Contacts of the strand formed by residues 396 - 411 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374C VAL* 3.9 11.9 - - + -
375C GLU 3.9 2.7 - - - -
377C THR* 5.1 0.4 - - - -
390C LEU* 4.0 24.2 - - + -
391C PRO* 3.4 36.6 - - + +
392C ALA 3.6 11.4 - - - +
393C VAL* 3.2 21.6 + - + +
394C ASN 4.8 2.4 - - - +
395C ASN* 1.3 76.8 - - - +
397C TYR* 1.3 63.0 + - - +
398C GLU* 3.8 12.3 - - - +
399C LEU* 3.7 33.9 - - + +
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Residues in contact with TYR 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C GLU* 2.9 35.5 + - - +
376C THR 3.8 12.8 - - - +
377C THR* 4.1 8.6 - - - +
379C ARG* 3.1 49.7 + - + -
395C ASN 3.7 2.8 + - - -
396C ILE* 1.3 74.2 - - - +
398C GLU* 1.3 84.5 + - + +
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Residues in contact with GLU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C GLU 4.1 0.5 - - - +
375C GLU* 3.0 31.0 + - + +
396C ILE* 3.5 5.4 - - - +
397C TYR* 1.3 106.0 + - + +
399C LEU* 1.3 62.3 + - - +
400C ARG* 2.7 36.4 + - + +
477C ALA* 3.5 32.5 - - + +
478C SER 5.6 0.2 - - - +
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Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TYR* 4.1 25.4 - - + -
373C GLU 4.1 0.9 - - - -
374C VAL* 3.7 25.8 - - + +
390C LEU* 4.2 25.8 - - + -
396C ILE* 3.7 22.2 - - + +
398C GLU* 1.3 72.5 - - - +
400C ARG* 1.3 65.9 + - - +
401C GLU* 3.9 1.2 + - - +
477C ALA* 4.5 0.7 - - - -
478C SER* 3.2 33.2 + - - +
480C MET* 3.4 41.5 - - + +
498C ILE* 4.8 2.7 - - + -
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Residues in contact with ARG 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 3.8 8.3 - - - +
373C GLU* 2.7 99.1 + - + +
375C GLU* 2.6 49.6 + - - +
381C VAL* 4.2 10.1 - - - +
398C GLU* 2.7 26.7 + - - +
399C LEU* 1.3 72.9 - - - +
401C GLU* 1.3 60.0 + - - +
475C PHE* 4.1 13.7 - - + -
476C GLN* 3.2 4.5 - - - -
477C ALA* 3.4 25.1 - - - +
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Residues in contact with GLU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C TYR* 3.9 9.9 - - + -
400C ARG* 1.3 73.9 - - - +
402C PRO* 1.4 82.7 - - + +
403C ILE* 3.3 15.4 + - - +
426C ARG* 2.5 36.4 + - - -
446C PRO* 3.3 13.8 - - + +
447C MET 5.0 0.9 - - - +
448C ALA* 4.3 8.0 - - + +
475C PHE* 3.8 3.1 - - - -
476C GLN* 2.6 33.5 + - - +
478C SER* 3.2 20.1 + - - -
480C MET* 3.3 28.6 - - + +
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Residues in contact with PRO 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C VAL* 3.7 20.6 - - + -
371C VAL 3.2 28.0 - - - +
372C TYR* 3.8 13.2 - - + -
401C GLU* 1.4 92.1 - - + +
403C ILE* 1.3 55.5 + - - +
446C PRO 3.7 0.5 - - - -
447C MET* 2.7 44.7 + - + +
472C PHE* 4.1 15.3 - - + -
474C ARG 3.6 6.5 - - - +
475C PHE* 3.7 12.7 - - + -
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLU* 3.7 32.5 - - - +
402C PRO* 1.3 75.3 - - - +
404C ALA* 1.3 63.0 + - - +
444C GLU* 3.8 35.9 - - + +
445C ILE 3.8 5.8 - - - +
446C PRO* 3.9 15.9 - - + -
447C MET* 4.9 0.7 - - - -
472C PHE* 4.0 2.6 - - - -
473C LYS* 3.1 27.7 + - + +
474C ARG* 2.8 43.2 + - + +
476C GLN* 3.7 17.5 - - + +
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Residues in contact with ALA 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C PRO 4.0 1.8 + - - -
403C ILE* 1.3 72.6 - - - +
405C GLU* 1.3 60.5 + - - +
406C CYS* 3.7 7.7 + - - -
443C TYR 3.6 0.2 - - - +
444C GLU* 3.4 4.0 - - - -
445C ILE 2.7 42.3 + - - +
447C MET* 3.7 34.5 - - + +
450C VAL* 3.9 13.7 - - + -
