Contacts of the strand formed by residues 396 - 411 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374D VAL* 3.9 11.0 - - + -
375D GLU 3.7 2.7 - - - -
376D THR* 4.7 0.2 - - - +
377D THR* 4.9 0.9 - - - -
390D LEU* 4.4 20.9 - - + -
391D PRO* 3.4 36.8 - - + +
392D ALA 3.4 11.0 - - - +
393D VAL* 3.5 27.4 + - + +
394D ASN 3.3 5.0 - - - +
395D ASN* 1.3 77.2 - - - +
397D TYR* 1.3 64.1 + - - +
398D GLU* 3.8 2.9 - - - +
399D LEU* 3.7 38.1 - - + +
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Residues in contact with TYR 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D GLU* 2.7 25.4 + - + +
376D THR 3.8 14.4 - - - +
377D THR* 3.8 10.8 - - - +
379D ARG* 3.0 48.9 + - + -
395D ASN 3.8 3.0 + - - -
396D ILE* 1.3 75.5 - - - +
398D GLU* 1.3 83.7 + - + +
400D ARG* 5.9 0.2 - - - -
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Residues in contact with GLU 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D GLU 4.2 0.2 - - - +
374D VAL* 3.6 1.6 - - - +
375D GLU* 2.7 38.3 + - + +
396D ILE* 3.8 3.4 - - - -
397D TYR* 1.3 102.3 + - + +
399D LEU* 1.3 61.6 + - - +
400D ARG* 2.7 35.6 + - - +
477D ALA* 3.5 33.1 - - + +
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Residues in contact with LEU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D TYR* 4.0 26.9 - - + -
373D GLU 4.0 0.9 - - - -
374D VAL* 3.8 25.1 - - + -
390D LEU* 4.0 28.3 - - + -
396D ILE* 3.7 22.7 - - + +
398D GLU* 1.3 72.1 - - - +
400D ARG* 1.3 64.0 + - - +
401D GLU 4.0 0.7 + - - -
477D ALA* 3.6 2.9 - - - -
478D SER 3.2 31.4 + - - +
480D MET* 3.5 41.5 - - + +
498D ILE* 4.7 2.2 - - + -
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Residues in contact with ARG 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D TYR* 3.8 6.9 - - - +
373D GLU* 2.6 100.9 + - + +
374D VAL 5.2 0.2 - - - -
375D GLU* 2.7 48.4 + - - +
381D VAL* 4.2 10.3 - - - +
398D GLU* 2.7 28.9 + - - +
399D LEU* 1.3 70.8 - - - +
401D GLU* 1.3 62.0 + - - +
475D PHE* 3.8 15.6 - - + -
476D GLN* 3.5 4.5 - - - +
477D ALA* 3.4 26.0 - - - +
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Residues in contact with GLU 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D TYR* 3.9 12.3 - - + -
399D LEU* 4.0 2.7 + - + +
400D ARG* 1.3 71.4 - - - +
402D PRO* 1.3 83.0 - - + +
403D ILE* 3.6 11.1 + - + +
426D ARG* 2.6 40.6 + - - -
446D PRO* 3.3 19.7 - - + +
448D ALA* 4.2 9.9 - - + +
475D PHE* 3.4 2.0 - - - -
476D GLN 2.8 34.1 + - - +
478D SER* 3.5 8.4 + - - -
480D MET* 3.4 30.0 - - + +
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Residues in contact with PRO 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D VAL* 3.7 22.7 - - + -
371D VAL 3.4 22.2 - - - +
372D TYR* 3.7 15.5 - - + -
400D ARG 4.0 2.0 - - - +
401D GLU* 1.3 96.3 - - + +
403D ILE* 1.3 54.4 + - - +
446D PRO 3.6 0.3 - - - -
447D MET* 2.7 41.1 + - + +
448D ALA 4.8 0.4 - - - +
472D PHE* 4.2 12.1 - - + -
474D ARG 3.8 1.8 - - - +
475D PHE* 3.7 21.5 - - + -
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Residues in contact with ILE 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401D GLU* 3.9 18.6 - - - +
402D PRO* 1.3 75.7 - - - +
404D ALA* 1.3 64.8 + - - +
444D GLU* 4.2 28.7 - - + +
445D ILE 4.0 7.6 - - - +
446D PRO* 3.8 28.0 - - + -
447D MET* 4.3 2.2 - - - -
472D PHE* 4.0 4.4 - - - -
473D LYS* 3.0 28.3 + - + +
474D ARG* 2.8 49.1 + - - +
476D GLN* 4.0 13.2 - - + +
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Residues in contact with ALA 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D ILE* 1.3 76.1 - - - +
