Contacts of the helix formed by residues 287 - 310 (chain A) in PDB entry 5IXC
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 CYS 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ASN 3.7 2.5 + - - -
286A LEU* 1.3 78.3 - - - +
288A ALA* 1.3 66.8 + - - +
289A GLU* 3.3 20.0 - - - +
290A GLU* 3.1 31.5 + - - +
291A GLN* 3.2 11.1 + - - +
486A TYR* 4.0 17.9 - - - -
487A GLU* 3.6 37.7 + - - +
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Residues in contact with ALA 288 (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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287A CYS* 1.3 74.0 - - - +
289A GLU* 1.3 65.2 + - + +
291A GLN* 3.1 8.7 + - - +
292A ALA* 2.9 30.1 + - - +
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A CYS* 3.3 17.1 - - - +
288A ALA* 1.3 81.8 + - + +
290A GLU* 1.3 57.7 + - - +
292A ALA* 3.5 7.7 + - - +
293A PHE* 2.9 29.1 + - - +
296A ARG* 4.7 0.9 + - - -
449A ARG* 5.7 3.1 + - - +
486A TYR* 3.4 47.2 + - + +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.9 22.9 - - + +
287A CYS* 3.1 23.8 + - - +
289A GLU* 1.3 78.3 - - - +
291A GLN* 1.3 57.5 + - - +
293A PHE* 3.3 3.1 + - + +
294A LEU* 2.9 30.2 + - + +
356A TYR* 2.6 33.1 + - + +
459A LEU* 3.7 20.4 - - + +
486A TYR* 4.0 14.5 - - + -
487A GLU* 4.9 3.8 - - - +
661A ARG* 4.3 4.9 + - - -
664A ARG* 2.9 33.8 + - - -
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 4.0 35.7 + - + +
287A CYS 3.2 14.3 + - - +
288A ALA* 3.1 12.2 + - - +
290A GLU* 1.3 75.1 - - - +
292A ALA* 1.3 64.9 + - - +
294A LEU* 3.3 25.7 + - - +
295A SER* 3.3 14.2 + - - -
663A GLY* 5.3 2.0 + - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA 2.9 15.5 + - - +
289A GLU* 3.6 7.6 - - - +
291A GLN* 1.3 74.2 - - - +
293A PHE* 1.3 65.4 + - - +
295A SER* 3.0 18.0 + - - -
296A ARG* 3.2 31.3 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLU 2.9 18.6 + - - +
290A GLU* 3.5 6.7 - - + +
292A ALA* 1.3 74.5 - - - +
294A LEU* 1.3 61.0 + - + +
296A ARG* 3.1 14.4 + - - +
297A ARG* 2.7 60.9 + - + -
355A THR* 3.8 15.5 - - + -
452A LEU* 3.7 37.7 - - + -
455A GLY* 4.3 7.2 - - - -
457A ASN 3.5 19.1 - - - -
459A LEU* 3.5 42.8 - - + -
486A TYR* 3.6 17.9 - + + +
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Residues in contact with LEU 294 (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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286A LEU* 4.4 13.0 - - + -
290A GLU* 2.9 18.0 + - + +
291A GLN* 3.4 27.4 - - - +
292A ALA 3.2 0.4 - - - -
293A PHE* 1.3 82.6 - - + +
295A SER* 1.3 56.6 + - - +
297A ARG* 4.2 0.8 - - - +
298A LYS* 2.9 60.8 + - + +
317A GLU* 4.6 0.4 - - - -
322A VAL* 5.5 3.1 - - + -
355A THR* 3.3 33.7 - - + -
356A TYR* 3.5 27.1 - - + +
663A GLY 5.6 0.7 - - - +
664A ARG 5.6 3.1 - - - +
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Residues in contact with SER 295 (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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291A GLN 3.3 7.8 + - - -
292A ALA* 3.0 12.2 + - - -
294A LEU* 1.3 76.5 - - - +
296A ARG* 1.3 68.8 + - - +
297A ARG 3.3 0.3 + - - -
298A LYS* 3.3 10.1 + - - +
299A GLN* 3.5 15.3 + - - +
317A GLU* 2.6 30.6 + - - +
