Contacts of the helix formed by residues 312 - 329 (chain D) in PDB entry 1ZUM
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 312 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D VAL 3.4 0.6 + - - -
311D GLN* 1.3 71.8 - - + +
313D ASP* 1.3 73.2 - - - +
314D ILE 3.2 1.2 + - - -
315D TYR* 3.3 21.2 + - - +
316D ASP* 4.7 4.0 + - - +
409D LYS* 3.9 22.6 - - + +
410D PHE 2.8 17.8 + - - +
411D LYS* 3.3 44.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 313 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D SER* 4.2 23.2 + - - -
311D GLN* 3.2 4.7 + - + +
312D GLU* 1.3 88.7 - - - +
314D ILE* 1.3 63.0 + - + +
10F ALA* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ILE* 3.9 19.5 - - + +
278D MET 3.4 28.7 - - - +
279D SER* 3.6 30.3 - - - +
281D ALA* 5.4 3.1 - - + +
283D MET* 3.7 26.2 - - + -
310D VAL* 3.8 10.1 - - + -
311D GLN 3.4 11.9 - - - +
313D ASP* 1.3 82.8 - - + +
315D TYR* 1.3 67.0 + - - +
316D ASP 3.5 2.0 - - - -
317D GLU* 3.3 11.6 + - - +
318D PHE* 2.9 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D VAL* 3.7 19.7 - - + -
311D GLN 3.0 9.8 + - - +
312D GLU* 3.3 19.3 + - - +
314D ILE* 1.3 76.7 - - - +
316D ASP* 1.3 76.4 + - - +
318D PHE* 3.2 1.0 + - - +
319D VAL* 2.8 58.4 + - + +
387D GLY* 3.8 4.7 - - - -
388D ASP* 2.7 50.0 + - - -
407D ILE* 3.9 8.6 + - + -
408D LEU 4.0 4.9 - - - -
409D LYS* 3.6 52.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D GLU 4.7 3.6 + - - +
313D ASP 5.6 0.2 - - - -
314D ILE 3.5 0.4 - - - -
315D TYR* 1.3 93.9 - - - +
317D GLU* 1.3 57.3 - - - +
319D VAL* 3.7 4.4 - - - +
320D GLU* 3.0 29.9 + - - +
409D LYS* 5.3 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D MET* 3.9 22.0 - - + +
314D ILE* 3.3 13.8 + - - +
316D ASP* 1.3 75.5 - - - +
318D PHE* 1.3 66.9 + - - +
320D GLU* 3.3 9.6 + - - +
321D ARG* 2.9 69.7 + - - +
97F ARG* 4.4 23.9 - - + +
98F ASP* 4.6 1.1 - - - +
3122F EDO 3.9 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ILE* 3.9 28.7 - - + -
283D MET* 4.0 27.0 - - + -
286D ALA* 4.1 15.7 - - + -
287D VAL* 4.1 11.4 - - + -
290D ALA* 3.7 24.9 - - + -
308D THR* 3.8 13.7 - - + -
310D VAL* 3.5 30.5 - - + -
314D ILE* 2.9 18.6 + - + +
315D TYR 3.6 3.4 - - - +
317D GLU* 1.3 75.4 - - - +
319D VAL* 1.3 61.3 + - + +
321D ARG* 3.4 3.0 + - - +
322D SER* 2.8 52.1 + - - -
405D MET* 5.4 1.3 - - + -
407D ILE* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D TYR* 2.8 58.8 + - + +
316D ASP* 3.7 5.6 - - - +
318D PHE* 1.3 79.7 - - + +
320D GLU* 1.3 63.8 + - - +
322D SER* 3.2 4.8 + - - -
323D VAL* 2.9 30.8 + - + +
368D LEU* 3.4 32.3 - - + -
407D ILE* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ASP 3.0 17.7 + - - +
317D GLU* 3.3 7.2 + - - +
319D VAL* 1.3 78.1 - - - +
321D ARG* 1.3 62.5 + - + +
323D VAL* 3.4 5.7 + - - +
324D ALA* 3.1 22.5 + - + +
90F ARG* 4.5 15.2 + - - -
93F ASP* 4.7 6.6 - - - +
