Contacts of the helix formed by residues 284 - 304 (chain B) in PDB entry 3NYN
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 284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLY 4.8 0.9 - - - +
283B PHE* 1.3 94.9 - - + +
285B GLU* 1.3 64.7 + - - +
286B ALA* 3.7 7.2 - - + +
287B ARG* 4.3 16.4 - - + +
288B ALA* 3.5 17.5 + - - +
379B ILE* 5.1 1.8 - - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 1.3 73.1 - - - +
286B ALA* 1.3 70.1 + - - +
287B ARG 3.1 1.2 + - - -
288B ALA* 3.3 4.2 + - - +
289B VAL* 3.1 35.4 + - + +
379B ILE* 4.8 16.1 - - + +
411B ARG 4.5 4.9 - - - +
412B PHE* 4.5 1.7 - - - -
413B SER* 3.2 46.0 + - - -
416B ALA* 3.7 11.6 - - + +
447B LEU* 4.7 6.9 - - + +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PRO* 4.5 4.2 - - + +
285B GLU* 1.3 79.1 - - - +
287B ARG* 1.3 61.3 + - - +
289B VAL* 3.5 6.5 + - - +
290B PHE* 3.2 21.0 + - - +
464B PRO* 4.8 8.0 - - + +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B HIS* 3.3 25.1 + - - -
278B MET* 5.8 4.0 - - - +
283B PHE* 3.3 44.9 - - + +
284B PRO* 4.0 17.4 + - + +
285B GLU 3.1 1.0 - - - -
286B ALA* 1.3 74.6 - - - +
288B ALA* 1.3 62.0 + - - +
289B VAL 3.0 1.6 - - - -
290B PHE* 2.8 22.9 + - - +
291B TYR* 3.1 45.8 + - + -
319B LEU* 4.7 0.8 - - - +
464B PRO* 3.8 25.1 - - + +
465B PHE* 3.2 49.7 - - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 4.5 6.7 - - + +
284B PRO 3.5 15.3 + - - +
285B GLU 3.3 4.1 + - - +
287B ARG* 1.3 79.8 - - - +
289B VAL* 1.3 57.3 + - - +
291B TYR* 3.7 1.7 + - - +
292B ALA* 3.1 22.7 + - - +
375B LEU* 3.9 3.1 - - + +
378B MET* 3.3 50.4 - - + +
379B ILE* 4.1 17.5 - - + -
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 3.1 28.2 + - + +
286B ALA* 3.6 7.4 - - - +
287B ARG 3.0 0.6 - - - -
288B ALA* 1.3 75.7 - - + +
290B PHE* 1.3 68.3 + - - +
292B ALA* 3.0 8.2 + - - +
293B ALA* 2.8 21.3 + - - +
375B LEU* 4.9 5.6 - - + -
379B ILE* 5.7 2.9 - - + -
416B ALA* 6.4 0.2 - - + -
447B LEU* 3.7 43.1 - - + +
448B PHE* 3.7 26.4 - - + -
451B LEU* 3.9 11.0 - - + -
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA 3.2 9.7 + - - +
287B ARG 2.8 14.7 + - - +
289B VAL* 1.3 75.3 - - - +
291B TYR* 1.3 71.9 + + + +
293B ALA* 2.8 24.5 + - - +
294B GLU* 3.0 39.5 + - + +
324B HIS* 4.0 4.9 - - - -
451B LEU* 4.3 21.5 - - + -
456B LEU* 3.4 25.8 - - + -
461B LEU* 4.2 11.0 - - + -
462B GLU 3.5 18.6 - - - -
463B PRO* 3.7 26.0 - - + -
464B PRO* 3.7 21.1 - - + -
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B LEU* 3.7 32.3 - - + -
283B PHE* 4.6 6.5 - + - -
287B ARG* 3.1 59.4 + - + -
288B ALA 4.0 6.7 - - - +
290B PHE* 1.3 95.2 - + - +
292B ALA* 1.3 57.8 + - - +
294B GLU* 3.3 6.4 + - - +
295B ILE* 2.8 40.7 + - + +
319B LEU* 3.9 15.8 - - + +
323B GLY 3.9 19.0 + - - -
325B ILE* 4.1 15.2 - - + +
378B MET* 4.0 18.2 - - - -
463B PRO* 5.3 0.2 - - + -
464B PRO* 4.8 7.0 - - + -
465B PHE* 4.0 11.7 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ALA 3.1 15.4 + - - +
289B VAL* 3.0 10.6 + - - +
291B TYR* 1.3 74.5 - - - +
293B ALA* 1.3 52.4 + - - +
295B ILE* 3.2 14.9 + - - +
296B CYS* 2.7 35.6 + - - +
371B LEU* 4.2 14.6 - - + +
375B LEU* 4.2 26.9 - - + -
378B MET* 4.2 4.0 - - + +
448B PHE* 4.6 9.4 - - + -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B VAL 2.8 10.2 + - - +
290B PHE 2.8 9.5 + - - +
292B ALA* 1.3 78.2 - - - +
294B GLU* 1.3 60.7 + - - +
296B CYS* 3.2 10.6 - - - +
297B CYS* 3.1 25.5 + - - -
448B PHE* 3.6 21.5 - - + -
451B LEU* 3.9 12.8 - - + -
453B PHE* 3.7 17.2 - - + -
456B LEU* 3.8 12.1 - - + -
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.5 27.5 - - + -
290B PHE* 3.0 39.7 + - + +
291B TYR* 3.7 3.5 - - - +
293B ALA* 1.3 71.7 - - - +
295B ILE* 1.3 59.0 + - - +
296B CYS 2.9 1.1 - - - -
297B CYS* 2.7 28.8 + - - +
298B GLY* 3.0 9.9 + - - -
324B HIS* 3.0 27.1 + - - +
325B ILE* 2.6 53.8 + - + +
456B LEU* 4.0 19.2 - - + +