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Residues in contact with ARG 296 (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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289A GLU 4.7 0.6 + - - -
292A ALA* 3.2 36.7 + - - +
293A PHE* 3.1 18.0 + - - +
295A SER* 1.3 79.2 - - - +
297A ARG* 1.3 62.4 + - - +
299A GLN* 3.1 35.8 + - - +
300A VAL* 3.6 8.5 - - - +
452A LEU 3.1 22.4 + - - -
453A GLU* 3.0 27.3 + - - +
454A ARG* 4.4 6.1 - - - +
455A GLY* 4.0 15.7 - - - +
486A TYR* 3.2 22.8 + - - -
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Residues in contact with ARG 297 (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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293A PHE* 2.7 45.0 + - + +
294A LEU* 4.2 3.1 - - - +
296A ARG* 1.3 74.1 - - - +
298A LYS* 1.3 63.9 + - - +
299A GLN 3.1 0.7 + - - -
300A VAL* 3.2 14.6 + - - +
301A VAL* 3.0 26.6 + - + +
351A LEU* 3.2 21.6 + - - +
352A ASP* 3.4 18.6 + - - +
354A VAL 2.9 25.4 + - - -
355A THR* 4.1 17.7 - - + +
377A SER* 5.3 1.2 + - - -
378A GLN* 5.0 1.4 - - - +
455A GLY* 2.8 35.4 + - - -
456A GLN* 3.1 24.0 + - - +
457A ASN* 3.2 19.1 + - - +
458A PRO* 3.7 8.9 - - - +
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Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 2.9 54.2 + - + +
295A SER 3.3 5.1 + - - +
297A ARG* 1.3 77.4 - - + +
299A GLN* 1.3 57.1 + - - +
301A VAL* 3.7 7.6 - - - +
302A ALA* 2.8 27.2 + - - +
317A GLU* 3.7 42.4 - - + +
320A VAL* 3.5 29.2 - - + +
322A VAL* 4.1 18.5 - - + +
355A THR* 5.1 7.6 - - - +
807A ARG* 4.0 17.4 - - - +
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Residues in contact with GLN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER 3.5 7.8 + - - +
296A ARG* 3.1 35.2 + - - +
298A LYS* 1.3 78.5 - - - +
300A VAL* 1.3 61.7 + - + +
302A ALA* 3.5 7.1 - - + +
303A LYS* 3.0 26.7 + - - +
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Residues in contact with VAL 300 (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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296A ARG 3.6 15.5 - - - +
297A ARG* 3.6 22.4 - - - +
299A GLN* 1.3 75.3 - - + +
301A VAL* 1.3 60.7 + - - +
303A LYS* 3.6 10.0 - - + +
304A ALA* 2.8 27.4 + - - +
352A ASP* 4.1 21.1 - - + +
378A GLN* 5.2 6.1 - - - +
454A ARG 4.3 6.1 - - - +
455A GLY 3.2 24.7 - - - +
456A GLN* 5.2 1.6 - - - -
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Residues in contact with VAL 301 (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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297A ARG* 3.0 31.4 + - - +
298A LYS* 3.7 5.4 - - - +
300A VAL* 1.3 75.0 - - - +
302A ALA* 1.3 54.1 + - - +
304A ALA* 3.7 1.0 - - - +
305A LEU* 2.8 47.2 + - + +
320A VAL* 3.5 23.1 - - + -
321A PRO 4.4 5.6 - - - +
352A ASP 3.3 20.6 - - - +
353A CYS* 3.6 27.8 - - - +
354A VAL 4.2 0.2 - - - +
355A THR* 4.1 14.6 - - - +
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Residues in contact with ALA 302 (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 LYS 2.8 19.7 + - - +
299A GLN* 3.5 10.3 - - + +
301A VAL* 1.3 73.2 - - - +
303A LYS* 1.3 65.8 + - - +
305A LEU* 3.4 5.9 + - - +
306A LYS* 3.1 25.1 + - - +
315A LEU* 4.1 37.8 + - + +
320A VAL* 4.1 10.1 - - + -
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Residues in contact with LYS 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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299A GLN 3.0 17.5 + - - +
