Contacts of the strand formed by residues 396 - 411 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374F VAL* 4.0 7.4 - - + -
375F GLU 4.0 2.2 - - - -
376F THR* 4.8 0.2 - - - +
377F THR* 4.5 0.7 - - - -
390F LEU* 3.9 22.7 - - + -
391F PRO* 3.3 38.8 - - + +
392F ALA 3.7 8.5 - - - +
393F VAL* 3.3 25.7 + - + +
394F ASN 4.6 3.4 - - - +
395F ASN* 1.3 77.0 - - - +
397F TYR* 1.3 63.1 + - - +
398F GLU 3.7 26.5 - - - +
399F LEU* 3.8 19.3 - - + +
480F MET 6.1 0.2 - - - +
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Residues in contact with TYR 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F GLU* 2.9 20.6 + - + +
376F THR 3.4 15.5 - - - +
377F THR* 3.8 9.8 - - - +
379F ARG* 3.1 47.6 + - + -
395F ASN 3.5 3.6 + - - -
396F ILE* 1.3 75.5 - - - +
398F GLU* 1.3 85.9 + - + +
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Residues in contact with GLU 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373F GLU 4.3 0.2 - - - +
374F VAL* 3.8 1.6 - - - -
375F GLU* 2.9 36.5 + - + +
396F ILE* 3.7 4.5 - - - +
397F TYR* 1.3 104.6 + - + +
399F LEU* 1.3 62.3 + - - +
400F ARG* 2.8 35.1 + - - +
477F ALA* 3.6 29.5 - - + +
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Residues in contact with LEU 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F TYR* 4.0 24.7 - - + -
373F GLU 4.2 0.4 - - - -
374F VAL* 3.6 26.2 - - + -
390F LEU* 4.1 27.8 - - + -
396F ILE* 3.8 19.3 - - + +
398F GLU* 1.3 73.1 - - - +
400F ARG* 1.3 63.3 + - - +
401F GLU 4.0 0.9 + - - -
477F ALA* 3.6 2.3 - - - -
478F SER* 3.1 33.7 + - - +
480F MET* 3.6 42.3 - - + +
498F ILE* 4.8 4.3 - - + -
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Residues in contact with ARG 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F TYR* 3.8 5.7 - - - -
373F GLU* 2.7 93.4 + - + +
374F VAL 5.2 0.2 - - - -
375F GLU* 2.7 45.7 + - - +
381F VAL* 4.7 7.3 - - - +
398F GLU* 2.8 25.1 + - + +
399F LEU* 1.3 72.8 - - - +
401F GLU* 1.3 62.4 + - - +
475F PHE* 3.6 17.0 - - + -
476F GLN* 3.4 10.1 - - - +
477F ALA* 3.3 28.0 - - - +
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Residues in contact with GLU 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F TYR* 3.6 15.5 - - + -
399F LEU 4.0 1.6 + - - -
400F ARG* 1.3 72.7 - - - +
402F PRO* 1.3 83.3 - - + +
403F ILE* 3.5 9.8 + - + +
426F ARG* 2.9 39.6 + - - -
446F PRO* 3.3 14.8 - - + +
448F ALA* 4.3 9.2 - - + +
475F PHE* 4.0 1.3 - - - -
476F GLN* 2.9 29.4 + - - +
478F SER* 3.2 22.3 - - - -
480F MET* 3.4 26.3 - - + +
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Residues in contact with PRO 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370F VAL* 3.7 26.9 - - + -
371F VAL 3.4 24.5 - - - +
372F TYR* 4.0 3.1 - - + -
401F GLU* 1.3 89.2 - - + +
403F ILE* 1.3 56.9 + - - +
446F PRO* 3.6 4.3 - - - +
447F MET* 2.8 43.4 + - + -
448F ALA 5.3 0.2 - - - +
472F PHE* 3.7 23.6 - - + -
474F ARG 3.4 6.5 - - - +
475F PHE* 3.7 9.6 - - + -
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Residues in contact with ILE 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401F GLU* 4.0 15.5 - - - +
402F PRO* 1.3 79.9 - - - +
404F ALA* 1.3 61.9 + - - +
444F GLU* 3.7 43.7 - - + +
445F ILE 3.9 2.0 - - - +
446F PRO* 4.2 21.3 - - + -
447F MET* 5.1 0.7 - - - -
472F PHE* 3.9 3.4 - - - -
473F LYS* 3.0 28.9 + - + +
474F ARG* 2.7 36.2 + - + +
476F GLN* 3.7 32.8 - - + +
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Residues in contact with ALA 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F PRO 4.1 0.8 + - - -
403F ILE* 1.3 74.1 - - - +
405F GLU* 1.3 62.6 + - - +
406F CYS* 3.6 6.7 + - - -
