Contacts of the helix formed by residues 327 - 343 (chain E) in PDB entry 1ZMD
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 LEU 327 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E ASP* 3.8 0.9 + - - +
325E PRO* 2.9 28.5 + - + +
326E MET* 1.3 82.2 - - - +
328E ALA* 1.3 65.9 + - - +
329E HIS* 3.7 12.8 - - + +
330E LYS* 3.2 12.0 + - + +
331E ALA* 3.1 21.1 + - - +
354E VAL* 4.5 4.0 - - + -
355E PRO 3.5 25.4 - - - +
356E SER* 3.9 17.3 - - - +
480E FAD 3.1 15.7 + - - +
481E NAI 3.6 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E PRO* 3.6 9.3 - - + +
45E CYS* 3.3 34.1 - - - -
50E CYS* 3.7 2.9 - - - -
327E LEU* 1.3 68.7 - - - +
329E HIS* 1.3 64.1 + - - +
331E ALA* 3.2 4.6 + - - +
332E GLU* 3.1 29.2 + - - +
480E FAD 2.9 33.1 + - - +
452F HIS* 3.6 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 329 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E LEU* 3.7 17.6 - - + +
328E ALA* 1.3 75.6 - - - +
330E LYS* 1.3 68.8 + - - +
332E GLU* 3.6 7.9 + - - +
333E ASP* 3.1 30.0 + - - +
354E VAL* 3.8 14.1 - - + -
355E PRO* 2.7 32.2 + - + -
356E SER* 5.1 2.2 - - - -
357E VAL* 5.4 2.5 - - + -
480E FAD 3.1 19.0 + + - -
481E NAI 5.2 2.0 - - - -
449F CYS* 3.8 12.3 - - - -
450F HIS 3.1 19.3 - - - +
451F ALA* 3.9 13.9 - - + -
452F HIS* 3.0 34.8 + - + +
457F GLU* 5.3 1.1 - - - +
460F ARG* 5.4 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 330 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E GLY* 3.3 20.7 + - - +
320E ASP* 5.9 0.2 - - - +
322E VAL* 3.6 1.2 + - - +
323E ALA 2.9 25.1 + - - -
324E GLY* 3.8 11.1 + - - -
325E PRO* 3.0 31.3 + - + +
326E MET* 5.8 0.2 - - - +
327E LEU* 3.2 16.5 + - + +
328E ALA 3.1 0.6 - - - -
329E HIS* 1.3 84.3 - - - +
331E ALA* 1.3 63.6 + - - +
333E ASP* 3.6 4.8 + - - +
334E GLU* 2.8 57.5 + - - +
349E ILE* 6.0 0.6 - - + +
351E TYR* 3.9 18.8 - - + -
354E VAL* 4.3 16.8 - - + -
449F CYS* 4.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLY* 3.5 29.6 - - - +
318E ILE* 3.9 1.6 - - - +
319E GLY* 3.9 18.4 - - - -
320E ASP* 5.5 0.2 - - - +
327E LEU 3.1 11.7 + - - +
328E ALA 3.2 8.2 + - - +
330E LYS* 1.3 76.1 - - - +
332E GLU* 1.3 57.6 + - - +
334E GLU* 3.2 5.2 + - - +
335E GLY* 2.9 24.4 + - - -
480E FAD 3.7 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E PRO* 3.4 36.8 - - + +
17E GLY* 4.3 0.7 - - - -
19E TYR* 4.7 7.2 + - - -
20E VAL* 3.7 26.1 - - + +
328E ALA 3.1 16.8 + - - +
329E HIS* 3.8 7.9 - - - +
331E ALA* 1.3 73.8 - - - +
333E ASP* 1.3 70.0 + - - +
335E GLY* 3.1 2.6 + - - -
336E ILE* 3.1 29.5 + - + +
452F HIS* 4.0 25.8 + - - -
457F GLU* 4.4 8.5 - - - +
460F ARG* 5.9 1.1 + - - +
473F ASN* 5.2 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 333 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E HIS 3.1 16.5 + - - +
330E LYS* 4.0 4.9 - - - +
332E GLU* 1.3 78.7 - - - +
334E GLU* 1.3 62.8 + - - +
336E ILE* 3.2 10.4 + - - +
337E ILE* 3.0 31.5 + - + +
349E ILE* 4.0 22.3 - - + +
447F ARG 4.5 3.1 - - - +
449F CYS* 3.1 31.5 + - - +
460F ARG* 2.8 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E PHE* 3.4 27.1 - - + -
318E ILE* 3.8 12.4 - - + +
319E GLY* 2.8 26.9 + - - -
322E VAL* 3.7 1.5 - - - +
323E ALA 4.1 0.9 - - - +
330E LYS* 2.8 38.3 + - - +
331E ALA 3.4 7.4 - - - +
333E ASP* 1.3 80.5 - - - +
335E GLY* 1.3 62.2 + - - +