300A VAL* 3.6 10.1 - - + +
302A ALA* 1.3 77.5 - - - +
304A ALA* 1.3 56.3 + - - +
306A LYS* 3.5 4.0 + - - +
307A GLN* 2.1 47.4 - - - +
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Residues in contact with ALA 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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300A VAL 2.8 22.3 + - - +
301A VAL 3.3 3.8 + - - +
303A LYS* 1.3 74.8 - - - +
305A LEU* 1.3 56.7 + - - +
307A GLN* 3.5 5.7 + - - +
308A ALA* 3.1 28.9 + - - +
349A GLY 4.6 5.1 - - - +
352A ASP* 3.3 38.8 - - + +
353A CYS* 4.0 7.6 - - - -
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Residues in contact with LEU 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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301A VAL* 2.8 40.4 + - + +
302A ALA 3.8 3.8 - - - +
304A ALA* 1.3 70.6 - - - +
306A LYS* 1.3 60.2 + - - +
308A ALA* 4.3 1.6 - - + -
309A LEU* 2.7 57.7 + - + +
311A LEU* 4.4 4.3 - - + -
315A LEU* 3.9 20.2 - - + -
320A VAL* 4.5 1.3 - - + -
321A PRO* 3.6 33.4 - - + -
353A CYS* 3.9 19.1 - - + -
800A LEU* 4.2 25.6 - - + +
804A LEU* 5.1 2.9 - - + -
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Residues in contact with LYS 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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302A ALA 3.1 14.0 + - - +
303A LYS* 3.7 2.9 - - - +
305A LEU* 1.3 78.8 - - - +
307A GLN* 1.3 71.6 + - - +
310A GLN* 2.8 24.3 + - - +
311A LEU* 2.8 46.5 + - + +
312A ASP 4.5 2.4 + - - -
313A ARG* 3.8 21.2 - - - +
314A ASP* 2.7 33.4 + - - +
315A LEU* 6.2 1.3 - - + +
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Residues in contact with GLN 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 LYS* 2.1 46.2 + - - +
304A ALA* 3.5 6.0 + - - +
305A LEU 3.2 0.4 - - - -
306A LYS* 1.3 80.3 - - - +
308A ALA* 1.3 67.6 + - - +
310A GLN* 3.3 28.7 + - - +
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Residues in contact with ALA 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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304A ALA 3.1 16.0 + - - +
305A LEU* 3.8 7.0 - - + +
307A GLN* 1.3 81.3 - - - +
309A LEU* 1.3 64.3 + - + +
310A GLN* 5.1 1.7 - - - +
348A LEU 5.3 2.9 - - - +
349A GLY 4.5 8.3 - - - +
350A LEU* 4.1 25.4 - - + -
353A CYS* 4.6 2.5 - - - -
797A LEU* 4.0 19.0 - - + +
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Residues in contact with LEU 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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305A LEU* 2.7 34.7 + - + +
308A ALA* 1.3 75.8 - - + +
310A GLN* 1.3 67.6 + - - +
311A LEU* 3.5 16.1 + - + -
797A LEU* 3.7 34.3 - - + +
800A LEU* 4.3 15.5 - - + -
801A ARG* 2.7 59.2 + - + +
804A LEU* 3.8 29.2 - - + -
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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
----------------------------------------------------------
306A LYS 2.8 13.1 + - - +
307A GLN* 3.3 24.8 + - - +
308A ALA 5.1 1.3 - - - +
309A LEU* 1.3 80.3 - - - +
311A LEU* 1.3 61.2 + - - +
312A ASP 4.2 0.2 + - - -
801A ARG* 4.6 2.6 + - - -
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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