Contacts of the strand formed by residues 382 - 394 (chain A) in PDB entry 4ZCH
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 GLU 382 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS 4.5 0.4 - - - -
376A VAL* 3.4 13.0 - - - +
377A HIS* 2.9 57.8 + - + +
380A GLY* 4.1 14.3 - - - +
381A ASP* 1.3 78.6 - - - +
383A LEU* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LYS* 3.8 35.7 - - + -
375A LYS 3.5 3.8 - - - -
376A VAL* 3.9 13.5 - - + -
381A ASP 4.3 0.2 + - - -
382A GLU* 1.3 76.8 - - - +
384A SER* 1.3 69.2 + - - +
385A LEU* 4.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ARG* 3.7 3.6 + - - +
374A LYS* 3.4 6.1 - - - +
375A LYS* 3.0 57.2 + - - +
383A LEU* 1.3 75.3 - - - +
385A LEU* 1.3 61.9 + - - +
386A VAL* 4.2 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 5.6 2.9 - - + +
372A GLN* 3.5 44.0 - - + +
373A ARG 3.4 9.9 - - - +
374A LYS* 3.8 18.2 - - + -
383A LEU* 4.9 13.6 - - + +
384A SER* 1.3 74.4 + - - +
386A VAL* 1.3 64.8 + - - +
387A THR 4.3 0.4 + - - -
419A GLN* 3.4 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLN* 3.3 4.3 - - - -
373A ARG* 2.8 69.6 + - + +
384A SER* 4.2 11.9 - - - +
385A LEU* 1.3 79.0 - - - +
387A THR* 1.3 74.2 + - - +
388A LEU* 3.6 5.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A HIS* 3.5 49.2 + - + +
370A LEU* 3.9 29.3 - - + +
371A ILE 3.7 5.8 - - - +
372A GLN* 3.6 22.6 + - - +
386A VAL* 1.3 81.7 - - - +
388A LEU* 1.3 61.0 + - - +
389A PHE 3.9 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A HIS* 5.5 1.6 + - - -
132A PRO 4.5 2.6 - - - +
133A HIS* 3.3 17.9 - - - +
354A ILE* 4.3 1.6 - - + -
371A ILE* 2.7 20.0 + - + +
373A ARG* 4.1 39.9 - - + +
386A VAL* 4.5 6.5 - - + +
387A THR* 1.3 76.9 - - - +
389A PHE* 1.4 91.2 + - + +
410A ALA* 4.1 27.1 - - + -
412A LEU* 4.4 1.6 - - + -
418A LEU* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A HIS* 4.1 14.6 - + - -
133A HIS* 3.8 6.1 - - - -
136A PHE* 3.9 20.2 - + + -
354A ILE* 4.1 24.2 - - + -
369A HIS 4.2 0.2 - - - +
370A LEU* 3.6 1.7 - - - -
371A ILE* 2.8 57.2 + - + +
387A THR* 3.9 1.8 - - - +
388A LEU* 1.4 107.4 - - + +
390A ARG* 1.3 60.4 + - - +
406A SER* 3.7 18.2 - - - +
407A ALA 4.2 5.6 - - - -
408A GLY* 3.3 38.6 - - - -
409A ILE 3.4 18.8 - - - -
410A ALA* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLN* 2.9 26.5 + - - -
62A LEU* 3.4 27.8 - - + +
64A GLN* 5.3 0.2 - - - +
100A TYR* 4.9 9.9 - - - -
102A SER* 4.4 0.9 + - - -
129A ASN* 3.8 14.8 - - - +
131A SER* 5.1 3.4 + - - -
133A HIS* 2.9 41.7 + - + +
134A GLY* 4.7 1.8 - - - -
369A HIS 3.6 3.4 - - - +
370A LEU* 3.7 28.2 - - + +
371A ILE* 6.2 0.2 - - - -
389A PHE* 1.3 75.5 - - - +
391A CYS* 1.3 71.9 + - - +
392A ILE* 3.5 35.6 - - + +
406A SER* 3.6 5.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 3.8 8.1 - - - -
368A GLY* 3.1 4.2 - - - -
369A HIS* 2.9 51.0 + - + +
390A ARG* 1.3 78.7 + - - +
392A ILE* 1.3 62.9 + - - +
404A CYS* 2.1 60.3 - - - -
405A TYR 3.4 17.3 - - - -
406A SER* 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 3.5 41.7 - - + -
100A TYR* 3.8 27.8 - - + +
102A SER* 2.9 36.6 + - - +
366A ALA* 4.2 16.8 - - + -
367A MET 3.5 13.7 - - - +
368A GLY* 5.7 0.9 - - - +
390A ARG* 3.5 28.7 - - + +
391A CYS* 1.3 76.1 - - - +
393A GLN* 1.3 67.8 + - - +
404A CYS* 3.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ARG* 5.8 6.1 + - - +
100A TYR 3.6 7.2 - - - -
101A ASN* 3.5 12.1 - - - +
242A GLN* 4.6 3.3 + - - +
360A TYR* 3.2 21.4 - - - -
366A ALA* 3.3 2.7 - - - -
367A MET 2.8 39.3 + - - +
392A ILE* 1.3 76.9 - - - +
394A ASN* 1.3 63.1 + - - +
395A MET* 4.0 11.9 - - - +
402A ASN* 2.9 46.3 + - + +
403A SER 3.1 18.7 - - - +
404A CYS* 3.4 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 3.6 18.2 - - + +
98A ARG* 2.8 35.9 + - - +
99A ALA* 3.2 5.7 - - - -
100A TYR 2.9 27.9 + - - +
101A ASN* 3.1 26.5 + - - +
365A TYR 2.8 24.0 + - - -
366A ALA* 4.0 3.4 - - - +
393A GLN* 1.3 74.9 - - - +
395A MET* 1.3 61.0 + - - +
396A PRO* 4.3 0.7 - - - +
402A ASN* 3.6 18.2 + - - -
----------------------------------------------------------
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