Contacts of the strand formed by residues 396 - 411 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B VAL* 4.3 6.7 - - + -
375B GLU 4.0 2.9 - - - -
376B THR* 5.0 0.2 - - - +
377B THR* 4.9 0.9 - - - -
390B LEU* 4.0 24.5 - - + -
391B PRO* 3.3 35.2 - - + +
392B ALA 3.2 10.7 + - - +
393B VAL* 3.5 24.7 + - + +
394B ASN 4.9 2.2 - - - +
395B ASN* 1.3 77.4 - - - +
397B TYR* 1.3 61.4 + - - +
398B GLU 3.8 26.2 - - - +
399B LEU* 3.9 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLU* 2.9 38.3 + - - +
376B THR 3.5 15.0 - - - +
377B THR* 3.8 10.9 - - - +
379B ARG* 2.8 38.9 + - + -
395B ASN 3.4 3.8 + - - -
396B ILE* 1.3 75.9 - - - +
398B GLU* 1.3 90.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU 4.2 0.2 - - - +
374B VAL* 3.8 1.0 - - - -
375B GLU* 2.8 37.0 + - + +
396B ILE* 3.8 5.7 - - - +
397B TYR* 1.3 109.0 + - + +
399B LEU* 1.3 61.1 + - - +
400B ARG* 3.0 31.4 + - - +
477B ALA* 3.7 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 4.0 23.8 - - + -
373B GLU 4.2 0.7 - - - -
374B VAL* 3.8 25.6 - - + +
390B LEU* 4.1 27.4 - - + -
396B ILE* 3.9 20.1 - - + +
398B GLU* 1.3 72.9 - - - +
400B ARG* 1.3 63.0 + - - +
401B GLU* 3.8 1.7 + - - +
477B ALA* 4.4 0.7 - - - -
478B SER* 3.1 34.0 + - - +
480B MET* 3.3 43.5 - - + +
498B ILE* 5.0 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 3.5 7.9 - - - +
373B GLU* 2.7 104.9 + - + +
375B GLU* 2.5 46.8 + - - +
381B VAL* 4.0 11.1 - - - +
398B GLU* 3.0 24.2 + - - +
399B LEU* 1.3 71.6 - - - +
401B GLU* 1.3 61.6 + - - +
475B PHE* 3.7 16.5 - - + -
476B GLN* 3.4 3.4 - - - +
477B ALA* 3.3 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 3.6 13.0 - - + -
399B LEU 3.8 1.2 + - - +
400B ARG* 1.3 73.5 - - - +
402B PRO* 1.3 83.7 - - + +
403B ILE* 3.6 10.2 + - + +
426B ARG* 2.7 37.2 + - - -
446B PRO* 3.3 18.1 - - + +
448B ALA* 4.2 8.1 - - + +
475B PHE* 3.5 2.0 - - - -
476B GLN* 3.0 29.3 + - - +
478B SER* 3.4 11.8 + - - -
480B MET* 3.3 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.7 22.2 - - + -
371B VAL 3.4 22.9 - - - +
372B TYR* 3.8 9.4 - - + -
401B GLU* 1.3 91.7 - - + +
403B ILE* 1.3 60.1 + - - +
446B PRO* 3.5 5.5 - - - +
447B MET* 2.8 38.4 + - + -
448B ALA 4.7 0.2 - - - +
472B PHE* 4.1 15.5 - - + -
474B ARG 3.4 6.5 - - - +
475B PHE* 3.8 16.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLU* 3.9 17.7 - - - +
402B PRO* 1.3 80.6 - - - +
404B ALA* 1.3 64.1 + - - +
444B GLU* 4.0 32.3 - - + +
445B ILE 3.8 7.4 - - - +
446B PRO* 4.0 22.7 - - + -
447B MET* 4.5 1.6 - - - -
472B PHE* 3.9 4.3 - - - -
473B LYS* 3.0 27.3 + - + -
474B ARG* 2.7 51.6 + - + +
476B GLN* 4.1 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 1.3 77.2 - - - +
405B GLU* 1.3 60.3 + - - +
406B CYS* 3.7 5.8 + - - -
443B TYR 3.6 0.9 - - - +
444B GLU* 3.4 4.0 - - - -
