Contacts of the helix formed by residues 369 - 385 (chain A) in PDB entry 4Z2A
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 369 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 2.5 31.1 - - - +
341A TYR 5.0 0.4 - - - -
342A SER* 3.7 10.5 - - - +
351A ILE* 3.8 13.5 - - + -
364A HIS* 3.5 29.4 - - + +
365A THR 3.9 10.1 + - - +
366A GLY 3.0 12.6 + - - +
368A SER* 1.3 79.5 - - - +
370A SER* 1.3 60.9 + - - +
371A ALA 3.5 0.2 - - - -
372A PRO* 3.6 2.6 - - - +
373A LEU* 3.7 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ILE* 4.0 5.4 - - - -
318A SER 3.7 13.2 - - - -
319A SER* 2.8 24.2 + - - -
340A THR* 2.9 41.3 + - - -
341A TYR 3.5 7.8 + - - -
342A SER* 3.5 3.3 - - - -
367A THR* 2.9 12.0 + - - -
369A ALA* 1.3 77.8 - - - +
371A ALA* 1.3 67.2 + - - +
373A LEU* 3.3 2.5 + - - -
374A ALA* 3.1 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A SER* 3.9 10.3 - - - +
252A ALA 4.3 6.1 - - - +
253A SER* 5.7 0.2 - - - -
290A VAL* 3.5 13.9 - - + +
291A TRP* 3.9 6.5 - - - -
292A ALA* 3.7 34.3 - - + +
317A ILE* 4.4 7.7 - - - +
367A THR 3.5 3.0 + - - +
368A SER 4.6 0.9 - - - +
370A SER* 1.3 80.0 - - - +
372A PRO* 1.3 64.8 - - + +
374A ALA* 3.1 5.5 + - - +
375A ALA* 2.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A CYS* 3.6 36.1 - - + +
201A GLU* 3.4 24.7 - - + +
202A VAL* 3.4 15.9 - - + +
251A SER* 3.8 14.6 - - - +
368A SER 3.0 23.8 - - - +
369A ALA 3.6 3.1 - - - +
370A SER 3.5 3.1 - - - -
371A ALA* 1.3 91.2 - - + +
373A LEU* 1.3 58.9 + - - +
375A ALA* 3.2 3.8 + - + -
376A GLY* 2.9 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.8 37.9 - - + -
124A LEU* 5.9 0.2 - - + -
132A LEU* 4.1 18.8 - - + -
201A GLU* 3.3 31.2 - - + +
215A VAL* 3.8 24.2 - - + +
340A THR* 4.0 8.7 - - - +
341A TYR 3.4 26.7 - - - +
351A ILE* 4.0 5.6 - - + -
369A ALA 3.7 9.0 - - - +
370A SER 3.3 6.5 + - - +
372A PRO* 1.3 75.8 - - - +
374A ALA* 1.3 63.6 + - - +
376A GLY* 3.2 2.8 + - - -
377A ILE* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 3.9 4.5 - - + -
317A ILE* 3.5 29.2 - - + -
340A THR* 3.9 3.0 - - + +
370A SER 3.1 8.8 + - - +
371A ALA 3.1 9.5 + - - +
373A LEU* 1.3 76.3 - - - +
375A ALA* 1.3 57.3 + - - +
377A ILE* 3.1 2.9 + - - +
378A ILE* 2.8 37.7 + - + +
429A LEU* 3.4 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A VAL* 4.3 3.7 - - + +
202A VAL* 4.2 9.9 - - + -
249A ILE* 4.0 20.7 - - + +
251A SER* 4.0 23.6 - - - -
290A VAL* 4.1 13.4 - - + +
371A ALA 2.8 16.5 + - - +
372A PRO* 3.2 10.5 + - + +
374A ALA* 1.3 73.1 - - - +
376A GLY* 1.3 54.5 + - - +
378A ILE* 3.3 3.2 + - - +
379A ALA* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.0 17.2 - - - +
215A VAL* 3.4 20.8 - - - +
216A ALA* 3.8 6.0 - - - +
372A PRO 2.9 13.1 + - - -
373A LEU 3.2 3.8 + - - -
374A ALA 3.2 0.2 - - - -
375A ALA* 1.3 73.4 - - - +
377A ILE* 1.3 63.6 + - - +
379A ALA* 3.1 5.9 + - - +
380A LEU* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.1 33.2 - - + +
134A VAL* 4.4 1.3 - - + -
215A VAL* 3.5 16.1 - - + +
340A THR* 4.9 0.7 - - + -
373A LEU 3.0 18.1 + - - +
374A ALA 3.6 6.7 - - - +
376A GLY* 1.3 75.8 - - - +
378A ILE* 1.3 58.5 + - - +
380A LEU* 3.3 7.6 + - - +