459B GLY* 5.9 1.0 - - - -
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.8 5.6 - - + -
291B TYR* 2.8 43.7 + - + +
292B ALA* 3.4 9.2 - - - +
294B GLU* 1.3 71.7 - - - +
296B CYS* 1.3 61.7 + - - +
298B GLY* 3.5 3.2 + - - +
299B LEU* 3.0 40.4 + - + +
312B LEU* 3.6 21.5 - - + -
317B ILE* 4.6 10.8 - - + -
325B ILE* 3.7 18.6 - - + +
327B ILE* 4.6 4.4 - - + +
371B LEU* 3.5 20.6 - - + -
374B LEU* 3.4 28.5 - - + -
378B MET* 4.5 3.6 - - + -
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Residues in contact with CYS 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ALA 2.7 17.2 + - - +
293B ALA* 3.2 15.7 - - - +
294B GLU 2.9 0.2 + - - -
295B ILE* 1.3 73.5 - - - +
297B CYS* 1.3 58.5 + - - +
299B LEU* 3.0 12.8 + - - +
300B GLU* 2.8 25.5 + - - +
368B TRP* 3.8 26.3 - - + -
371B LEU* 4.6 8.5 - - + +
439B ALA* 4.6 4.0 - - - -
442B VAL* 4.3 10.8 - - + -
443B LYS* 4.1 27.1 - - - -
448B PHE* 5.6 2.7 - - + -
453B PHE* 4.4 7.0 - - + -
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Residues in contact with CYS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PHE* 3.5 28.0 - - + -
293B ALA 3.1 13.7 + - - -
294B GLU 2.7 13.2 + - - +
296B CYS* 1.3 75.4 - - - +
298B GLY* 1.3 57.0 + - - +
300B GLU* 3.3 8.7 + - - +
301B ASP* 2.8 37.9 + - - +
443B LYS* 5.4 5.2 - - - +
453B PHE* 4.1 23.1 - - - -
456B LEU* 4.1 13.2 - - - -
457B GLY* 4.7 11.9 - - - -
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B SER* 5.1 0.4 - - - -
245B PHE* 3.7 24.1 - - - +
246B VAL* 4.9 1.3 - - - +
294B GLU 3.0 10.6 + - - -
295B ILE 3.5 1.5 + - - -
297B CYS* 1.3 77.2 - - - +
299B LEU* 1.3 56.4 + - - +
301B ASP* 3.3 6.9 - - - +
302B LEU* 2.8 32.7 + - - +
327B ILE* 3.7 19.1 - - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ILE* 3.0 35.9 - - + +
296B CYS* 3.0 9.9 + - - +
298B GLY* 1.3 74.7 - - - +
300B GLU* 1.3 56.6 + - - +
302B LEU* 3.0 5.2 + - + +
303B HIS* 2.7 51.2 + - + +
309B TYR* 4.3 22.0 - - + -
312B LEU* 4.3 11.2 - - + -
327B ILE* 4.4 7.2 - - + -
367B ASP* 3.7 39.9 - - + +
368B TRP* 4.7 10.1 - - + -
371B LEU* 4.6 11.4 - - + -
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B CYS 2.8 13.2 + - - +
297B CYS* 3.5 11.9 - - - +
299B LEU* 1.3 76.3 - - - +
301B ASP* 1.3 63.0 + - - +
303B HIS* 3.7 4.9 - - - +
304B ARG* 2.8 66.3 + - - +
368B TRP* 4.9 2.7 - - - -
439B ALA* 3.0 37.2 - - + +
440B ARG* 4.5 4.0 + - - +
443B LYS* 2.8 33.2 + - - -
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B VAL* 6.1 1.8 - - + -
243B SER* 3.2 37.5 + - - +
244B ARG 4.4 2.6 + - - -
245B PHE* 4.4 7.7 - - - -
246B VAL* 5.6 0.2 - - + -
297B CYS* 2.8 27.3 + - - +
298B GLY* 3.3 6.7 - - - +
300B GLU* 1.3 79.9 - - - +
302B LEU* 1.3 64.1 + - + +
304B ARG* 3.4 12.1 + - - +
305B GLU* 3.4 20.0 + - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B VAL* 4.6 11.2 - - + -
246B VAL* 4.4 15.7 - - + -
298B GLY 2.8 17.7 + - - +
299B LEU* 3.0 13.2 + - + +
301B ASP* 1.3 72.6 - - - +
303B HIS* 1.3 62.5 + - + +
305B GLU* 2.9 23.8 + - - +
307B ILE* 3.2 50.3 + - + +
309B TYR* 4.5 14.1 - - + -
327B ILE* 3.4 38.1 - - + -
330B LEU* 3.9 21.8 - - + -
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Residues in contact with HIS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LEU* 2.7 31.3 + - + +
300B GLU* 3.8 4.0 - - - +
302B LEU* 1.3 71.2 - - + +
304B ARG* 1.3 58.0 + - - +
305B GLU 3.0 4.5 - - - -
306B ARG* 2.8 24.0 + - - +
307B ILE 3.3 19.5 - - - +
364B PHE* 3.4 50.0 - + + +
367B ASP* 2.7 33.1 + - + +
368B TRP* 3.4 36.8 + + - -
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLU* 2.8 51.4 + - - +
301B ASP* 3.6 9.4 - - - +
302B LEU 3.2 0.2 - - - -
303B HIS* 1.3 77.2 - - - +
305B GLU* 1.3 65.4 + - + +
306B ARG* 3.4 5.2 + - - +
440B ARG* 5.4 12.5 - - - +
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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