Contacts of the helix formed by residues 302 - 321 (chain A) in PDB entry 4RPP
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 PRO 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A HIS* 4.8 8.5 - - + -
298A GLY 4.9 0.2 - - - +
300A GLU 4.3 3.6 - - - +
301A ILE* 1.3 89.6 - - + +
303A ALA* 1.3 59.6 + - - +
304A GLU* 3.4 26.7 - - - +
305A LYS* 2.9 43.6 + - + +
306A VAL* 3.3 8.5 + - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLY* 4.7 5.9 + - - +
301A ILE 3.4 2.6 + - - -
302A PRO* 1.3 69.9 - - - +
304A GLU* 1.3 65.2 + - - +
305A LYS 3.2 0.2 - - - -
306A VAL* 3.4 26.2 + - - +
307A PHE* 4.4 3.6 + - - +
340B PRO* 5.1 14.8 - - + +
341B THR 4.8 13.7 - - - +
342B ARG* 5.7 7.9 - - + +
345B GLY* 5.1 13.0 - - - -
377B MET* 5.5 4.5 - - + -
381B ILE* 5.6 1.3 - - + -
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A PRO* 3.4 20.9 - - - +
303A ALA* 1.3 84.6 + - - +
305A LYS* 1.3 65.6 + - + +
307A PHE* 3.1 31.3 - - - -
345B GLY 5.9 0.7 - - - -
377B MET* 4.4 9.6 - - - +
380B LEU* 3.8 31.7 - - + +
381B ILE* 3.7 39.9 - - + +
384B GLU* 3.7 25.0 - - + +
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Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A HIS* 6.3 0.7 - - - +
301A ILE* 4.6 7.9 - - + -
302A PRO* 2.9 36.2 + - + +
304A GLU* 1.3 88.0 - - + +
306A VAL* 1.3 64.0 + - - +
307A PHE 3.4 0.4 - - - -
308A LEU* 3.2 24.3 + - + +
309A ALA* 3.3 5.2 + - - +
35B ILE* 3.1 49.7 + - + +
37B SER 4.1 10.1 + - - -
38B PRO* 4.6 3.0 - - - +
39B PRO* 4.3 4.2 - - - +
384B GLU* 2.9 38.5 + - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A VAL* 6.0 0.8 - - + +
294A ARG* 4.6 9.4 - - + -
297A LEU* 4.6 10.5 - - + -
298A GLY* 3.6 28.9 - - - +
301A ILE* 3.7 15.7 - - + -
302A PRO 3.4 15.0 - - - +
303A ALA* 3.5 15.3 - - - +
304A GLU 3.3 1.4 - - - -
305A LYS* 1.3 77.1 - - - +
307A PHE* 1.3 65.6 + - - +
309A ALA* 3.0 14.7 + - - +
310A GLN* 3.0 12.0 + - + +
342B ARG* 3.0 30.5 - - - +
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA 4.4 2.8 + - - +
304A GLU* 3.1 30.3 - - - -
306A VAL* 1.3 80.3 - - - +
308A LEU* 1.3 90.0 + - + +
310A GLN* 3.5 11.8 + - - +
311A LYS* 3.1 47.6 + - + +
345B GLY 5.2 2.5 - - - -
346B SER* 4.0 28.0 - - - -
349B ALA* 3.7 27.6 - - + -
350B ASN* 5.5 0.9 - - - +
353B LEU* 3.8 19.7 - - + -
381B ILE* 4.7 2.5 - - + -
384B GLU* 4.4 2.2 - - + -
385B ALA* 3.5 32.5 - - + -
388B ALA* 4.1 2.9 - - + -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LYS* 3.2 19.0 + - + +
307A PHE* 1.3 101.1 - - + +
309A ALA* 1.3 60.1 + - - +
311A LYS* 3.3 3.0 + - - +
312A MET* 2.9 30.6 + - - +
33B LEU* 4.0 27.7 - - + +
34B ASP 5.2 4.5 - - - +
35B ILE* 3.9 20.2 - - + +
384B GLU* 3.5 33.7 - - - +
