Contacts of the strand formed by residues 396 - 411 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A VAL* 3.8 23.1 - - + -
375A GLU 3.8 2.7 - - - -
376A THR* 4.7 0.2 - - - +
377A THR* 4.6 1.1 - - - -
390A LEU* 4.4 19.5 - - + -
391A PRO* 3.4 26.7 - - + +
392A ALA 3.3 10.9 + - - +
393A VAL* 3.6 26.1 + - + +
394A ASN 3.3 3.8 - - - +
395A ASN* 1.3 77.6 - - - +
397A TYR* 1.3 63.8 + - - +
398A GLU* 3.8 11.9 - - - +
399A LEU* 3.8 27.1 - - + +
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Residues in contact with TYR 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 2.7 38.7 + - + +
376A THR 3.6 13.4 - - - +
377A THR* 4.1 5.8 - - - +
379A ARG* 3.2 46.7 + - + -
395A ASN 3.7 2.4 + - - -
396A ILE* 1.3 76.2 - - - +
398A GLU* 1.3 85.6 + - + +
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLU 4.0 0.7 - - - +
374A VAL* 3.8 0.2 - - - -
375A GLU* 3.0 26.9 + - - +
396A ILE* 3.6 3.6 - - - -
397A TYR* 1.3 109.1 + - + +
399A LEU* 1.3 62.2 + - - +
400A ARG* 2.8 37.6 + - - +
477A ALA* 3.4 33.4 - - + +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 3.9 23.1 - - + -
373A GLU 4.1 0.9 - - - -
374A VAL* 3.7 27.4 - - + -
390A LEU* 4.2 24.9 - - + -
396A ILE* 3.8 22.6 - - + +
398A GLU* 1.3 71.5 - - - +
400A ARG* 1.3 64.3 + - - +
401A GLU* 4.0 0.5 + - - +
477A ALA* 3.7 0.9 - - - -
478A SER* 3.1 33.5 + - - +
480A MET* 3.3 44.0 - - + +
498A ILE* 5.0 4.0 - - + -
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Residues in contact with ARG 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A TYR* 3.7 9.5 - - - +
373A GLU* 2.7 86.3 + - + +
375A GLU* 2.7 49.0 + - - +
381A VAL* 4.3 10.3 - - - +
398A GLU* 2.8 29.0 + - - +
399A LEU* 1.3 73.6 - - - +
401A GLU* 1.3 61.8 + - - +
475A PHE* 3.8 21.4 - - + -
476A GLN* 3.3 4.5 - - - +
477A ALA* 3.5 25.6 - - - +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 4.1 11.0 - - + -
399A LEU* 4.0 1.0 + - + +
400A ARG* 1.3 72.7 - - - +
402A PRO* 1.3 82.2 - - + +
403A ILE* 3.5 13.9 + - + +
426A ARG* 2.6 33.4 + - - -
446A PRO* 3.0 17.0 - - + +
448A ALA* 4.4 7.9 - - + +
475A PHE* 3.4 3.7 - - - -
476A GLN* 2.7 35.4 + - - +
478A SER* 3.0 20.8 + - - -
480A MET* 3.2 26.1 - - + +
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Residues in contact with PRO 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A VAL* 3.6 22.2 - - + -
371A VAL 3.3 26.7 - - - +
372A TYR* 3.8 13.7 - - + -
400A ARG 4.1 2.0 - - - +
401A GLU* 1.3 96.7 - - + +
403A ILE* 1.3 59.1 + - - +
446A PRO* 3.6 1.2 - - - +
447A MET* 2.9 35.9 + - + -
448A ALA 4.6 1.1 - - - +
472A PHE* 4.2 12.3 - - + -
474A ARG 3.6 5.8 - - - +
475A PHE* 3.7 12.5 - - + -
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Residues in contact with ILE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A GLU* 3.7 25.8 - - - +
402A PRO* 1.3 80.3 - - - +
404A ALA* 1.3 62.9 + - - +
444A GLU* 3.9 39.5 - - + +
445A ILE 4.0 7.2 - - - +
446A PRO* 4.0 17.9 - - + -
447A MET* 4.6 2.0 - - - -
472A PHE* 3.8 3.1 - - - -
473A LYS* 2.9 29.4 + - + +
474A ARG* 2.8 30.8 + - + +
476A GLN* 4.1 23.8 - - + +
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ILE* 1.3 74.2 - - - +
405A GLU* 1.3 60.4 - - - +
406A CYS* 3.7 3.1 + - - -
444A GLU* 3.5 2.8 - - - -
445A ILE 2.9 39.6 + - - +
447A MET* 3.8 32.5 - - + +