381A THR* 2.9 30.6 + - - +
429A LEU* 3.7 35.9 - - + -
431A ALA* 3.9 34.8 - - + +
434A MET* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 3.7 17.3 - - + -
288A ILE* 4.0 13.2 - - + -
290A VAL* 3.7 25.1 - - + -
315A LEU* 3.8 27.8 - - + -
374A ALA* 2.8 26.0 + - + +
375A ALA* 3.6 4.3 - - - +
376A GLY 3.2 0.2 - - - -
377A ILE* 1.3 78.1 - - + +
379A ALA* 1.3 57.0 + - - +
381A THR* 3.2 7.6 + - - -
382A LEU* 2.9 27.7 + - - +
393A MET* 3.8 33.6 - - + +
397A VAL* 5.1 3.1 - - + -
429A LEU* 5.3 2.7 - - + -
434A MET* 4.5 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY* 4.5 2.4 - - - -
147A ILE* 3.5 31.2 - - + +
149A VAL* 4.1 9.9 - - + -
216A ALA* 4.0 17.7 - - + -
219A ALA* 4.7 0.9 - - + -
249A ILE* 3.5 11.8 - - + +
375A ALA 2.9 14.4 + - - +
376A GLY 3.1 9.6 + - - +
378A ILE* 1.3 73.2 - - - +
380A LEU* 1.3 64.5 + - - +
382A LEU 3.3 0.9 + - - +
383A GLU* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.9 2.0 - - + -
137A ALA* 3.9 22.0 - - + -
138A TRP* 4.3 5.6 - - + +
142A TYR* 3.4 18.8 - - + +
143A THR* 3.4 35.0 - - - +
144A GLY 3.4 1.3 - - - +
215A VAL* 3.7 34.3 - - + +
216A ALA* 4.0 4.5 - - - -
376A GLY 3.1 11.4 + - - +
377A ILE* 3.3 6.5 + - - +
379A ALA* 1.3 73.7 - - - +
381A THR* 1.3 62.8 - - - +
383A GLU* 3.3 8.1 + - - +
384A ALA* 3.1 20.8 + - - +
431A ALA* 4.3 13.2 - - + -
435A VAL* 3.8 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ILE 2.9 14.2 + - - -
378A ILE 3.5 8.1 - - - -
379A ALA 3.2 0.2 - - - -
380A LEU* 1.3 77.4 - - - +
382A LEU* 1.3 57.8 + - - +
384A ALA* 3.0 16.3 + - - +
385A ASN 3.1 9.4 + - - -
388A LEU* 3.8 9.2 - - + +
393A MET* 3.9 11.4 - - - -
396A LEU* 3.4 32.8 - - + -
434A MET* 3.3 33.5 - - + +
435A VAL* 4.2 8.9 + - - +
438A ALA* 3.6 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.8 11.7 - - + -
248A HIS* 3.7 37.9 - - + -
249A ILE* 4.1 11.4 - - + -
282A ARG* 3.5 29.2 - - - +
288A ILE* 4.1 7.6 - - + -
378A ILE 2.9 12.9 + - - +
379A ALA 3.3 4.9 + - - +
381A THR* 1.3 73.0 - - - +
383A GLU* 1.3 67.4 + - - +
385A ASN 3.7 15.3 - - - +
386A LYS* 3.0 35.8 + - - +
388A LEU* 3.9 8.5 - - + +
393A MET* 3.8 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLY 4.1 6.9 - - - +
142A TYR* 3.4 22.4 - - + +
143A THR 3.0 11.1 + - - -
144A GLY* 2.7 28.6 + - - -
145A HIS* 3.4 42.6 + - - +
147A ILE* 3.7 13.5 - - + +
379A ALA 3.0 13.7 + - - +
380A LEU 3.5 8.9 - - - +
381A THR 3.3 0.2 - - - -
382A LEU* 1.3 77.3 - - - +
384A ALA* 1.3 61.5 + - - +
385A ASN 3.3 0.3 + - - -
386A LYS* 4.1 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.4 19.5 + - + -
380A LEU 3.1 11.8 + - - +
381A THR 3.0 13.5 + - - +
383A GLU* 1.3 77.3 - - - +
385A ASN* 1.3 60.3 + - - +
435A VAL* 3.8 36.8 - - + +
438A ALA* 4.1 5.6 - - + -
439A GLN* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A THR 3.1 4.2 + - - -
382A LEU* 3.0 8.2 + - - +
384A ALA* 1.3 81.0 - - - +
386A LYS* 1.3 62.1 + - - +
387A ASP* 2.9 27.2 + - - +
388A LEU* 3.2 45.2 + - + +
438A ALA* 3.0 28.9 + - + +
439A GLN* 5.1 0.8 - - - +
441A TRP* 4.1 14.1 + - - -
----------------------------------------------------------
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