337E ILE* 3.6 8.7 - - + +
338E CYS* 3.0 28.2 + - - +
349E ILE* 5.0 5.2 - - + -
351E TYR* 2.3 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 335 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLY 4.1 2.2 - - - -
21E ALA* 3.7 14.1 - - - +
318E ILE* 3.2 25.3 - - - +
331E ALA 2.9 12.4 + - - -
332E GLU 3.1 3.9 + - - -
334E GLU* 1.3 75.6 - - - +
336E ILE* 1.3 53.6 + - - +
338E CYS* 3.6 3.1 - - - +
339E VAL* 2.7 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 336 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E VAL* 3.5 31.2 - - + -
24E LYS* 4.1 20.2 - - + -
332E GLU* 3.1 11.6 + - + +
333E ASP* 3.6 12.1 - - - +
335E GLY* 1.3 74.5 - - - +
337E ILE* 1.3 62.8 + - + +
339E VAL* 2.8 24.2 - - - +
340E GLU* 2.9 41.2 + - - +
447F ARG* 5.1 2.2 - - - +
460F ARG* 5.6 6.7 - - - +
464F LEU* 5.6 4.3 - - + -
472F ILE* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E PHE* 3.7 20.0 - - + -
333E ASP* 3.0 19.5 + - + +
334E GLU* 3.6 8.5 - - - +
336E ILE* 1.3 77.9 - - + +
338E CYS* 1.3 59.6 + - - +
340E GLU* 3.8 18.7 - - - +
341E GLY 2.9 21.8 + - - -
346E ALA 4.3 2.4 - - - +
347E VAL* 3.5 19.2 - - + +
348E HIS 3.5 34.3 - - - +
349E ILE* 3.6 27.8 - - + -
447F ARG* 4.3 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E LEU* 4.0 12.8 - - - -
307E ARG 4.5 3.8 - - - +
308E PHE* 4.0 15.3 - - + -
316E TYR* 3.5 44.2 - - - -
318E ILE* 3.8 17.9 - - + -
334E GLU 3.0 22.0 + - - +
335E GLY* 3.6 4.5 - - - +
337E ILE* 1.3 78.4 - - - +
339E VAL* 1.3 62.7 + - - +
341E GLY* 3.2 3.8 + - - -
342E MET* 3.1 23.1 + - - +
347E VAL* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 4.7 1.1 - - + -
21E ALA 3.5 18.8 - - - +
24E LYS* 3.8 21.3 - - + -
25E ALA* 3.9 10.3 - - + -
28E LEU* 3.7 13.5 - - + +
30E PHE* 3.8 2.9 - - - -
145E LEU* 4.2 14.4 - - + -
335E GLY 2.7 25.5 + - - +
336E ILE* 2.8 21.1 - - - +
338E CYS* 1.3 73.4 - - - +
340E GLU* 1.3 65.1 + - - +
342E MET* 3.0 41.6 + - + +
343E ALA 3.1 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LYS* 3.8 15.5 + - - -
28E LEU* 3.8 24.1 - - + +
336E ILE* 2.9 34.6 + - + +
337E ILE* 3.8 15.3 - - - +
339E VAL* 1.3 76.9 - - - +
341E GLY* 1.3 53.9 + - - +
343E ALA* 3.2 11.3 + - - +
344E GLY 3.4 0.2 + - - -
345E GLY* 2.7 32.3 + - - -
346E ALA 4.8 8.0 - - - +
447F ARG* 3.0 43.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E ARG* 2.9 27.9 + - - -
337E ILE 2.9 10.5 + - - -
338E CYS 3.2 3.6 + - - -
339E VAL 3.2 0.2 - - - -
340E GLU* 1.3 75.6 - - - +
342E MET* 1.3 55.7 + - - +
344E GLY* 2.8 19.6 + - - -
345E GLY 3.6 4.3 - - - -
347E VAL* 3.4 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 342 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 3.3 38.1 - - + -
30E PHE* 3.5 19.6 - - + -
143E ASN* 3.9 24.5 - - - +
145E LEU* 5.0 6.5 - - + -
316E TYR* 3.8 34.5 - - + +
338E CYS* 3.1 15.1 + - - +
339E VAL* 3.0 42.3 + - + +
341E GLY* 1.3 75.8 - - - +
343E ALA* 1.3 56.9 + - - +
344E GLY 3.3 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E LEU* 4.4 18.8 - - + +
30E PHE* 3.6 21.5 - - + -
339E VAL 3.1 7.1 + - - +
340E GLU* 3.6 9.4 - - - +
341E GLY 3.1 1.0 - - - -
342E MET* 1.3 75.9 - - - +
344E GLY* 1.3 59.3 + - - +
345E GLY 3.5 0.7 - - - -
----------------------------------------------------------
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