Contacts of the strand formed by residues 359 - 364 (chain A) in PDB entry 1ZQ1
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 ALA 359 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS 2.8 17.3 + - - +
331A GLY* 3.4 0.5 - - - -
332A ILE 2.7 32.9 + - - +
357A GLY 4.1 0.2 + - - -
358A VAL* 1.3 71.4 - - - +
360A VAL* 1.3 58.4 + - - +
361A CYS* 4.0 0.7 - - - -
388A ILE* 4.8 6.1 - - + -
402A LEU* 3.7 29.9 - - + +
406A LEU* 4.1 13.9 - - + -
412A LEU* 4.2 11.2 - - + +
415A VAL* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE* 3.3 9.9 - - + +
334A ILE* 3.4 35.4 - - + -
350A ILE* 4.0 15.7 - - + -
353A ALA* 4.1 25.8 - - + -
354A VAL* 4.2 14.4 - - + +
358A VAL* 3.6 13.0 + - + +
359A ALA* 1.3 76.1 - - - +
361A CYS* 1.3 64.4 + - - +
386A GLY 5.5 0.4 + - - -
387A VAL* 3.6 16.3 - - + +
388A ILE* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ILE 2.9 10.0 + - - +
333A VAL* 3.7 16.4 - - + +
334A ILE* 2.8 31.5 + - - +
360A VAL* 1.3 79.2 - - - +
362A MSE 1.3 61.7 + - - +
387A VAL* 4.4 2.0 - - - -
388A ILE* 3.2 16.6 - - - -
390A CYS* 3.4 23.1 - - - -
398A ALA* 5.4 1.3 - - + -
402A LEU* 4.0 30.5 - - - -
419A MSE 4.1 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 3.4 27.8 - - + +
336A GLY* 3.9 9.2 - - - -
340A GLY* 3.7 31.6 - - - +
341A HIS 4.3 0.2 - - - +
342A THR* 3.6 23.1 - - - +
361A CYS* 1.3 73.2 - - - +
363A THR* 1.3 75.2 + - - +
371A VAL* 3.8 14.4 - - + +
373A LEU* 4.3 9.4 - - + -
382A LEU* 3.8 31.4 - - + -
387A VAL* 3.8 18.1 - - + +
388A ILE 2.9 12.6 + - - +
389A PRO* 4.5 0.7 - - + -
390A CYS* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A VAL* 4.1 8.8 - - + +
334A ILE 3.1 4.9 + - - +
335A GLU* 3.5 16.3 - - - +
336A GLY* 2.9 20.4 + - - -
340A GLY* 4.4 0.9 - - - -
362A MSE 1.3 87.8 - - - +
364A SER* 1.3 62.1 + - - +
371A VAL* 3.5 12.1 - - - +
390A CYS* 3.9 10.8 - - + +
391A GLU 5.7 0.7 - - - +
393A MSE 3.7 19.5 - - - +
395A PRO* 3.5 23.0 - - + +
398A ALA* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 4.6 1.3 - - - -
336A GLY 3.7 6.1 - - - -
338A GLY 3.1 28.7 + - - -
340A GLY 4.6 1.6 - - - -
363A THR* 1.3 79.0 - - - +
365A GLN* 1.3 62.3 + - - +
366A CYS* 2.8 37.8 + - - +
367A ILE* 4.0 0.7 + - - +
371A VAL* 3.7 9.6 - - - +
395A PRO* 3.5 19.9 - - - +
259B THR* 3.7 9.2 - - - -
----------------------------------------------------------
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