Contacts of the helix formed by residues 375 - 393 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E CYS* 3.4 6.7 - - - -
27E ASP 3.2 15.4 + - - -
28E LEU 2.9 24.4 + - - +
29E PRO 3.5 9.4 - - - +
30E GLY* 3.5 4.3 - - - -
108E PRO* 3.4 15.4 - - - +
319E PHE 4.7 3.5 + - - +
322E PRO* 4.8 2.6 - - - +
374E GLY* 1.3 72.1 - - - -
376E PRO* 1.3 57.0 - - - +
377E TYR* 3.0 26.7 + - - +
378E LEU* 3.1 24.0 + - + +
379E ALA* 2.7 37.2 + - - +
451E TRP* 4.7 3.9 - - + -
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Residues in contact with PRO 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E ALA* 4.0 11.9 - - + +
242E MET* 4.1 24.9 - - + -
243E GLN* 3.4 43.1 - - + +
246E LYS* 5.8 1.8 - - - +
275E MET* 5.1 6.3 - - + -
374E GLY 3.8 7.9 - - - +
375E ASN* 1.3 82.7 - - - +
377E TYR* 1.3 62.0 + - + +
379E ALA* 4.0 7.9 - - + -
380E PHE* 2.8 51.3 + - + -
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Residues in contact with TYR 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E CYS* 3.8 26.0 - - + -
32E MET* 4.3 2.4 - - - +
92E ASN* 3.8 5.7 + - - -
108E PRO* 3.2 26.7 - - + +
109E ARG* 3.6 31.7 + - + -
112E ALA* 4.2 5.9 - - + +
236E LEU* 4.1 9.9 - - + -
239E ALA* 3.3 26.2 - - + +
240E ASP* 2.4 38.3 + - - -
243E GLN* 3.5 29.1 - - + +
375E ASN* 3.0 18.2 + - - +
376E PRO* 1.3 80.2 - - + +
378E LEU* 1.3 61.0 + - - +
380E PHE* 4.2 1.4 - - - +
381E SER* 2.8 30.5 + - - -
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Residues in contact with LEU 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 3.9 20.0 - - + +
108E PRO* 4.1 11.7 - - + -
111E ILE* 3.7 36.8 - - + -
319E PHE* 3.9 21.8 - - + +
375E ASN* 3.1 18.7 + - + +
377E TYR* 1.3 74.3 - - - +
379E ALA* 1.3 56.0 + - - +
381E SER* 3.2 3.7 + - - -
382E ALA* 2.7 39.2 + - - +
443E PHE* 3.7 8.3 - - + -
447E LEU* 4.6 6.7 - - + -
451E TRP* 3.5 39.0 - - + -
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Residues in contact with ALA 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E MET* 4.5 8.7 - - + -
319E PHE* 3.5 27.7 + - - +
320E THR* 4.2 4.3 - - - +
375E ASN 2.7 22.2 + - - +
376E PRO* 3.8 8.7 - - + +
378E LEU* 1.3 72.9 - - - +
380E PHE* 1.3 65.5 + - + +
382E ALA* 3.3 1.4 + - - +
383E MET* 2.9 44.6 + - + +
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Residues in contact with PHE 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE* 3.5 42.1 - + + -
132E ALA* 4.3 19.7 - - + -
235E LEU* 3.9 25.1 - - + -
238E ALA* 3.7 16.2 - - + -
239E ALA* 3.6 34.8 - - + -
242E MET* 4.7 4.3 - - + -
275E MET* 3.9 16.2 - - + -
277E CYS* 3.6 22.7 - - - -
376E PRO* 2.8 33.1 + - + +
379E ALA* 1.3 74.6 - - + +
381E SER* 1.3 62.7 + - - +
383E MET* 3.3 10.5 + - + +
384E LEU* 3.0 19.6 + - - +
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Residues in contact with SER 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ILE* 3.7 7.9 + - - -
112E ALA* 3.4 26.2 + - - -
115E ALA* 3.6 15.8 - - - +
235E LEU* 3.8 11.2 - - - +
377E TYR 2.8 21.6 + - - -
378E LEU 3.6 3.1 - - - -
380E PHE* 1.3 77.8 - - - +
382E ALA* 1.3 62.7 + - - +
384E LEU* 3.1 4.7 + - - +
385E MET* 2.9 26.3 + - - +
443E PHE* 3.9 16.8 - - - -
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Residues in contact with ALA 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E LEU* 3.5 23.4 - - + +
319E PHE* 3.9 21.1 - - + -
378E LEU 2.7 21.4 + - - +
379E ALA 3.7 2.7 - - - +
381E SER* 1.3 73.2 - - - +
383E MET* 1.3 63.3 + - - +
385E MET* 3.3 3.3 + - - +
386E ALA* 3.0 19.8 + - - +
437E LEU* 3.8 26.0 - - + +
443E PHE* 3.8 5.7 - - + -
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Residues in contact with MET 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E PHE* 4.2 6.1 - - + -
275E MET* 4.4 0.4 - - + -
277E CYS* 3.6 28.5 - - - -
279E GLN* 3.7 34.1 - - - +
305E TYR* 3.7 4.8 + - - -
309E LEU* 3.6 13.0 - - + +
316E LEU* 3.9 6.3 - - + -
320E THR* 3.7 19.5 - - + -
367E PHE* 3.9 17.9 - - + -
370E PRO* 3.7 16.8 - - + -
379E ALA* 2.9 37.4 + - + +
380E PHE* 3.5 9.9 - - + +
382E ALA* 1.3 76.3 - - - +
384E LEU* 1.3 57.4 + - - +
386E ALA 3.3 0.5 + - - -
387E GLY 2.9 24.1 + - - -
