Contacts of the helix formed by residues 327 - 343 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ASP* 3.7 1.2 + - - +
325D PRO* 2.9 27.5 + - + +
326D MET* 1.3 82.4 - - - +
328D ALA* 1.3 65.2 + - - +
329D HIS* 3.5 13.5 - - + +
330D LYS* 3.3 11.0 - - + +
331D ALA* 3.1 21.0 + - - +
354D VAL* 4.3 4.5 - - + -
355D PRO 3.7 23.3 - - - +
356D SER* 3.8 16.8 - - - +
480D FAD 3.1 20.0 + - - +
481D NAI 3.7 43.3 - - + +
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Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C HIS* 3.8 13.0 - - + -
16D PRO* 3.9 12.5 - - + +
45D CYS* 3.6 31.9 - - - -
50D CYS* 3.9 1.1 - - - -
327D LEU* 1.3 69.9 - - - +
329D HIS* 1.3 57.9 + - - +
331D ALA* 3.2 3.2 + - - +
332D GLU* 3.0 33.1 + - - +
480D FAD 2.8 33.3 + - + +
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Residues in contact with HIS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C CYS* 3.7 22.9 - - - -
450C HIS 3.1 26.0 - - - +
451C ALA* 3.9 10.0 - - + -
452C HIS* 3.0 29.5 + - + +
457C GLU* 5.3 0.9 - - - +
460C ARG* 5.2 2.7 - - - +
327D LEU* 3.8 15.0 - - + +
328D ALA* 1.3 74.9 - - - +
330D LYS* 1.3 62.0 + - - +
332D GLU* 3.9 8.2 - - - +
333D ASP* 3.1 30.8 + - - +
354D VAL* 3.7 14.9 - - + +
355D PRO* 2.8 30.1 + - + -
356D SER* 5.3 1.8 - - - -
357D VAL* 5.6 1.8 - - + -
480D FAD 3.3 19.6 + + - -
481D NAI 5.4 1.6 - - - -
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Residues in contact with LYS 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C CYS* 4.6 7.4 - - - -
319D GLY* 3.1 21.2 + - - +
320D ASP* 5.2 0.4 - - - +
322D VAL* 3.8 2.6 + - - +
323D ALA 2.9 27.2 + - - -
324D GLY* 3.8 8.6 + - - -
325D PRO* 3.2 31.9 + - + +
326D MET* 5.7 0.4 - - - +
327D LEU* 3.3 17.5 - - + +
329D HIS* 1.3 83.4 - - - +
331D ALA* 1.3 65.0 + - - +
333D ASP* 3.5 2.6 + - - +
334D GLU* 2.8 62.8 + - - +
349D ILE* 4.5 2.2 - - + +
351D TYR* 3.8 17.7 - - + -
354D VAL* 4.4 12.1 - - + -
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D PRO* 4.5 0.2 - - + -
17D GLY* 3.4 21.7 - - - +
318D ILE* 3.7 3.1 - - - +
319D GLY* 3.6 30.3 - - - -
320D ASP 4.6 0.2 - - - +
327D LEU 3.1 9.3 + - - +
328D ALA 3.2 6.7 + - - +
330D LYS* 1.3 78.6 - - - +
332D GLU* 1.3 64.8 + - - +
334D GLU* 3.4 1.5 + - - +
335D GLY 3.0 18.4 + - - -
480D FAD 3.8 23.8 - - - +
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C HIS* 3.9 27.0 + - - -
457C GLU* 4.4 9.4 - - - +
460C ARG* 5.8 2.0 + - - +
473C ASN* 5.2 6.6 + - - -
16D PRO* 3.5 37.5 - - + +
17D GLY* 4.3 0.7 - - - -
19D TYR* 4.7 7.1 + - - -
20D VAL* 3.9 24.3 - - + +
328D ALA 3.0 21.0 + - - +
329D HIS* 3.9 7.6 - - - +
330D LYS 3.3 0.2 - - - -
331D ALA* 1.3 76.1 - - - +
333D ASP* 1.3 67.1 + - - +
335D GLY* 3.1 3.1 + - - -
336D ILE* 3.0 29.5 + - + +
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Residues in contact with ASP 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447C ARG 4.6 3.3 - - - +
449C CYS* 3.1 30.9 + - - +
460C ARG* 2.9 36.8 + - - -
329D HIS 3.1 17.7 + - - +
330D LYS 3.9 4.0 - - - +
332D GLU* 1.3 79.4 - - - +
334D GLU* 1.3 62.4 + - - +
336D ILE* 3.2 10.2 + - - +
337D ILE* 3.0 33.2 + - + +
349D ILE* 4.3 14.8 - - + +
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Residues in contact with GLU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D PHE* 3.4 24.6 - - + -
318D ILE* 3.7 13.8 - - + +
319D GLY* 2.8 30.1 + - - -
322D VAL* 3.6 3.2 - - - +
323D ALA 3.9 1.9 - - - +
330D LYS* 2.8 51.7 + - - +
331D ALA 3.8 3.4 - - - +
332D GLU 3.3 0.2 - - - -
333D ASP* 1.3 74.9 - - - +
335D GLY* 1.3 58.3 + - - +
337D ILE* 3.5 8.8 - - - +
338D CYS* 2.9 33.3 + - - +
349D ILE* 4.0 10.5 - - + -
351D TYR* 2.4 26.2 + - - +
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Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 4.1 4.5 - - - -
