Contacts of the strand formed by residues 396 - 411 (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 ILE 396 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374E VAL* 4.0 8.3 - - + -
375E GLU 4.1 2.5 - - - -
376E THR* 4.8 0.2 - - - +
377E THR* 5.0 0.2 - - - -
390E LEU* 3.8 28.5 - - + -
391E PRO* 3.3 36.1 - - + +
392E ALA 3.6 9.9 - - - +
393E VAL* 3.2 21.6 + - + +
394E ASN 4.7 2.6 - - - +
395E ASN* 1.3 76.0 - - - +
397E TYR* 1.3 64.6 + - - +
398E GLU 3.9 4.5 - - - +
399E LEU* 3.9 39.0 - - + +
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Residues in contact with TYR 397 (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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375E GLU* 3.0 42.4 + - + +
376E THR 3.4 16.4 - - - +
377E THR* 3.8 8.2 - - - +
379E ARG* 2.8 43.9 + - + -
395E ASN 3.7 3.6 + - - -
396E ILE* 1.3 76.1 - - - +
398E GLU* 1.3 84.2 + - + +
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Residues in contact with GLU 398 (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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373E GLU 4.3 0.2 - - - +
374E VAL* 3.8 1.2 - - - -
375E GLU* 2.9 32.4 + - + +
396E ILE* 3.9 4.8 - - - +
397E TYR* 1.3 104.8 - - + +
399E LEU* 1.3 62.6 + - - +
400E ARG* 2.7 35.7 + - - +
477E ALA* 3.5 31.1 - - + +
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Residues in contact with LEU 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E TYR* 4.0 16.6 - - + -
373E GLU 4.1 0.4 - - - -
374E VAL* 3.7 26.7 - - + +
390E LEU* 4.5 14.1 - - + -
396E ILE* 3.9 28.8 - - + +
398E GLU* 1.3 73.4 - - - +
400E ARG* 1.3 73.2 + - - +
477E ALA* 3.4 3.0 - - - +
478E SER* 3.0 33.1 + - - +
480E MET* 3.5 44.0 - - + +
481E VAL* 5.6 0.2 - - - -
498E ILE* 4.8 3.4 - - + -
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Residues in contact with ARG 400 (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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372E TYR* 3.7 8.0 - - - +
373E GLU* 2.8 97.0 + - + +
375E GLU* 2.7 47.9 + - - +
381E VAL* 4.5 9.7 - - - +
398E GLU* 2.7 24.9 + - - +
399E LEU* 1.3 75.5 - - - +
401E GLU* 1.3 59.9 + - - +
475E PHE* 4.1 11.9 - - + -
476E GLN* 3.4 4.7 - - - -
477E ALA* 3.3 24.9 - - - +
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Residues in contact with GLU 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E TYR* 4.0 12.6 - - + -
399E LEU* 6.0 0.2 - - + -
400E ARG* 1.3 74.6 - - - +
402E PRO* 1.3 81.4 - - + +
403E ILE* 3.4 12.4 + - - +
426E ARG* 3.0 32.6 + - - -
446E PRO* 3.1 21.2 - - + +
448E ALA* 4.2 8.5 - - + +
475E PHE* 3.8 1.8 - - - -
476E GLN 2.8 37.6 + - - +
478E SER* 3.2 20.5 + - - -
480E MET* 3.2 26.9 - - + +
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Residues in contact with PRO 402 (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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370E VAL* 3.7 22.2 - - + -
371E VAL 3.4 23.3 - - - +
372E TYR* 3.9 12.1 - - + -
401E GLU* 1.3 92.4 - - + +
403E ILE* 1.3 54.5 + - - +
446E PRO* 3.6 3.6 - - - +
447E MET* 2.7 44.3 + - + +
472E PHE* 4.0 14.4 - - + -
474E ARG 3.6 5.8 - - - +
475E PHE* 3.6 19.0 - - + -
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Residues in contact with ILE 403 (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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401E GLU* 3.7 21.1 - - - +
402E PRO* 1.3 73.4 - - - +
404E ALA* 1.3 65.3 + - - +
444E GLU* 4.0 28.7 - - + +
445E ILE 3.9 6.1 - - - +
446E PRO* 4.0 26.9 - - + -
447E MET* 4.7 0.9 - - - -
472E PHE* 3.9 5.5 - - - -
473E LYS* 3.0 26.3 + - + +
474E ARG* 2.6 43.0 + - - +
476E GLN* 4.0 27.4 - - + +
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Residues in contact with ALA 404 (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* 1.3 75.5 - - - +
405E GLU* 1.3 61.0 + - - +
406E CYS* 3.7 14.4 + - - -
443E TYR 3.6 0.2 - - - +
444E GLU* 3.3 5.4 - - - -