445B ILE 2.7 40.8 + - - +
447B MET* 3.8 31.6 - - + +
450B VAL* 4.2 12.3 - - + -
470B TYR* 4.3 10.1 - - + -
471B ASN 3.4 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ALA* 1.3 70.5 - - - +
406B CYS* 1.3 61.0 + - - +
407B HIS* 3.2 33.1 + - - +
430B THR* 4.6 10.2 - - + +
442B THR* 4.0 11.2 - - - +
443B TYR 3.7 2.5 - - - +
444B GLU* 4.5 13.4 - - + +
469B ASP 3.7 1.7 - - - +
470B TYR* 3.3 19.6 - - - -
471B ASN* 3.0 30.7 + - - +
473B LYS* 3.2 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ALA* 3.8 14.6 - - - -
405B GLU* 1.3 75.9 - - - +
407B HIS* 1.3 62.3 + - - +
408B MET* 3.7 11.0 + - + +
441B LEU 3.6 0.9 - - - +
442B THR* 3.0 7.4 - - - -
443B TYR 2.6 42.4 + - - +
445B ILE* 3.7 31.6 - - + -
450B VAL* 4.5 8.3 - - - -
454B PHE* 5.1 2.0 - - + -
468B LEU* 4.1 15.9 - - + -
469B ASP 3.6 4.7 - - - -
470B TYR* 4.0 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ALA* 4.1 5.2 - - + +
117B TYR* 5.9 11.9 - + + -
405B GLU* 3.2 31.9 + - + -
406B CYS* 1.3 70.1 - - - +
408B MET* 1.3 60.2 + - - +
409B LEU* 5.2 5.4 - - + -
441B LEU 3.6 4.0 - - - +
442B THR* 4.1 20.2 - - + -
467B SER 3.5 4.0 - - - +
468B LEU* 3.7 0.9 - - - -
469B ASP* 2.8 56.6 + - + +
471B ASN* 3.3 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B CYS* 4.1 15.5 - - + +
407B HIS* 1.3 77.7 - - - +
409B LEU* 1.3 62.9 + - - +
410B LEU* 3.8 13.6 - - + +
418B VAL* 4.2 7.6 - - - -
422B CYS* 3.8 27.8 - - - -
439B VAL 3.2 2.1 - - - +
440B ALA* 3.4 3.3 - - - -
441B LEU* 2.6 54.6 + - + +
443B TYR* 3.8 27.8 - - + -
454B PHE* 4.8 6.3 - - - -
458B LEU* 3.8 28.3 - - + -
466B ALA* 5.3 0.9 - - + -
467B SER 3.3 9.4 - - - +
468B LEU* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B VAL 5.5 6.5 - - - +
109B GLU* 5.6 1.1 - - - -
110B ALA* 4.6 8.5 - - + +
113B LEU* 4.0 28.0 - - + -
117B TYR* 5.8 0.4 - - - +
150B ILE* 4.6 16.2 - - + -
407B HIS* 5.2 4.3 - - + -
408B MET* 1.3 79.0 - - - +
410B LEU* 1.3 60.6 + - - +
435B HIS* 4.4 9.0 - - - +
438B GLN* 3.6 32.3 - - + +
439B VAL 3.4 5.6 - - - +
440B ALA* 4.2 20.4 - - + -
465B TYR 3.2 3.5 - - - +
466B ALA* 3.2 4.0 - - - -
467B SER* 2.9 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B MET* 3.8 28.9 - - + +
409B LEU* 1.3 78.5 - - - +
411B PRO* 1.4 80.6 - - + +
414B TYR* 3.9 3.1 - - + -
415B LEU* 3.7 40.2 - - + +
418B VAL* 3.8 24.5 - - + -
438B GLN* 3.5 8.2 + - - +
439B VAL* 2.7 45.3 + - + +
441B LEU* 4.1 13.5 - - + -
465B TYR 3.9 0.7 - - - -
466B ALA* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 1.4 92.7 - - + +
412B GLN* 1.3 65.3 + - - +
413B ALA* 3.2 4.5 - - + +
414B TYR* 3.0 36.9 + - + +
437B ASN 3.6 12.1 - - - +
438B GLN* 4.0 7.6 - - - +
465B TYR* 3.6 42.4 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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