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Residues in contact with LEU 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ALA* 3.9 26.5 - - + +
116E GLU* 5.0 1.1 - - + +
119E LEU* 4.2 13.7 - - + -
128E ALA* 3.8 24.5 - - + -
130E PHE* 4.4 1.8 - - + -
235E LEU* 3.7 25.8 - - + -
281E LEU* 3.9 17.0 - - + -
305E TYR* 3.5 16.3 + - + +
380E PHE 3.0 13.1 + - - +
381E SER 3.5 7.6 - - - +
383E MET* 1.3 75.3 - - - +
385E MET* 1.3 55.4 + - + +
387E GLY* 3.1 1.7 + - - -
388E LEU* 2.7 59.5 + - + +
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Residues in contact with MET 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ALA* 5.1 5.4 - - - -
118E TYR* 3.7 28.7 - - + -
381E SER 2.9 20.2 + - - +
382E ALA 3.7 6.5 - - - +
384E LEU* 1.3 76.7 - - - +
386E ALA* 1.3 57.4 + - - +
388E LEU* 3.9 5.8 - - - +
389E ASP* 3.0 31.2 + - - +
436E TYR* 3.4 33.3 - - + +
437E LEU* 4.0 12.3 - - + +
439E GLU* 3.3 28.7 - - + +
442E VAL* 3.7 35.7 - - + -
443E PHE* 4.3 8.5 - - + -
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Residues in contact with ALA 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E GLY* 3.3 17.3 - - - +
309E LEU* 4.2 3.1 - - + -
312E HIS* 3.9 18.5 - - + -
316E LEU* 3.9 17.9 - - + -
382E ALA 3.0 15.6 + - - +
383E MET 3.6 4.0 - - - +
385E MET* 1.3 76.9 - - - +
387E GLY* 1.3 64.3 + - - +
389E ASP* 3.5 3.1 + - - +
390E GLY 3.1 16.8 + - - -
436E TYR* 3.8 22.8 - - + -
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Residues in contact with GLY 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E TYR* 3.6 46.7 - - - -
309E LEU* 4.4 1.1 - - - +
383E MET 2.9 12.2 + - - -
384E LEU 3.5 3.1 - - - -
386E ALA* 1.3 77.2 - - - +
388E LEU* 1.3 59.6 + - - +
390E GLY* 3.2 3.8 + - - -
391E ILE* 3.1 24.3 + - - +
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Residues in contact with LEU 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E TYR* 4.0 35.0 - - + -
119E LEU* 3.7 35.0 - - + -
122E THR* 4.6 4.3 - - + -
124E ILE* 4.0 24.4 - - + +
281E LEU* 4.2 8.7 - - + -
384E LEU* 2.7 42.4 + - + +
385E MET* 3.9 6.3 - - - +
387E GLY* 1.3 70.8 - - - +
389E ASP* 1.3 59.7 + - - +
391E ILE* 3.2 18.4 + - + +
392E LYS* 2.9 32.6 + - - +
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Residues in contact with ASP 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E HIS* 2.7 30.5 + - - +
385E MET 3.0 18.3 + - - +
386E ALA 3.7 4.7 - - - +
388E LEU* 1.3 75.7 - - - +
390E GLY* 1.3 56.4 + - - +
392E LYS* 4.3 5.8 - - - +
393E ASN* 2.9 61.1 + - - +
395E ILE* 4.1 5.9 - - - +
436E TYR* 3.9 17.9 - - + +
439E GLU* 4.9 10.3 - - + +
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Residues in contact with GLY 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E HIS* 3.3 22.9 - - - +
308E GLY* 3.7 15.0 - - - -
386E ALA 3.1 11.1 + - - -
387E GLY 3.2 2.7 + - - -
388E LEU 3.2 0.2 - - - -
389E ASP* 1.3 77.2 - - - +
391E ILE* 1.3 54.9 + - - +
394E LYS* 3.0 9.9 + - - -
395E ILE* 2.8 35.8 + - - -
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Residues in contact with ILE 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ILE* 3.8 27.1 - - + -
281E LEU* 3.6 31.2 - - + -
301E THR* 3.5 37.2 - - + +
304E HIS* 3.8 9.8 + - + +
305E TYR* 3.8 13.2 - - + +
387E GLY 3.1 15.3 + - - +
388E LEU* 3.2 15.0 + - + +
390E GLY* 1.3 72.1 - - - +
392E LYS* 1.3 67.0 + - - +
394E LYS* 3.2 19.9 + - - +
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Residues in contact with LYS 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E TYR* 3.3 17.2 + - - +
122E THR* 3.3 33.7 - - - +
124E ILE* 4.1 19.7 - - - +
388E LEU* 2.9 16.7 + - - +
389E ASP* 3.7 9.2 - - - +
391E ILE* 1.3 79.0 - - - +
393E ASN* 1.3 65.9 + - - +
394E LYS* 3.6 6.4 + - - +
439E GLU* 5.9 4.0 - - - +
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Residues in contact with ASN 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E ASP* 2.9 51.8 + - - +
392E LYS* 1.3 82.5 - - - +
394E LYS* 1.3 70.0 + - - +
395E ILE* 3.2 17.7 + - + +
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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