445E ILE 2.7 42.1 + - - +
447E MET* 3.9 26.7 - - + +
450E VAL* 4.3 6.5 - - + -
470E TYR* 4.4 6.1 - - + -
471E ASN 3.5 11.2 - - - +
473E LYS* 4.3 2.5 - - - -
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Residues in contact with GLU 405 (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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404E ALA* 1.3 70.8 - - - +
406E CYS* 1.3 61.7 + - - +
407E HIS* 3.1 32.2 + - - +
430E THR* 4.5 9.9 - - + +
442E THR* 3.9 17.1 + - - +
443E TYR 3.5 5.2 - - - +
444E GLU* 4.6 9.8 - - + +
469E ASP 3.9 0.2 - - - +
470E TYR* 3.2 5.0 - - - +
471E ASN* 3.1 43.5 + - - +
473E LYS* 3.3 42.8 + - + +
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Residues in contact with CYS 406 (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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404E ALA* 3.9 17.5 - - - -
405E GLU* 1.3 75.9 - - - +
407E HIS* 1.3 61.7 + - - +
408E MET* 3.6 10.0 + - + +
441E LEU 3.6 1.4 - - - +
442E THR* 3.2 5.3 - - - -
443E TYR 2.8 35.0 + - - +
445E ILE* 3.7 35.9 - - + -
450E VAL* 4.4 8.1 - - - -
454E PHE* 5.0 1.8 - - - -
468E LEU* 3.9 17.5 - - + -
469E ASP 3.5 4.7 - - - -
470E TYR* 4.0 13.0 - - - -
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Residues in contact with HIS 407 (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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110E ALA* 5.7 1.7 - - - +
117E TYR* 6.3 3.8 - + - -
405E GLU* 3.1 39.0 + - + -
406E CYS* 1.3 70.3 - - - +
408E MET* 1.3 59.0 + - - +
409E LEU* 5.6 3.6 - - + -
441E LEU 3.8 3.6 - - - -
442E THR* 3.9 20.6 - - + -
467E SER 3.5 1.4 - - - +
469E ASP* 2.7 62.6 + - + +
471E ASN* 3.4 18.4 + - - -
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Residues in contact with MET 408 (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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110E ALA* 6.0 0.2 - - - -
406E CYS* 3.6 21.8 - - + +
407E HIS* 1.3 80.8 - - - +
409E LEU* 1.3 69.0 + - - +
410E LEU* 4.0 9.4 - - + -
418E VAL* 3.9 5.8 - - + -
422E CYS* 3.8 26.7 - - - -
439E VAL 3.4 1.2 - - - +
440E ALA 3.6 0.2 - - - -
441E LEU* 2.6 72.0 + - + +
443E TYR* 4.2 8.3 - - + -
454E PHE* 5.0 5.4 - - - -
458E LEU* 3.5 27.8 - - + -
467E SER 3.1 13.2 - - - +
468E LEU* 4.6 8.3 - - + -
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Residues in contact with LEU 409 (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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108E VAL 6.0 1.6 - - - +
109E GLU* 6.1 0.7 - - - -
110E ALA* 4.0 17.9 - - + +
113E LEU* 4.2 22.9 - - + -
117E TYR* 6.0 0.2 - - - +
150E ILE* 5.3 7.0 - - + -
407E HIS* 5.6 2.7 - - + -
408E MET* 1.3 83.6 - - - +
410E LEU* 1.3 60.8 + - - +
435E HIS* 4.6 14.8 - - + +
438E GLN* 3.6 33.9 - - + +
439E VAL 3.5 5.8 - - - +
440E ALA* 4.1 16.6 - - + -
465E TYR 3.3 6.2 - - - +
467E SER* 3.0 40.1 + - - +
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Residues in contact with LEU 410 (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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408E MET* 4.0 23.8 - - + +
409E LEU* 1.3 79.2 - - - +
411E PRO* 1.4 79.8 - - + +
414E TYR* 4.0 4.7 - - + -
415E LEU* 3.7 29.8 - - + +
418E VAL* 3.6 31.2 - - + -
438E GLN* 3.9 8.2 + - - -
439E VAL* 2.9 34.8 + - + +
441E LEU* 3.9 22.0 - - + -
462E SER* 5.5 0.4 - - - -
465E TYR 3.9 0.2 - - - -
466E ALA* 3.8 18.8 - - + +
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Residues in contact with PRO 411 (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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410E LEU* 1.4 95.7 - - + +
412E GLN* 1.3 66.5 + - - +
413E ALA* 3.3 4.2 + - + +
414E TYR* 3.4 39.0 + - + +
415E LEU 4.1 0.2 + - - -
437E ASN* 3.7 15.0 - - - +
438E GLN* 3.9 11.9 - - - +
439E VAL* 4.4 0.4 - - - +
465E TYR* 3.8 37.7 - - + +
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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