Contacts of the helix formed by residues 375 - 393 (chain D) in PDB entry 3ZXR
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 ASN 375 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D CYS* 3.6 3.2 - - - -
27D ASP 3.2 15.8 + - - -
28D LEU 2.8 24.4 + - - +
29D PRO 3.5 9.0 - - - +
30D GLY* 3.6 8.5 - - - -
108D PRO* 3.3 15.5 - - - +
319D PHE 4.6 4.2 + - - +
322D PRO* 4.8 2.4 - - - +
374D GLY* 1.3 74.0 - - - -
376D PRO* 1.4 52.1 - - - +
377D TYR* 3.0 31.5 + - - +
378D LEU* 3.1 20.0 + - + +
379D ALA* 2.7 36.9 + - - +
451D TRP* 4.7 4.9 - - + -
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Residues in contact with PRO 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ALA* 4.0 11.9 - - + +
242D MET* 4.0 26.0 - - + -
243D GLN* 3.4 42.2 - - + +
246D LYS* 5.7 2.7 - - + +
275D MET* 5.1 7.0 - - + -
374D GLY 3.7 7.6 - - - +
375D ASN* 1.4 83.9 - - - +
377D TYR* 1.3 69.7 + - + +
379D ALA* 4.0 7.9 - - + -
380D PHE* 2.9 43.2 + - + -
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Residues in contact with TYR 377 (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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26D CYS* 3.7 26.0 - - + -
32D MET* 4.3 2.4 - - - +
92D ASN* 3.8 5.4 + - - -
108D PRO* 3.2 26.0 - - + +
109D ARG* 3.5 29.7 + - + -
112D ALA* 4.1 12.7 - - + +
236D LEU* 4.1 4.0 - - + -
239D ALA* 3.4 25.8 - - + -
240D ASP* 2.5 39.8 + - - -
243D GLN* 3.5 29.1 - - + +
375D ASN* 3.0 18.7 + - - +
376D PRO* 1.3 83.5 - - + +
378D LEU* 1.3 62.7 + - - +
380D PHE* 4.3 0.9 - - - +
381D SER* 2.8 27.8 + - - -
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Residues in contact with LEU 378 (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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28D LEU* 3.8 19.5 - - + +
108D PRO* 4.0 12.3 - - + -
111D ILE* 3.7 36.3 - - + -
319D PHE* 4.0 24.0 - - + +
375D ASN* 3.1 19.8 + - + +
377D TYR* 1.3 73.1 - - - +
379D ALA* 1.3 60.3 + - - +
381D SER* 4.4 3.6 - - - -
382D ALA* 2.8 32.4 + - - +
443D PHE* 3.8 7.0 - - + -
447D LEU* 4.5 10.5 - - + -
451D TRP* 3.6 36.1 - - + -
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Residues in contact with ALA 379 (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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275D MET* 4.4 9.0 - - + -
319D PHE* 3.6 26.4 + - - +
320D THR* 4.3 5.0 - - - +
371D ASP 5.9 0.2 - - - +
375D ASN 2.7 22.3 + - - +
376D PRO* 3.3 8.3 + - + +
378D LEU* 1.3 69.7 - - - +
380D PHE* 1.3 69.2 + - + +
382D ALA* 3.2 3.1 + - - +
383D MET* 2.9 45.2 + - + +
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Residues in contact with PHE 380 (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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130D PHE* 3.5 43.3 - + + -
132D ALA* 4.3 19.7 - - + -
235D LEU* 3.8 32.1 - - + -
238D ALA* 3.7 15.3 - - + -
239D ALA* 3.6 27.8 - - + -
242D MET* 4.7 6.5 - - + -
275D MET* 3.9 13.9 - - + -
277D CYS* 3.7 21.8 - - - -
376D PRO* 2.9 28.9 + - + +
379D ALA* 1.3 77.9 - - + +
381D SER* 1.3 64.2 + - - +
383D MET* 3.3 11.1 + - + +
384D LEU* 3.0 19.2 + - - +
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Residues in contact with SER 381 (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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111D ILE* 4.0 7.4 - - - -
112D ALA* 3.4 26.3 + - - -
115D ALA* 3.5 14.1 - - - +
235D LEU* 3.9 11.5 - - - +
377D TYR 2.8 21.5 + - - -
378D LEU 3.8 2.7 - - - -
380D PHE* 1.3 79.3 - - - +
382D ALA* 1.3 58.2 + - - +
384D LEU* 3.1 4.2 + - - +
385D MET* 2.9 31.9 + - - +
443D PHE* 4.0 16.6 - - - -
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Residues in contact with ALA 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D LEU* 3.5 23.6 - - + +
319D PHE* 3.9 20.9 - - + -
378D LEU 2.8 22.8 + - - +
379D ALA 3.7 2.7 - - - +
381D SER* 1.3 73.6 - - - +
383D MET* 1.3 57.2 + - - +
385D MET* 3.3 3.1 + - - +
386D ALA* 3.0 24.1 + - - +
437D LEU* 3.8 26.2 - - + +
443D PHE* 3.8 5.3 - - + -
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Residues in contact with MET 383 (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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130D PHE* 4.2 5.8 - - + -
275D MET* 4.4 0.4 - - + -
277D CYS* 3.6 28.5 - - - -
279D GLN* 3.6 34.3 - - - +
305D TYR* 3.6 4.6 + - - -
309D LEU* 3.7 12.9 - - + +
316D LEU* 3.9 5.8 - - - -
320D THR* 3.8 15.7 - - + -
367D PHE* 3.8 18.2 - - + -
370D PRO* 3.6 17.7 - - + -
379D ALA* 2.9 40.8 + - + +
380D PHE* 3.3 10.1 + - + +
382D ALA* 1.3 72.9 - - - +