470C TYR* 4.4 7.0 - - + -
471C ASN 3.7 7.4 - - - +
473C LYS* 4.6 0.2 - - - -
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Residues in contact with GLU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C ILE 3.9 1.6 + - - -
404C ALA* 1.3 70.7 - - - +
406C CYS* 1.3 61.2 + - - +
407C HIS* 3.2 30.5 + - + -
430C THR* 4.6 7.8 - - + +
442C THR* 4.0 17.1 + - - +
443C TYR 3.6 4.9 - - - +
444C GLU* 4.7 10.0 - - + +
469C ASP 3.5 2.4 - - - +
470C TYR* 3.3 2.4 - - - -
471C ASN* 2.9 44.3 + - - +
473C LYS* 3.6 50.1 + - + +
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Residues in contact with CYS 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404C ALA* 3.9 16.8 - - - -
405C GLU* 1.3 75.8 - - - +
407C HIS* 1.3 62.4 + - - +
408C MET* 4.0 11.3 + - + +
441C LEU 3.9 0.2 - - - +
442C THR* 3.1 7.2 + - - -
443C TYR 2.8 41.4 + - - +
445C ILE* 3.7 34.5 - - + -
450C VAL* 4.3 6.7 - - - -
454C PHE* 5.2 1.6 - - - -
468C LEU* 4.4 11.9 - - + -
469C ASP 3.4 6.1 - - - +
470C TYR* 3.8 18.2 - - + +
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Residues in contact with HIS 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ALA* 4.4 4.8 - - + +
117C TYR* 6.5 2.5 - + + -
405C GLU* 3.2 40.7 + - + -
406C CYS* 1.3 70.0 - - - +
408C MET* 1.3 64.2 + - - +
409C LEU* 5.2 5.6 - - + -
441C LEU 3.5 4.5 - - - +
442C THR* 4.1 18.6 - - + -
467C SER 3.9 0.5 - - - +
468C LEU 3.6 1.4 - - - -
469C ASP* 2.7 63.4 + - + +
471C ASN* 4.5 8.7 - - - -
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Residues in contact with MET 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C CYS* 4.1 17.5 - - + +
407C HIS* 1.3 80.4 - - - +
409C LEU* 1.3 66.3 - - - +
410C LEU* 4.0 7.4 - - + -
418C VAL* 3.9 7.2 - - + -
422C CYS* 3.6 28.7 - - - -
439C VAL 3.4 1.6 - - - +
440C ALA* 3.5 3.1 - - - -
441C LEU* 2.6 72.2 + - + +
443C TYR* 4.4 12.1 - - + +
445C ILE* 5.4 0.2 - - - -
454C PHE* 4.9 2.5 - - - -
458C LEU* 3.5 28.3 - - + -
466C ALA* 5.9 2.5 - - + -
467C SER 3.3 9.9 - - - +
468C LEU* 4.6 12.6 - - + -
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Residues in contact with LEU 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 5.9 2.5 - - + +
109C GLU* 5.7 1.6 - - - -
110C ALA* 4.1 9.4 - - + +
113C LEU* 3.7 30.1 - - + -
117C TYR* 5.7 1.3 - - + +
150C ILE* 4.3 20.0 - - + -
407C HIS* 5.2 4.3 - - + -
408C MET* 1.3 82.7 - - - +
410C LEU* 1.3 62.7 + - - +
435C HIS* 4.6 2.2 - - - +
438C GLN* 4.3 19.5 - - + -
439C VAL 3.5 15.9 - - - +
440C ALA* 3.9 20.2 - - + -
465C TYR 3.8 2.8 - - - +
466C ALA* 3.5 2.1 - - - -
467C SER* 3.1 42.6 + - - +
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Residues in contact with LEU 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C MET* 3.9 17.9 - - + +
409C LEU* 1.3 79.4 - - - +
411C PRO* 1.4 75.2 - - + +
414C TYR* 4.2 4.5 - - + -
415C LEU* 3.7 31.9 - - + +
418C VAL* 3.7 34.8 - - + -
438C GLN* 3.2 9.6 + - - +
439C VAL* 2.8 48.8 + - + +
441C LEU* 4.1 21.1 - - + -
465C TYR 4.2 0.7 - - - -
466C ALA* 3.9 13.9 - - + -
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Residues in contact with PRO 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410C LEU* 1.4 97.0 - - + +
412C GLN* 1.3 64.2 + - - +
413C ALA* 3.2 7.4 + - + +
414C TYR* 3.4 37.8 + - + -
415C LEU* 3.8 7.8 + - - +
437C ASN 3.6 14.8 - - - +
438C GLN* 3.2 9.6 - - - +
439C VAL* 4.9 0.6 - - - +
465C TYR* 3.7 29.2 - - + +
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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