 4.6 5.2 - - - +
331D SER* 5.6 0.2 + - - -
386D SER* 5.8 1.0 - - - -
387D PRO* 5.3 3.5 - - - +
388D SER* 3.5 37.4 + - - +
482D ARG* 5.2 1.0 + - - -
484D ASP* 5.3 2.2 - - - +
491D ARG* 3.3 32.9 + - - +
492D VAL* 1.3 69.7 - - - +
494D ALA* 1.3 58.2 + - - +
495D LEU 2.9 10.9 + - - -
496D ALA* 3.1 21.0 + - - +
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D GLY* 5.2 2.2 + - - -
300D PHE* 3.7 22.0 - - + -
329D GLU* 3.3 37.7 + - - +
331D SER* 4.1 11.0 + - - +
334D LEU* 4.5 4.3 - - + -
366D THR* 3.4 22.4 + - - +
492D VAL* 3.4 1.2 - - + +
493D ASP* 1.3 76.8 - - - +
495D LEU* 1.3 57.6 + - - +
496D ALA 3.5 3.5 + - - +
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D LEU* 4.3 13.2 - - + -
364D ILE* 6.4 0.9 - - + -
366D THR* 3.9 27.6 - - + -
367D ALA* 5.8 1.7 - - - +
485D VAL* 3.2 26.9 - - + +
487D ILE* 5.3 4.3 - - + -
492D VAL* 3.6 35.9 - - + +
493D ASP 2.9 0.8 + - - -
494D ALA* 1.3 75.9 - - - +
496D ALA* 1.3 65.9 + - - +
497D LEU* 4.9 0.7 - - - +
511D LEU* 3.6 22.5 - - + +
515D MET* 3.7 44.0 - - + -
518D LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D ALA* 5.5 3.6 - - - +
369D THR* 5.4 3.6 - - - +
387D PRO* 3.5 27.7 - - + +
388D SER* 4.8 4.5 - - - +
482D ARG* 4.9 0.9 - - - +
483D VAL 3.4 16.2 - - - +
484D ASP* 4.2 18.2 - - - +
485D VAL* 4.3 3.6 - - - +
492D VAL 3.8 5.1 + - - +
493D ASP* 3.1 17.5 + - - +
494D ALA 4.5 3.6 - - - +
495D LEU* 1.3 83.7 - - - +
497D LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D ALA* 4.9 20.0 - - + +
369D THR* 5.6 4.7 - - - -
387D PRO* 3.7 6.5 - - - -
452D LEU* 6.4 3.1 - - + -
482D ARG* 3.5 6.4 - - - +
483D VAL* 2.9 50.9 + - + +
495D LEU 4.9 0.2 - - - +
496D ALA* 1.3 77.2 - - - +
498D ILE* 1.3 68.1 + - - +
499D THR* 3.6 32.8 - - + -
507D ARG* 4.5 22.9 - - + +
511D LEU* 3.8 26.2 - - + -
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D THR* 4.9 3.9 + - - +
372D TYR* 3.4 52.9 + - + +
384D VAL* 4.8 4.9 - - + -
385D ASP 5.8 0.9 - - - +
387D PRO* 3.7 32.9 - - + +
390D LEU* 4.1 32.1 - - + -
399D LEU* 4.7 2.0 - - + -
448D ALA* 5.1 3.3 - - - +
452D LEU* 5.9 2.6 - - - +
480D MET* 3.5 28.3 - - + -
481D VAL 3.3 12.3 - - - +
482D ARG* 5.1 1.1 - - - -
497D LEU* 1.3 80.2 - - - +
499D THR* 1.3 62.9 + - - +
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Residues in contact with THR 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D ALA* 6.4 0.9 - - - -
449D GLU* 5.0 2.3 + - - -
480D MET* 3.5 9.4 - - - -
481D VAL* 2.8 42.9 + - - +
483D VAL* 4.2 6.5 - - + -
497D LEU* 3.6 22.2 - - + -
498D ILE* 1.3 76.2 - - - +
500D HIS* 1.3 64.5 + - - +
504D SER* 3.7 31.2 - - - -
507D ARG* 3.5 38.7 + - + +
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Residues in contact with HIS 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426D ARG* 3.6 46.7 + - - +
449D GLU* 5.4 0.2 - - - +
478D SER* 3.7 21.2 + - - -
479D ASP* 3.1 33.1 + - + -
480D MET* 3.4 9.0 - - - +
499D THR* 1.3 78.3 + - - +
501D ARG* 1.3 67.4 + - - +
502D ASP* 3.2 46.5 + - + -
503D ASN 3.3 5.5 + - - -
504D SER* 3.1 17.7 + - - -
507D ARG* 4.6 5.0 + - - +
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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