Contacts of the helix formed by residues 346 - 356 (chain B) 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 ILE 346 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL* 5.2 2.0 - - + -
316B ILE* 3.2 49.8 - - + +
317B SER 4.9 0.2 - - - +
318B SER* 4.2 14.1 - - - +
321B ILE* 3.2 33.9 - - + -
342B THR* 3.5 22.2 - - + -
343B PRO* 2.8 22.5 + - + +
344B ASN 2.8 1.2 + - - -
345B ASP* 1.3 86.7 - - - +
347B ILE* 1.3 66.0 + - - +
348B PRO* 3.1 4.0 - - - -
349B SER* 2.9 19.8 + - - +
350B ILE* 3.4 3.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B THR* 3.9 11.0 - - - +
343B PRO 3.8 9.6 - - - +
344B ASN* 3.5 28.7 - - + +
346B ILE* 1.3 75.3 - - - +
348B PRO* 1.3 58.2 - - + +
350B ILE* 2.9 10.9 + - - +
351B GLU* 2.7 38.7 + - - +
378B THR* 4.6 5.6 - - + +
381B LYS* 4.6 22.9 - - + +
382B LEU* 3.4 42.8 - - + -
385B ALA* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER* 6.3 0.4 - - - -
344B ASN 3.3 11.2 - - - +
345B ASP 4.5 4.5 - - - +
346B ILE* 2.9 6.0 - - - +
347B ILE* 1.3 93.4 - - + +
349B SER* 1.3 62.0 + - - +
351B GLU* 3.0 17.0 + - + +
352B ARG* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER* 3.4 26.1 - - - -
321B ILE* 3.2 28.9 - - - +
322B ASP* 3.3 26.1 - - - +
325B VAL* 4.8 0.9 - - - +
346B ILE* 2.9 17.3 + - - +
348B PRO* 1.3 74.5 - - - +
350B ILE* 1.3 63.6 + - - +
352B ARG* 3.4 7.5 + - - +
353B ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 3.5 23.1 - - + -
334B ILE* 3.7 20.9 - - + -
342B THR* 4.0 22.0 - - + +
346B ILE* 3.9 6.1 - - + +
347B ILE* 2.9 9.9 + - + +
349B SER* 1.3 77.1 + - - +
351B GLU* 1.3 67.3 + - - +
352B ARG 3.1 0.3 + - - -
353B ALA* 3.1 8.3 + - - +
354B VAL* 3.0 29.7 + - + +
360B VAL* 3.8 15.7 - - + -
382B LEU* 3.5 25.6 - - + -
385B ALA* 5.1 1.8 - - + -
387B VAL* 3.5 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ILE* 2.7 16.4 + - - +
348B PRO* 3.2 19.8 - - - +
350B ILE* 1.3 76.9 - - - +
352B ARG* 1.3 59.1 + - - +
354B VAL* 3.7 5.9 + - - +
355B GLU* 3.0 41.9 + - + +
384B LYS* 4.4 6.1 - - - +
385B ALA* 4.0 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 5.5 2.5 - - - +
325B VAL* 6.1 2.0 - - + -
348B PRO 3.0 10.8 + - - +
349B SER* 3.6 11.4 - - - +
350B ILE 3.1 0.2 - - - -
351B GLU* 1.3 73.9 - - - +
353B ALA* 1.3 54.2 - - - +
354B VAL 3.0 1.8 - - - -
355B GLU* 2.8 18.2 + - - +
356B GLU* 2.7 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ILE* 4.6 4.5 - - + -
325B VAL* 3.2 34.9 - - + +
332B ILE* 5.0 1.8 - - + -
349B SER 3.2 7.8 + - - +
350B ILE* 3.1 12.7 + - - +
352B ARG* 1.3 77.6 - - - +
354B VAL* 1.3 59.1 + - - +
356B GLU* 3.1 9.2 + - - -
358B VAL* 2.8 45.9 + - + +
360B VAL* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ILE* 3.0 21.8 - - + +
351B GLU 3.7 5.4 - - - +
352B ARG 3.0 0.6 - - - -
353B ALA* 1.3 73.7 - - - +
355B GLU* 1.3 54.3 + - + +
356B GLU 2.9 4.5 - - - -
357B GLY* 2.7 25.6 + - - -
358B VAL 3.7 8.2 + - - +
360B VAL* 3.9 20.2 - - + -
385B ALA 3.2 28.0 - - - +
386B GLY* 3.8 21.8 - - - +
412B LEU* 3.9 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLU* 3.0 29.3 - - + +
352B ARG* 2.8 19.5 + - - +
354B VAL* 1.3 73.8 - - + +
356B GLU* 1.3 62.0 + - + +
357B GLY 3.1 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B VAL* 4.1 24.1 - - + +
330B LYS* 5.3 4.5 + - - -
352B ARG* 2.7 17.9 + - + +
353B ALA* 3.3 13.5 - - - +
354B VAL 2.9 0.6 - - - -
355B GLU* 1.3 81.4 - - + +
357B GLY* 1.3 59.3 + - - -
358B VAL* 3.3 6.8 + - + +
----------------------------------------------------------
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