Contacts of the strand formed by residues 362 - 371 (chain A) in PDB entry 2ZB5
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 GLN 362 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL 3.3 2.9 - - - +
358A ILE* 4.1 4.1 - - - +
359A ALA* 3.0 35.0 + - - +
360A ASP* 3.7 5.8 - - + +
361A ASN* 1.3 80.0 - - - +
363A ALA* 1.3 69.2 + - - +
364A LYS* 3.1 40.1 - - + +
414A SER* 3.7 15.1 + - - -
415A VAL 3.2 18.2 - - - +
416A ASP* 4.8 7.2 - - - +
417A LEU* 4.5 0.4 - - - -
472A TRP* 4.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA* 4.7 0.9 - - + -
297A ALA* 4.1 17.9 - - + -
321A LEU* 6.0 0.2 - - + -
357A VAL 3.4 5.8 - - - +
358A ILE* 4.1 8.7 - - + +
362A GLN* 1.3 72.2 - - - +
364A LYS* 1.3 58.7 + - - +
365A TRP* 3.5 33.3 - - + -
413A LEU 3.7 0.2 - - - +
414A SER* 3.0 8.5 - - - -
415A VAL* 2.9 34.9 + - + +
417A LEU* 4.2 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLY* 3.1 7.8 - - - -
357A VAL* 2.9 34.3 + - + +
359A ALA* 6.1 2.0 - - + +
362A GLN* 3.1 28.7 - - + +
363A ALA* 1.3 79.1 - - - +
365A TRP* 1.3 62.8 + - - +
412A VAL* 4.4 15.3 - - + +
413A LEU 3.3 3.4 - - - +
414A SER* 3.9 14.8 + - - -
443A LEU* 3.9 14.6 - - + +
452A TYR* 3.7 27.8 - - + +
470A LEU* 6.3 0.6 - - + +
472A TRP* 2.7 57.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET* 3.5 56.2 - - + +
289A VAL 3.0 20.6 + - - -
290A ALA* 3.5 19.5 - - + -
297A ALA* 3.7 20.6 - - + -
298A ALA 4.4 0.9 - - - -
299A LEU* 3.8 30.7 - - + -
321A LEU* 5.1 2.2 - - + -
354A HIS* 3.9 8.3 - - + -
355A ARG 3.8 5.2 - - - -
356A GLY* 3.4 19.3 - - - +
363A ALA* 3.5 26.9 - - + -
364A LYS* 1.3 74.3 - - - +
366A ALA* 1.3 60.7 + - - +
367A VAL* 4.2 3.6 - - + -
412A VAL* 3.0 8.0 - - - +
413A LEU* 2.8 46.4 + - + +
415A VAL* 4.4 9.0 - - + -
443A LEU* 3.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A HIS* 3.5 0.7 + - - -
355A ARG 5.6 0.4 + - - -
365A TRP* 1.3 73.3 - - - +
367A VAL* 1.3 66.3 + - - +
410A TYR* 5.9 0.7 - - + -
411A GLY 3.0 9.0 - - - +
412A VAL* 4.6 4.9 - - + -
441A MET* 3.2 38.3 + - + +
443A LEU* 3.6 26.9 - - + +
454A LEU* 3.7 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET* 4.0 10.5 - - - -
349A LEU* 3.8 19.7 - - + -
350A TYR 4.3 0.2 - - - +
351A LEU* 3.7 20.0 - - + -
354A HIS* 3.6 28.0 - - + +
365A TRP* 4.7 2.2 - - + -
366A ALA* 1.3 84.8 - - - +
368A PRO* 1.3 74.7 - - + +
369A THR* 3.3 0.8 + - - +
411A GLY 2.8 30.3 + - - +
413A LEU* 3.7 26.9 - - + -
441A MET* 3.8 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.8 1.7 - - - -
350A TYR* 3.1 52.4 + - + +
352A SER* 5.7 0.4 - - - +
354A HIS* 4.1 10.5 - - + -
367A VAL* 1.3 84.1 - - + +
369A THR* 1.3 61.7 + - - +
399A TRP* 3.6 37.9 - - + -
408A PRO* 4.5 4.9 - - + -
409A SER 3.4 10.1 - - - +
435A ILE* 4.6 4.9 - - + -
437A HIS 5.1 0.2 - - - +
438A GLY* 5.1 6.5 - - - -
440A GLY 6.1 1.1 - - - -
441A MET* 4.2 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 4.8 1.6 - - + -
346A ILE* 3.8 27.6 - - + -
348A ARG 3.3 13.0 - - - +
349A LEU* 3.2 24.6 - - + +
367A VAL 3.3 8.5 + - - -
368A PRO* 1.3 75.5 - - - +
370A THR* 1.3 71.3 + - - +
408A PRO* 4.4 1.1 - - - +
409A SER* 2.6 55.4 + - - +
411A GLY* 3.4 16.1 - - - -
427A ILE* 5.3 2.5 - - + +
429A SER* 4.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASP* 2.9 27.3 + - - +
348A ARG* 3.0 36.7 + - - +
350A TYR* 3.9 22.3 - - + +
369A THR* 1.3 81.2 - - - +
371A ARG* 1.3 64.0 + - - +
374A ASP* 4.9 0.4 - - - -
401A PRO* 4.2 7.0 - - + -
406A ARG* 3.6 43.7 + - + +
407A ILE 4.9 0.7 - - - -
408A PRO* 4.4 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ASP* 5.4 3.4 + - - -
345A VAL* 3.3 15.7 - - + +
346A ILE* 3.7 19.1 - - + +
347A ASP 4.2 0.2 - - - +
369A THR 3.9 0.4 + - - -
370A THR* 1.3 79.8 - - - +
372A THR* 1.3 58.5 + - - +
373A ASP* 3.0 39.4 + - - +
374A ASP* 2.9 34.9 + - - +
377A ARG* 4.5 6.7 - - - +
406A ARG* 3.1 5.5 + - - -
407A ILE 4.9 1.2 + - - -
409A SER* 3.5 25.1 - - - +
429A SER* 2.7 51.4 + - - +
430A GLY* 4.3 3.6 - - - +
431A PHE* 3.7 19.4 - - + -
----------------------------------------------------------
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