443F TYR 3.5 0.9 - - - +
444F GLU* 3.3 4.0 - - - -
445F ILE 2.7 42.2 + - - +
447F MET* 3.7 33.9 - - + -
450F VAL* 4.1 12.1 - - + -
470F TYR* 4.5 6.5 - - + -
471F ASN 3.4 7.0 - - - +
473F LYS* 4.5 0.2 - - - -
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Residues in contact with GLU 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F ALA* 1.3 68.7 - - - +
406F CYS* 1.3 61.6 + - - +
407F HIS* 2.8 34.4 + - - +
430F THR* 4.6 9.8 - - + +
442F THR* 4.4 12.8 - - - +
443F TYR 3.6 5.2 - - - +
444F GLU* 4.2 11.8 - - + +
469F ASP 3.5 2.9 - - - +
470F TYR* 3.2 3.8 - - - -
471F ASN* 2.9 43.5 + - - +
473F LYS* 3.0 48.8 + - + +
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Residues in contact with CYS 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404F ALA 3.8 13.7 - - - -
405F GLU* 1.3 71.8 - - - +
407F HIS* 1.3 62.9 + - - +
408F MET* 3.8 9.6 + - + +
441F LEU 3.5 2.4 - - - +
442F THR* 3.3 3.3 - - - -
443F TYR* 2.7 39.7 + - + +
445F ILE* 3.8 32.5 - - + -
450F VAL* 4.2 13.2 - - - -
454F PHE* 5.1 1.1 - - + -
468F LEU* 3.9 17.0 - - + -
469F ASP 3.6 4.3 - - - -
470F TYR* 3.8 16.8 - - - -
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Residues in contact with HIS 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F ALA* 4.8 2.5 - - + +
114F ALA* 5.8 1.4 - - + +
117F TYR* 6.1 10.5 - + + -
405F GLU* 2.8 37.6 + - + -
406F CYS* 1.3 70.7 - - - +
408F MET* 1.3 59.7 + - - +
409F LEU* 5.2 5.8 - - + -
441F LEU 3.6 3.6 - - - -
442F THR* 4.0 22.4 - - + -
467F SER 3.4 4.0 - - - +
468F LEU* 3.8 0.3 - - - -
469F ASP* 2.8 64.0 + - + +
471F ASN* 3.7 16.8 - - - -
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Residues in contact with MET 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F CYS* 4.2 14.1 - - + +
407F HIS* 1.3 79.6 - - - +
409F LEU* 1.3 69.3 + - - +
410F LEU* 3.9 11.7 - - + -
418F VAL* 4.4 3.8 - - + -
422F CYS* 3.6 31.2 - - - -
439F VAL 3.7 0.2 - - - +
440F ALA* 3.6 0.3 - - - +
441F LEU* 2.7 66.5 + - + +
443F TYR* 3.9 19.1 - - + -
454F PHE* 4.8 6.7 - - - -
458F LEU* 3.5 31.6 - - + -
466F ALA* 5.6 0.2 - - + -
467F SER 3.4 7.0 - - - +
468F LEU* 4.5 11.2 - - + -
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Residues in contact with LEU 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLU* 5.7 1.8 - - - -
110F ALA* 4.1 10.3 - - + +
113F LEU* 3.8 28.7 - - + -
117F TYR* 5.8 0.2 - - - +
150F ILE* 4.8 12.8 - - + -
407F HIS* 5.2 3.8 - - + -
408F MET* 1.3 82.1 - - - +
410F LEU* 1.3 60.2 + - - +
435F HIS* 4.7 7.6 - - - +
438F GLN* 3.9 34.3 - - + +
439F VAL 3.7 9.0 - - - +
440F ALA* 4.2 18.2 - - + -
465F TYR 3.2 4.6 - - - +
466F ALA* 3.1 4.7 - - - -
467F SER* 2.9 48.6 + - - +
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Residues in contact with LEU 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408F MET* 3.9 20.4 - - + +
409F LEU* 1.3 79.0 - - - +
411F PRO* 1.4 74.2 - - + +
414F TYR* 4.2 2.9 - - + -
415F LEU* 3.5 43.7 - - + +
418F VAL* 3.5 22.0 - - + -
438F GLN* 3.6 8.3 + - - -
439F VAL* 2.7 47.7 + - + +
441F LEU* 3.7 22.7 - - + -
465F TYR 3.8 0.7 - - - -
466F ALA* 4.0 14.8 - - + -
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Residues in contact with PRO 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410F LEU* 1.4 91.5 - - + +
412F GLN* 1.3 66.7 + - - +
413F ALA* 4.6 3.6 - - + +
414F TYR* 3.1 43.8 + - + +
415F LEU 3.9 3.8 + - - -
437F ASN* 3.6 15.7 - - - +
438F GLN* 4.3 6.9 - - + +
462F SER* 6.0 0.2 - - - -
465F TYR* 3.6 33.0 - - + +
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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