387B ALA* 5.2 4.7 - - + -
388B ALA* 3.6 32.1 - - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL* 4.6 9.6 - - + -
297A LEU* 5.0 3.4 - - + -
301A ILE* 4.4 15.7 - - + -
305A LYS 3.3 6.1 + - - +
306A VAL 3.0 10.3 + - - +
308A LEU* 1.3 78.1 - - - +
310A GLN* 1.3 63.0 + - - +
312A MET* 3.4 8.5 + - - +
313A MET* 3.0 50.3 + - + +
35B ILE* 4.0 12.9 - - + +
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Residues in contact with GLN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A VAL* 4.2 21.9 - - + +
294A ARG* 2.8 34.4 + - + +
306A VAL* 3.0 11.9 + - - +
307A PHE* 3.6 15.2 - - - +
309A ALA* 1.3 77.2 - - - +
311A LYS* 1.3 58.5 + - - +
313A MET* 3.4 1.8 + - - +
314A ILE* 3.0 46.7 + - + +
326A CYS* 3.6 23.3 - - - -
347A ASP* 5.3 2.9 + - - +
350A ASN* 6.1 0.2 - - - +
351A ALA* 4.0 11.1 - - - +
354A ASP* 3.3 21.7 + - - +
346B SER* 5.8 3.5 - - - -
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A PHE* 3.1 34.3 + - + +
308A LEU 3.9 3.1 - - - +
310A GLN* 1.3 79.2 - - + +
312A MET* 1.3 64.0 + - - +
314A ILE* 4.1 5.5 - - - +
315A GLY* 3.0 20.6 + - - -
350A ASN* 5.4 0.8 + - - +
354A ASP* 2.5 47.1 + - - +
30B MET* 3.7 39.4 - - + +
33B LEU* 4.2 5.6 - - + -
350B ASN* 3.2 22.8 + - - +
353B LEU* 3.5 29.7 - - + +
388B ALA* 5.1 0.4 - - + -
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL* 3.6 41.1 - - + +
280A PHE* 4.4 3.8 - - + -
308A LEU 2.9 17.5 + - - +
309A ALA* 3.6 6.5 - - - +
311A LYS* 1.3 76.7 - - - +
313A MET* 1.3 76.1 + - + +
315A GLY* 3.3 1.9 + - - -
316A ARG* 3.0 65.0 + - - +
30B MET 3.2 14.7 + - - +
31B CYS* 3.4 21.4 - - - +
33B LEU* 3.5 23.1 - - + +
35B ILE* 6.4 0.2 - - + -
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Residues in contact with MET 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ILE* 3.7 34.8 - - + -
277A VAL* 4.1 7.4 - - + -
280A PHE* 3.5 41.1 - - + -
290A ILE* 4.6 1.8 - - + -
292A VAL* 4.0 23.3 - - + -
297A LEU* 4.1 17.3 - - + -
309A ALA* 3.0 44.8 + - + +
310A GLN 4.0 2.5 - - - +
312A MET* 1.3 84.7 - - + +
314A ILE* 1.3 67.0 + - - +
316A ARG 3.5 0.2 + - - -
317A CYS* 3.0 31.4 + - - -
324A VAL* 4.7 0.7 - - - -
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Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A VAL* 4.8 4.5 - - + -
310A GLN* 3.0 45.4 + - + +
311A LYS* 4.1 3.8 - - - +
313A MET* 1.3 76.1 - - - +
315A GLY* 1.3 57.9 + - - +
317A CYS* 3.4 1.0 + - - +
318A ASN* 2.9 37.6 + - - +
324A VAL* 4.0 25.8 - - + -
326A CYS* 4.9 5.4 - - + +
351A ALA 4.4 0.4 - - - +
354A ASP* 3.3 44.2 - - + +
355A GLY* 3.5 22.7 - - - +
356A ALA* 3.7 15.0 - - + +
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Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A LYS 3.0 16.3 + - - -
