Contacts of the strand formed by residues 467 - 477 (chain E) 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 SER 467 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110E ALA* 3.1 30.4 - - - +
111E GLN* 5.0 8.1 - - - -
407E HIS 3.5 2.1 - - - +
408E MET* 3.1 25.7 - - - +
409E LEU* 3.0 20.0 + - - +
455E PHE* 5.9 0.2 - - - -
458E LEU* 4.8 0.7 - - - -
459E LYS* 5.9 1.6 - - - +
465E TYR 3.7 1.7 + - - -
466E ALA* 1.3 72.7 - - - +
468E LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E HIS* 4.3 16.6 - - - -
406E CYS* 3.9 18.6 - - + -
407E HIS 4.0 0.4 - - - -
408E MET* 4.6 8.5 - - + -
450E VAL* 4.5 2.5 - - + -
454E PHE* 3.7 31.6 - - + -
455E PHE* 3.6 44.8 - - + -
458E LEU* 4.3 11.2 - - + -
466E ALA 3.9 2.2 + - - -
467E SER* 1.3 71.6 - - - +
469E ASP* 1.3 72.9 + - - +
470E TYR* 3.8 43.0 - - + -
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Residues in contact with ASP 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E HIS* 5.5 3.0 + - - -
82E VAL* 3.2 33.1 + - - +
110E ALA* 5.1 13.4 - - + +
111E GLN* 5.7 2.4 - - - -
114E ALA* 3.4 28.1 - - - +
406E CYS 3.5 0.5 - - - -
407E HIS* 2.7 66.3 + - + +
467E SER 5.3 0.2 - - - +
468E LEU* 1.3 73.7 - - - +
470E TYR* 1.3 62.0 + - - +
471E ASN* 5.0 2.3 - - - +
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Residues in contact with TYR 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E HIS* 5.3 9.2 - - - -
82E VAL* 3.3 25.7 - - + +
83E ASP* 4.4 8.3 + - - +
294E GLN* 3.3 33.1 + - - +
344E GLY* 4.4 0.7 - - - -
345E LEU* 3.6 35.2 + - + +
346E LEU* 5.8 3.1 - - + -
404E ALA* 4.4 7.6 - - + -
405E GLU 3.2 13.9 - - - +
406E CYS* 4.0 9.4 - - - -
447E MET* 3.9 18.4 - - + -
450E VAL* 4.2 18.9 - - + +
451E VAL* 5.1 2.9 - - - +
455E PHE* 6.1 0.9 - + - -
468E LEU* 3.8 33.2 - - + -
469E ASP* 1.3 79.4 - - - +
471E ASN* 1.3 66.6 + - - +
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Residues in contact with ASN 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E VAL* 5.4 10.0 - - + +
85E SER* 5.5 5.8 - - - +
294E GLN* 5.5 2.2 - - - -
404E ALA* 3.5 4.6 - - - +
405E GLU* 3.1 41.6 + - - +
407E HIS* 3.4 24.9 + - - -
447E MET* 4.6 5.2 - - - -
469E ASP* 5.0 2.3 - - - +
470E TYR* 1.3 77.2 - - - +
472E PHE* 1.3 87.7 + - - +
473E LYS* 4.9 1.8 - - - +
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Residues in contact with PHE 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E GLN* 5.0 5.9 + - - +
402E PRO* 4.0 22.4 - - + -
403E ILE 4.1 5.2 - - - -
447E MET* 4.0 20.5 - - + +
471E ASN* 1.3 91.0 + - - +
473E LYS* 1.3 65.2 + - - +
474E ARG* 3.7 37.5 - - - -
475E PHE* 3.9 28.5 - + - -
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Residues in contact with LYS 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E ILE* 3.0 17.9 + - + +
404E ALA 4.3 0.4 - - - -
405E GLU* 3.3 46.9 + - + +
444E GLU* 3.5 30.3 + - - +
471E ASN* 5.3 1.1 - - - +
472E PHE* 1.3 86.2 - - - +
474E ARG* 1.3 75.9 + - + +
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Residues in contact with ARG 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E PRO* 3.6 1.6 - - - +
403E ILE* 2.6 50.2 + - + +
444E GLU* 3.1 34.6 + - - -
472E PHE* 3.7 14.6 - - - -
473E LYS* 1.3 89.5 - - + +
475E PHE* 1.3 67.3 + - - +
476E GLN* 3.2 45.8 + - - +
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Residues in contact with PHE 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371E VAL* 3.3 31.4 - - + -
373E GLU* 3.4 45.8 - - + +
383E TYR* 3.8 29.2 - + - -
400E ARG* 4.1 10.6 - - + -
401E GLU 3.4 3.8 - - - -
402E PRO* 3.6 24.9 - - + -
472E PHE* 3.9 21.7 - + - -
474E ARG* 1.3 90.3 - - - +
476E GLN* 1.3 63.7 + - - +
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Residues in contact with GLN 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E ARG* 3.7 3.4 - - - +
401E GLU* 2.8 39.0 + - - +
403E ILE* 4.0 18.9 - - + +
474E ARG* 3.2 28.6 + - - +
475E PHE* 1.3 76.2 - - - +
477E ALA* 1.3 77.3 + - + +
478E SER* 3.3 6.6 + - - -
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Residues in contact with ALA 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E GLU* 3.5 36.3 - - + +
399E LEU 3.4 8.5 - - - -
400E ARG* 3.3 9.3 - - + +
476E GLN* 1.3 85.0 - - + +
478E SER* 1.3 60.3 + - - +
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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