450A VAL* 4.2 11.4 - - + -
470A TYR* 4.2 16.2 - - + -
471A ASN 3.5 8.3 - - - +
473A LYS* 4.7 0.4 - - - -
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Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ILE 4.1 1.0 + - - -
404A ALA* 1.3 70.3 - - - +
406A CYS* 1.3 61.3 + - - +
407A HIS* 3.2 35.5 + - + -
430A THR* 4.5 7.8 - - + +
442A THR* 4.1 14.1 + - - +
443A TYR 3.4 9.2 - - - +
444A GLU* 4.7 11.1 - - + +
469A ASP 3.5 1.7 - - - +
470A TYR* 3.2 19.8 - - - -
471A ASN* 2.9 28.7 + - - +
473A LYS* 3.5 41.8 + - + +
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Residues in contact with CYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ALA 3.8 11.9 - - - -
405A GLU* 1.3 73.7 - - - +
407A HIS* 1.3 63.1 + - - +
408A MET* 3.9 8.3 + - + +
441A LEU 3.6 0.9 - - - +
442A THR* 3.2 5.3 - - - -
443A TYR* 2.8 39.9 + - + +
445A ILE* 3.8 30.5 - - + -
450A VAL* 4.0 17.0 - - - -
454A PHE* 5.2 0.2 - - - -
468A LEU* 3.9 19.3 - - + -
469A ASP 3.3 5.2 - - - -
470A TYR* 3.9 15.5 - - - -
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Residues in contact with HIS 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 5.3 3.4 - - + +
117A TYR* 5.9 9.8 - + + -
405A GLU* 3.2 40.1 + - + -
406A CYS* 1.3 68.8 - - - +
408A MET* 1.3 63.3 + - - +
409A LEU* 5.9 0.7 - - + -
441A LEU 3.5 5.2 - - - +
442A THR* 4.1 19.0 + - + -
467A SER 3.3 3.5 - - - +
469A ASP* 2.7 62.7 + - + +
471A ASN* 4.0 14.5 + - - -
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Residues in contact with MET 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ALA* 5.6 0.4 - - - -
406A CYS* 4.1 11.2 - - + +
407A HIS* 1.3 80.3 - - - +
409A LEU* 1.3 65.7 + - - +
410A LEU* 3.9 6.7 - - + +
418A VAL* 3.8 4.3 - - + -
422A CYS* 3.6 30.1 - - - -
439A VAL 3.5 0.5 - - - +
440A ALA* 3.3 6.4 - - - +
441A LEU* 2.7 69.8 + - + +
443A TYR* 4.4 11.2 - - + -
454A PHE* 4.6 7.4 - - - -
458A LEU* 3.5 30.7 - - + -
466A ALA* 5.4 1.3 - - + -
467A SER 3.1 12.8 - - - +
468A LEU* 4.4 11.4 - - + -
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 6.0 2.9 - - + +
109A GLU* 6.0 1.1 - - - -
110A ALA* 4.4 9.4 - - + +
113A LEU* 4.1 27.6 - - + -
150A ILE* 4.8 13.9 - - + -
407A HIS* 6.4 0.2 - - + -
408A MET* 1.3 83.9 - - - +
410A LEU* 1.3 61.2 + - - +
435A HIS* 5.1 5.6 - - - +
438A GLN* 3.5 41.7 - - + +
439A VAL 3.5 4.3 - - - +
440A ALA* 3.8 19.3 - - + -
465A TYR 3.1 8.6 - - - +
466A ALA* 3.2 1.6 - - - -
467A SER* 3.1 40.3 + - - +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A MET* 3.9 16.2 - - + +
409A LEU* 1.3 78.5 - - - +
411A PRO* 1.4 71.8 - - + +
414A TYR* 4.0 4.5 - - + -
415A LEU* 3.5 39.9 - - + +
418A VAL* 3.6 25.8 - - + -
438A GLN* 4.0 6.0 - - - +
439A VAL* 2.7 53.1 + - + +
441A LEU* 3.8 25.6 - - + -
462A SER* 5.6 0.4 - - - -
465A TYR 3.8 0.2 - - - -
466A ALA* 4.1 13.9 - - + +
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Residues in contact with PRO 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A LEU* 1.4 88.6 - - + +
412A GLN* 1.3 66.1 + - - +
413A ALA* 2.9 6.2 + - + +
414A TYR* 3.1 38.2 + - + +
415A LEU 4.3 1.4 + - - -
437A ASN* 3.8 15.0 - - - +
438A GLN* 4.3 10.5 - - + +
439A VAL* 4.8 0.2 - - - -
465A TYR* 3.6 39.0 - - + +
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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