21D ALA* 3.7 24.5 - - - +
318D ILE* 4.1 10.5 - - - +
331D ALA 3.0 14.7 + - - -
332D GLU 3.1 3.8 + - - -
334D GLU* 1.3 78.6 - - - +
336D ILE* 1.3 61.4 + - - +
338D CYS* 3.7 3.0 - - - +
339D VAL* 3.2 30.5 + - - +
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Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ARG* 5.3 2.5 - - - +
460C ARG* 5.3 7.0 - - - +
464C LEU* 5.5 5.6 - - + -
472C ILE* 4.3 14.1 - - + -
20D VAL* 3.6 24.9 - - + -
24D LYS* 4.2 22.0 - - + +
332D GLU* 3.0 20.1 + - + +
333D ASP* 3.2 13.4 + - - +
335D GLY* 1.3 76.4 - - - +
337D ILE* 1.3 67.5 + - + +
339D VAL* 3.3 9.1 + - - +
340D GLU* 2.9 50.8 + - + +
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Residues in contact with ILE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ARG* 4.6 9.6 - - - +
308D PHE* 3.7 26.5 - - + -
333D ASP* 3.0 22.8 + - + +
334D GLU* 3.5 9.0 - - - +
336D ILE* 1.3 80.4 - - + +
338D CYS* 1.3 59.8 + - - +
340D GLU* 3.7 17.1 - - - +
341D GLY 2.8 24.6 + - - -
346D ALA 5.2 0.2 - - - +
347D VAL* 3.4 23.3 - - + +
348D HIS 3.7 32.8 - - - +
349D ILE* 3.7 18.6 - - + -
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Residues in contact with CYS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D LEU* 4.0 10.8 - - + -
307D ARG 4.6 4.5 - - - +
308D PHE* 4.0 16.4 - - + -
316D TYR* 3.6 37.3 - - - -
318D ILE* 3.8 11.0 - - + -
334D GLU 2.9 21.1 + - - +
335D GLY* 3.7 4.9 - - - +
337D ILE* 1.3 80.5 - - - +
339D VAL* 1.3 62.8 + - + +
341D GLY* 3.2 3.5 + - - -
342D MET* 3.1 35.2 + - - +
347D VAL* 5.1 0.7 - - - -
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.9 2.5 - - + -
21D ALA* 3.8 22.4 - - + +
24D LYS* 3.6 30.7 - - + -
25D ALA* 3.8 22.9 - - + +
28D LEU* 3.7 10.2 - - + +
30D PHE* 3.8 2.8 - - + -
145D LEU* 4.5 5.6 - - + -
335D GLY 3.2 18.3 + - - +
336D ILE 3.4 8.3 - - - +
338D CYS* 1.3 72.6 - - - +
340D GLU* 1.3 65.9 + - - +
341D GLY 3.1 1.1 - - - -
342D MET* 3.1 31.1 + - + +
343D ALA* 3.1 16.6 + - - +
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Residues in contact with GLU 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ARG* 2.9 44.8 + - - -
468C PHE* 5.9 1.0 - - - -
24D LYS* 4.0 16.5 + - - -
28D LEU* 4.0 20.1 - - + +
336D ILE* 2.9 38.6 + - + +
337D ILE* 3.7 12.2 - - - +
339D VAL* 1.3 75.6 - - - +
341D GLY* 1.3 62.4 + - - +
343D ALA* 3.0 14.3 + - - +
344D GLY 3.3 0.5 + - - -
345D GLY* 3.0 21.9 + - - -
346D ALA 4.7 10.0 - - - +
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Residues in contact with GLY 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D ARG* 5.0 9.0 - - - +
316D TYR* 5.6 2.0 - - - -
337D ILE 2.8 11.3 + - - -
338D CYS 3.5 4.0 - - - -
339D VAL 3.1 0.4 - - - -
340D GLU* 1.3 77.8 - - - +
342D MET* 1.3 53.0 + - - +
344D GLY* 2.8 23.4 + - - -
345D GLY 3.6 7.8 - - - +
347D VAL* 3.4 26.9 - - - +
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Residues in contact with MET 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 3.8 30.3 - - + -
30D PHE* 3.7 18.3 - - + -
143D ASN* 4.3 16.2 - - + +
145D LEU* 4.3 15.9 - - + -
316D TYR* 3.7 49.3 + - + +
338D CYS* 3.1 34.2 + - - +
339D VAL* 3.1 26.9 + - + +
341D GLY* 1.3 76.9 - - - +
343D ALA* 1.3 55.8 + - - +
344D GLY 3.1 2.6 + - - -
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Residues in contact with ALA 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.3 19.7 - - + +
30D PHE* 3.9 17.7 - - + -
339D VAL 3.1 10.0 + - - +
340D GLU* 3.0 14.1 + - - +
342D MET* 1.3 76.4 - - - +
344D GLY* 1.3 56.5 + - - +
345D GLY 3.5 1.3 + - - -
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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) + - + + + + + -
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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