Contacts of the strand formed by residues 480 - 487 (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 MET 480 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372D TYR* 4.1 14.8 - - + -
390D LEU* 5.6 0.2 - - - +
399D LEU* 3.5 33.0 - - + +
401D GLU* 3.4 32.5 - - + +
426D ARG* 4.4 2.2 - - - +
448D ALA* 6.0 0.9 - - - -
478D SER* 2.8 45.0 + - - +
479D ASP* 1.3 73.3 + - - +
481D VAL* 1.3 64.5 + - - +
498D ILE* 3.5 24.7 - - + -
499D THR* 3.5 5.6 - - - +
500D HIS* 3.4 31.4 - - - +
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Residues in contact with VAL 481 (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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390D LEU* 5.4 1.6 - - - -
393D VAL* 6.5 1.1 - - + -
480D MET* 1.3 78.8 - - - +
482D ARG* 1.3 62.0 + - - +
483D VAL* 4.1 0.8 + - + -
497D LEU 3.9 0.2 - - - +
498D ILE* 3.3 8.6 - - - +
499D THR* 2.8 48.1 + - + +
501D ARG* 3.6 49.1 - - + +
504D SER* 3.7 28.5 - - - +
532D ILE* 4.3 22.0 - - + -
165F THR* 5.3 0.7 - - + -
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Residues in contact with ARG 482 (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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387D PRO* 3.1 36.3 + - + +
388D SER* 3.5 24.4 + - - +
390D LEU* 3.9 35.1 + - + +
391D PRO 5.5 0.2 + - - -
392D ALA* 6.3 0.4 - - - +
481D VAL* 1.3 74.1 - - - +
483D VAL* 1.3 66.1 + - - +
484D ASP* 3.0 38.1 + - - +
491D ARG* 3.8 19.0 - - - +
493D ASP* 5.2 0.8 + - - -
496D ALA* 4.9 1.0 - - + +
497D LEU 3.5 10.1 - - - +
498D ILE* 4.6 1.3 - - + +
531D ALA 3.9 0.2 - - - +
532D ILE* 3.4 27.4 - - - +
533D GLY 4.8 1.2 + - - -
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Residues in contact with VAL 483 (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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481D VAL* 5.0 1.3 - - + +
482D ARG* 1.3 74.8 - - - +
484D ASP* 1.3 64.6 + - - +
485D VAL* 4.5 0.7 - - - +
496D ALA* 3.4 7.6 - - - +
497D LEU* 2.9 56.9 + - + -
499D THR* 4.2 14.1 - - + -
504D SER* 4.3 14.8 - - - +
508D GLY* 4.5 7.9 - - - +
511D LEU* 4.8 8.7 - - + -
530D ALA* 4.0 24.7 - - + -
531D ALA 3.3 10.1 - - - +
532D ILE* 4.3 12.8 - - + -
537D ILE* 4.3 7.2 - - + -
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Residues in contact with ASP 484 (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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388D SER* 5.6 0.2 - - - -
482D ARG* 3.0 42.1 + - - +
483D VAL* 1.3 74.1 - - - +
485D VAL* 1.3 63.5 + - - +
486D LEU* 4.2 6.0 + - + +
491D ARG* 3.6 33.2 + - + +
493D ASP* 5.3 1.9 - - - +
496D ALA* 4.2 9.6 - - - +
530D ALA* 3.3 3.3 - - - +
531D ALA* 2.7 49.4 + - + +
533D GLY* 4.9 10.8 + - - +
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Residues in contact with VAL 485 (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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483D VAL* 4.0 2.9 + - + +
484D ASP* 1.3 76.2 - - - +
486D LEU* 1.3 61.4 + - - +
487D ILE* 4.4 12.6 - - + -
491D ARG* 3.9 3.6 - - - +
492D VAL* 2.9 30.5 + - - +
495D LEU* 3.2 51.4 - - + +
496D ALA* 4.2 3.2 - - - +
511D LEU* 3.5 35.4 - - + -
512D VAL* 5.7 0.9 - - + -
515D MET* 5.0 0.4 - - + -
528D ILE* 4.7 6.1 - - + -
529D GLN 3.4 16.6 - - - +
530D ALA* 5.1 3.1 - - + -
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Residues in contact with LEU 486 (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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484D ASP* 4.6 14.4 - - + +
485D VAL* 1.3 77.4 - - - +
487D ILE* 1.3 63.8 + - - +
489D GLY* 3.8 25.8 - - - +
490D GLU 3.2 20.0 - - - +
491D ARG* 3.9 15.9 - - + +
492D VAL 4.3 0.2 - - - +
527D ALA 3.6 0.7 - - - +
529D GLN* 3.0 74.2 + - + +
531D ALA* 4.7 11.2 - - + -
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Residues in contact with ILE 487 (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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333D ALA* 3.1 36.0 - - + +
334D LEU* 6.0 0.2 - - + -
485D VAL* 4.4 9.9 - - + -
486D LEU* 1.3 79.0 - - - +
488D ASN* 1.3 71.9 + - + +
490D GLU* 3.1 22.4 + - - +
492D VAL* 4.1 9.4 - - + +
495D LEU* 5.3 4.5 - - + -
515D MET* 4.9 8.1 - - + -
519D ILE* 3.6 28.0 - - + -
526D ILE* 4.7 4.9 - - + -
527D ALA 3.2 7.0 - - - +
528D ILE* 3.6 33.7 - - + -
550E LEU* 4.0 8.5 - - + -
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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