312A MET 3.7 3.4 - - - -
313A MET 3.3 0.2 - - - -
314A ILE* 1.3 77.1 - - - +
316A ARG* 1.3 55.5 + - - +
318A ASN* 3.3 2.5 + - - -
319A ARG* 2.9 28.4 + - - +
354A ASP 5.2 2.0 + - - -
27B LEU* 3.5 22.2 - - - +
30B MET* 4.8 6.7 - - - -
31B CYS* 3.5 10.5 - - - -
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL 4.7 2.6 + - - -
278A ARG 5.6 2.0 + - - -
280A PHE* 3.7 29.7 - - + +
281A ASP* 3.0 38.2 + - - +
284A LEU* 3.8 7.4 - - + +
312A MET* 3.0 48.3 + - - +
315A GLY* 1.3 74.2 - - - +
317A CYS* 1.3 57.6 + - - +
319A ARG* 3.3 17.9 + - - +
320A ALA* 2.9 30.1 + - - +
31B CYS* 2.9 43.9 + - + +
32B ARG* 4.8 3.8 - - - +
33B LEU 4.6 5.1 + - - -
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Residues in contact with CYS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PHE* 3.6 21.5 - - - -
284A LEU* 3.7 14.1 - - - -
290A ILE* 3.6 25.8 - - - -
313A MET 3.0 25.1 + - - +
314A ILE 3.8 1.6 - - - +
316A ARG* 1.3 73.5 - - - +
318A ASN* 1.3 61.0 + - - +
320A ALA* 3.2 1.4 + - - -
321A GLY 2.8 24.4 + - - -
322A LYS 2.9 28.8 + - - +
323A PRO 4.7 0.9 - - - -
324A VAL* 3.7 20.0 - - + -
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Residues in contact with ASN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ILE* 2.9 23.1 + - - +
315A GLY* 3.5 6.1 - - - +
317A CYS* 1.3 77.5 - - - +
319A ARG* 1.3 61.2 + - - +
321A GLY* 3.2 12.6 + - - +
322A LYS 5.0 0.2 - - - -
324A VAL* 4.1 6.6 - - - +
354A ASP 4.4 2.8 + - - -
355A GLY* 3.0 41.0 + - - +
357A ASP* 4.3 0.2 - - - +
394A LEU* 4.2 18.2 - - + +
398A LEU* 4.2 13.9 - - + +
443A ARG* 4.6 7.3 - - - +
445A ARG* 3.9 30.9 + - + +
27B LEU* 4.3 11.2 - - + +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A ASP* 5.6 1.2 + - - -
315A GLY 2.9 13.5 + - - +
316A ARG* 3.4 24.9 - - - +
318A ASN* 1.3 77.7 - - - +
320A ALA* 1.3 59.0 + - - +
321A GLY 3.6 0.2 + - - -
398A LEU* 4.5 8.8 - - + +
401A LEU* 4.6 13.7 - - + -
443A ARG* 3.4 17.3 + - - +
27B LEU* 4.0 23.9 - - + +
28B GLU* 5.5 7.7 - - + +
31B CYS* 3.3 35.9 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LEU* 3.9 20.2 - - + -
316A ARG 2.9 16.6 + - - +
317A CYS* 3.9 2.9 - - - +
318A ASN 3.2 0.2 - - - -
319A ARG* 1.3 74.2 - - - +
321A GLY* 1.3 58.9 + - - +
322A LYS* 3.5 18.4 + - + +
443A ARG* 2.6 29.9 + - - +
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A CYS 2.8 5.2 + - - -
318A ASN* 3.2 12.1 + - - -
319A ARG 3.3 1.0 + - - -
320A ALA* 1.3 79.7 - - - +
322A LYS* 1.3 60.3 + - - +
439A HIS* 5.2 4.5 - - - +
443A ARG* 3.5 29.0 + - - +
445A ARG* 6.0 4.5 - - - -
466A TYR* 3.9 17.8 + - - -
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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