94F LEU* 4.9 2.3 - - - +
97F ARG* 3.5 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D MET* 3.7 25.7 - - - +
284D ASP* 3.9 17.9 + - - -
287D VAL* 3.9 20.4 - - + +
317D GLU* 2.9 50.8 + - + +
318D PHE 3.8 2.9 - - - +
320D GLU* 1.3 77.2 - - + +
322D SER* 1.3 58.5 + - - +
324D ALA* 3.3 8.2 + - - +
325D ARG* 2.9 28.6 + - - +
97F ARG* 3.6 37.3 - - - +
98F ASP* 3.9 5.9 + - - -
203F TYR* 5.8 0.4 + - - -
3122F EDO 4.5 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 4.1 13.9 + - - +
290D ALA* 5.6 0.5 - - - +
291D HIS* 5.0 3.1 + - - -
318D PHE* 2.8 46.2 + - - -
319D VAL 3.5 4.9 - - - -
321D ARG* 1.3 76.7 - - - +
323D VAL* 1.3 56.6 + - - +
325D ARG* 3.3 4.5 + - - +
326D ALA* 2.9 29.5 + - - +
405D MET* 3.5 30.1 - - - +
407D ILE* 4.3 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D VAL* 2.9 22.1 + - + +
320D GLU* 3.7 5.8 - - - +
322D SER* 1.3 72.7 - - - +
324D ALA* 1.3 66.8 + - - +
326D ALA* 3.3 7.5 + - - +
327D LYS* 3.0 50.4 + - + +
368D LEU* 3.6 48.0 - - + +
369D CYS* 4.1 7.0 - - + -
385D VAL* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D GLU 3.1 13.9 + - - +
321D ARG* 3.3 12.5 + - - +
323D VAL* 1.3 77.8 - - - +
325D ARG* 1.3 61.3 + - - +
327D LYS* 3.3 10.0 + - - +
328D SER* 3.1 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D VAL* 4.7 10.3 - - + -
288D GLU* 2.7 39.6 + - - +
291D HIS* 3.5 39.2 + - + +
321D ARG 2.9 16.5 + - - +
322D SER* 3.6 7.6 - - - +
324D ALA* 1.3 77.8 - - - +
326D ALA* 1.3 61.8 + - - +
328D SER* 3.1 28.1 + - - -
329D ARG* 3.2 12.8 + - - +
340D GLU* 3.3 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D HIS* 4.0 11.2 - - - -
295D PHE* 4.3 15.0 - - + -
322D SER 2.9 17.9 + - - +
323D VAL 3.6 3.8 - - - +
325D ARG* 1.3 76.0 - - - +
327D LYS* 1.3 62.1 + - - +
329D ARG* 3.4 9.7 + - - +
369D CYS* 3.9 9.0 - - - -
383D PRO* 3.4 25.1 - - + +
385D VAL* 3.6 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D VAL* 3.0 40.0 + - + +
324D ALA* 3.6 7.2 - - - +
325D ARG 3.3 0.2 - - - -
326D ALA* 1.3 78.1 - - - +
328D SER* 1.3 59.4 + - - +
329D ARG 3.5 4.2 + - - +
368D LEU 4.6 3.9 + - - -
369D CYS* 4.0 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D ALA 3.1 12.6 + - - -
325D ARG* 3.1 27.9 + - - -
327D LYS* 1.3 74.5 - - - +
329D ARG* 1.3 64.3 + - - +
330D VAL* 3.2 14.2 + - - +
340D GLU* 4.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D HIS* 3.1 39.1 + - + +
292D PHE* 5.9 1.2 - - - +
295D PHE* 3.3 39.8 + - - +
296D PHE* 4.3 3.8 - - - +
297D ASN 4.9 2.6 - - - +
298D GLN 5.1 0.6 - - - +
325D ARG* 3.2 12.4 + - - +
326D ALA 3.5 13.7 - - - +
327D LYS 3.3 5.0 - - - +
328D SER* 1.3 73.9 - - - +
330D VAL* 1.3 62.8 + - - +
331D VAL* 3.5 11.3 + - - +
340D GLU* 3.3 52.7 + - + +
341D GLN* 3.1 33.1 + - + +
383D PRO* 4.1 11.8 - - + +
----------------------------------------------------------
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