384D LEU* 1.3 59.9 + - - +
386D ALA* 3.3 0.7 + - - -
387D GLY* 2.8 27.2 + - - -
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ALA* 3.9 26.0 - - + +
116D GLU* 5.2 0.9 - - - -
119D LEU* 4.2 15.3 - - + -
128D ALA* 3.9 11.7 - - + -
130D PHE* 4.4 2.4 - - + -
235D LEU* 3.7 24.5 - - + -
281D LEU* 3.9 27.1 - - + -
305D TYR* 3.5 16.1 + - + +
380D PHE 3.0 12.7 + - - +
381D SER 3.1 7.4 + - - +
383D MET* 1.3 75.1 - - - +
385D MET* 1.3 56.5 + - + +
387D GLY 3.2 0.7 + - - -
388D LEU* 2.7 62.2 + - + +
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Residues in contact with MET 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ALA* 5.2 5.4 - - - -
118D TYR* 3.6 35.4 - - + -
381D SER 2.9 19.7 + - - +
382D ALA 3.7 7.0 - - - +
384D LEU* 1.3 78.2 - - - +
386D ALA* 1.3 61.5 + - - +
388D LEU* 3.4 5.6 + - - +
389D ASP* 3.0 25.5 + - - +
436D TYR* 3.4 32.8 - - - +
437D LEU* 3.9 15.5 - - + +
439D GLU* 3.4 28.9 - - + +
442D VAL* 3.8 27.6 - - + -
443D PHE* 4.4 7.0 - - + -
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Residues in contact with ALA 386 (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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308D GLY* 3.3 18.2 - - - +
309D LEU* 4.3 1.8 - - + -
312D HIS* 3.9 18.5 - - + -
316D LEU* 4.0 17.5 - - + -
382D ALA 3.0 17.8 + - - +
383D MET 3.7 4.0 - - - +
385D MET* 1.3 75.2 - - - +
387D GLY* 1.3 63.9 + - - +
389D ASP* 3.4 3.3 + - - +
390D GLY 3.1 17.7 + - - -
436D TYR* 3.8 22.6 - - + -
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Residues in contact with GLY 387 (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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305D TYR* 3.6 45.8 - - - -
309D LEU* 4.5 1.2 - - - +
383D MET 2.8 14.3 + - - -
384D LEU 3.6 2.2 - - - -
386D ALA* 1.3 77.4 - - - +
388D LEU* 1.3 60.2 + - - +
390D GLY* 3.2 4.5 + - - -
391D ILE* 3.1 24.1 + - - +
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Residues in contact with LEU 388 (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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118D TYR* 4.0 33.2 - - + -
119D LEU* 3.8 34.8 - - + -
122D THR* 4.7 3.8 - - + -
124D ILE* 4.0 23.6 - - + +
281D LEU* 4.2 9.6 - - + -
384D LEU* 2.7 44.4 + - + +
385D MET* 3.9 5.8 - - - +
387D GLY* 1.3 70.2 - - - +
389D ASP* 1.3 60.1 + - - +
391D ILE* 3.2 17.2 + - + +
392D LYS* 2.9 33.3 + - - +
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Residues in contact with ASP 389 (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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312D HIS* 2.7 31.0 + - - +
385D MET 3.0 18.1 + - - +
386D ALA 3.7 4.5 - - - +
388D LEU* 1.3 76.7 - - - +
390D GLY* 1.3 57.2 + - - +
392D LYS* 4.3 5.7 - - - +
393D ASN* 2.9 59.8 + - - +
395D ILE* 4.1 5.9 - - - +
436D TYR* 3.9 19.2 - - + +
439D GLU* 5.0 9.9 - - + +
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Residues in contact with GLY 390 (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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304D HIS* 3.3 22.6 - - - +
308D GLY* 3.8 6.9 - - - -
386D ALA 3.1 10.5 + - - -
387D GLY 3.2 2.6 + - - -
389D ASP* 1.3 75.5 - - - +
391D ILE* 1.3 57.8 + - - +
394D LYS* 2.8 9.4 + - - -
395D ILE* 2.8 42.9 + - - +
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Residues in contact with ILE 391 (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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124D ILE* 3.8 29.6 - - + -
281D LEU* 3.6 31.4 - - + -
301D THR* 3.6 39.5 - - + +
304D HIS* 3.8 9.1 + - + +
305D TYR* 3.9 12.3 - - + +
387D GLY 3.1 14.8 + - - +
388D LEU* 3.6 11.0 - - + +
390D GLY* 1.3 72.4 - - - +
392D LYS* 1.3 66.7 + - - +
394D LYS* 3.0 21.1 + - - +
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Residues in contact with LYS 392 (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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118D TYR* 3.4 16.8 + - - +
122D THR* 3.2 34.7 + - - +
124D ILE* 4.1 19.9 - - - +
388D LEU* 2.9 17.7 + - - +
389D ASP* 3.9 8.7 - - - +
391D ILE* 1.3 80.2 - - - +
393D ASN* 1.3 64.6 + - - +
394D LYS* 3.6 5.5 + - - +
439D GLU* 6.0 3.4 - - - +
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Residues in contact with ASN 393 (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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389D ASP* 2.9 52.4 + - - +
392D LYS* 1.3 82.5 - - - +
394D LYS* 1.3 71.5 + - - +
395D ILE* 3.2 17.2 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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