405D GLU* 1.3 63.0 + - - +
406D CYS* 3.5 5.8 - - - -
444D GLU* 3.6 0.2 - - - -
445D ILE 2.8 45.1 + - - +
447D MET* 3.6 30.4 - - + +
450D VAL* 4.3 11.9 - - + -
470D TYR* 4.3 7.9 - - + -
471D ASN 3.3 13.9 - - - +
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Residues in contact with GLU 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D ALA* 1.3 71.2 - - - +
406D CYS* 1.3 60.6 + - - +
407D HIS* 3.2 36.4 + - - +
430D THR* 4.8 8.2 - - + +
442D THR* 4.3 11.3 + - - +
443D TYR 3.7 4.9 - - - +
444D GLU* 4.5 9.9 - - + -
469D ASP 3.8 0.9 - - - +
470D TYR* 3.1 4.7 - - - -
471D ASN* 3.0 51.0 + - - +
473D LYS* 2.8 43.9 + - + +
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Residues in contact with CYS 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404D ALA 3.5 17.0 - - - -
405D GLU* 1.3 73.5 - - - +
407D HIS* 1.3 63.8 + - - +
408D MET* 3.4 11.7 - - + +
442D THR* 3.2 4.3 - - - -
443D TYR 2.7 36.5 + - - +
445D ILE* 3.8 31.9 - - + -
450D VAL* 4.2 12.3 - - - -
454D PHE* 5.1 0.9 - - - -
468D LEU* 4.1 16.4 - - + -
469D ASP 3.4 4.0 - - - -
470D TYR* 3.8 15.9 - - - -
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Residues in contact with HIS 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA* 4.7 4.2 - - + +
117D TYR* 6.1 9.6 - + + -
405D GLU* 3.2 37.7 + - + -
406D CYS* 1.3 70.5 - - - +
408D MET* 1.3 60.1 + - - +
409D LEU* 5.5 3.8 - - + -
441D LEU 3.5 5.8 - - - +
442D THR* 3.8 21.5 - - + -
467D SER 3.8 0.7 - - - +
469D ASP* 2.8 60.6 + - + +
471D ASN* 3.4 16.3 + - - -
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Residues in contact with MET 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ALA* 5.0 0.2 - - - -
406D CYS* 3.4 24.2 - - + +
407D HIS* 1.3 78.3 - - - +
409D LEU* 1.3 65.6 + - - +
410D LEU* 3.9 9.9 - - + -
418D VAL* 3.3 34.1 - - + -
422D CYS* 4.3 16.2 - - - -
439D VAL 3.7 0.2 - - - +
440D ALA* 3.4 4.0 - - - -
441D LEU* 2.6 63.6 + - + +
443D TYR* 5.3 2.7 - - + +
454D PHE* 4.7 4.5 - - - -
458D LEU* 3.6 23.1 - - + -
466D ALA* 4.6 2.2 - - + +
467D SER 3.3 13.2 - - - +
468D LEU* 4.9 6.3 - - - -
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Residues in contact with LEU 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D VAL 5.4 4.9 - - - +
109D GLU* 5.5 1.8 - - - -
110D ALA* 4.3 9.6 - - + +
113D LEU* 3.8 28.9 - - + -
117D TYR* 5.6 1.6 - - - +
150D ILE* 4.8 12.3 - - + -
407D HIS* 5.5 3.4 - - + -
408D MET* 1.3 82.5 - - - +
410D LEU* 1.3 61.0 + - - +
435D HIS* 4.6 5.4 - - - +
438D GLN* 3.7 32.8 - - + +
439D VAL 3.6 2.0 - - - +
440D ALA* 3.9 29.4 - - + +
465D TYR 3.0 15.6 - - - +
466D ALA* 3.1 2.3 - - - -
467D SER* 3.1 32.4 + - - +
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Residues in contact with LEU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408D MET* 3.9 20.6 - - + -
409D LEU* 1.3 80.4 - - - +
411D PRO* 1.3 76.6 - - + +
414D TYR* 4.2 3.4 - - + -
415D LEU* 3.7 37.7 - - + +
418D VAL* 3.7 19.7 - - + -
438D GLN* 3.5 8.2 + - - -
439D VAL* 2.7 46.7 + - + +
441D LEU* 3.8 26.9 - - + -
462D SER* 5.4 0.2 - - - -
465D TYR* 3.8 1.8 - - + -
466D ALA* 3.7 16.6 - - + -
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Residues in contact with PRO 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410D LEU* 1.3 98.4 - - + +
412D GLN* 1.3 64.1 + - - +
413D ALA* 3.2 6.0 + - + +
414D TYR* 3.2 35.6 + - + +
437D ASN* 3.3 14.1 - - + +
438D GLN* 4.1 12.3 - - - +
439D VAL* 4.6 0.4 - - - -
465D TYR* 3.6 41.7 - - + +
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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