Contacts of the helix formed by residues 286 - 302 (chain B) in PDB entry 3NIE
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 HIS 286 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B ARG* 5.2 13.0 - - - +
287B GLU* 1.3 62.8 + - - +
288B LYS* 3.5 4.9 - - + +
289B SER* 3.8 16.8 + - - +
290B ASN* 3.2 37.1 + - - +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B HIS* 1.3 71.5 - - - +
288B LYS* 1.3 62.1 + - - +
290B ASN* 3.6 8.6 + - - +
291B ARG* 3.1 32.9 + - + +
320B TYR* 2.8 40.8 + - - -
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 5.8 5.8 - - - +
295A ASN* 5.9 4.5 - - - +
286B HIS* 3.5 3.3 - - + +
287B GLU* 1.3 76.1 - - - +
289B SER* 1.3 59.6 + - - +
291B ARG* 3.5 10.1 + - - +
292B ASP* 2.9 50.1 + - - +
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Residues in contact with SER 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG* 3.6 39.4 + - - -
271B SER* 3.8 12.6 - - - -
272B SER* 4.1 16.5 + - - +
286B HIS* 3.8 16.9 + - - +
287B GLU 3.4 0.4 - - - -
288B LYS* 1.3 76.4 - - - +
290B ASN* 1.3 66.4 + - - +
292B ASP* 3.3 3.9 + - - -
293B GLN* 3.0 25.1 + - - +
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Residues in contact with ASN 290 (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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220B ARG* 4.9 11.2 + - - +
228B ILE* 3.7 38.0 + - + +
229B LEU* 5.7 1.7 - - + +
230B LEU* 4.8 12.3 - - - +
286B HIS 3.2 26.3 + - - +
287B GLU* 3.9 10.5 + - - +
289B SER* 1.3 79.3 - - - +
291B ARG* 1.3 62.9 + - - +
293B GLN* 3.2 3.9 + - - +
294B LEU* 3.1 28.9 + - + +
320B TYR* 4.3 11.2 - - + +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B GLU* 3.1 23.5 + - - +
288B LYS* 3.8 11.7 - - + +
289B SER 3.3 0.2 - - - -
290B ASN* 1.3 79.8 - - - +
292B ASP* 1.3 65.7 + - - +
295B ASN* 3.0 28.0 + - + +
320B TYR* 3.6 19.1 - - + +
324B PHE* 3.9 20.1 - - + -
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 4.8 11.1 - - - +
270B GLY* 3.6 24.8 - - - +
271B SER* 4.4 3.8 - - - -
272B SER 5.4 2.1 + - - -
288B LYS* 2.9 40.4 + - - +
289B SER* 3.8 5.4 + - - +
291B ARG* 1.3 82.3 - - - +
293B GLN* 1.3 60.6 + - - +
295B ASN* 3.6 7.0 - - - +
296B ILE* 3.2 23.0 + - - +
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Residues in contact with GLN 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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220B ARG* 3.8 16.5 + - + +
221B TRP* 3.6 12.2 + - - +
223B ARG 5.5 1.0 + - - -
228B ILE* 3.3 29.2 - - + -
268B PHE* 2.8 38.4 + - - +
270B GLY 3.4 5.1 + - - -
271B SER* 2.9 35.9 + - - +
289B SER 3.0 16.8 + - - +
290B ASN* 3.2 5.4 + - - +
292B ASP* 1.3 74.3 - - - +
294B LEU* 1.3 60.0 + - - +
296B ILE* 3.1 7.4 - - - +
297B ILE* 2.9 34.3 + - + +
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Residues in contact with LEU 294 (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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225B PRO* 4.3 33.9 - - + +
228B ILE* 4.3 9.6 - - + +
229B LEU* 3.8 29.8 - - + -
290B ASN* 3.1 16.8 + - + +
293B GLN* 1.3 72.1 - - - +
295B ASN* 1.3 58.6 + - - +
297B ILE* 2.9 11.6 + - + +
298B PHE* 2.6 67.8 + - + -
320B TYR* 3.9 17.5 - - + -
321B ILE* 5.1 2.5 - - + -
324B PHE* 4.0 18.2 - - + -
353B PHE* 5.1 0.4 - - + -
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Residues in contact with ASN 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 3.0 19.3 + - + +
292B ASP* 3.6 9.0 - - - +
294B LEU* 1.3 79.4 - - - +
296B ILE* 1.3 57.7 + - - +
298B PHE* 3.3 0.8 + - - -
299B ASN* 2.8 44.9 + - - +
324B PHE* 3.6 19.5 - - + -
325B PRO* 5.5 1.0 - - - +
327B ARG* 2.7 32.6 + - - +
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Residues in contact with ILE 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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275A PRO 6.5 0.9 - - - -
267B LEU 4.8 3.1 - - - +
268B PHE* 3.9 21.1 - - + -
269B PRO* 3.6 42.0 - - + +
270B GLY* 3.6 21.8 - - - +
292B ASP 3.2 10.2 + - - +
293B GLN* 3.1 14.6 - - - +
295B ASN* 1.3 77.0 - - - +
297B ILE* 1.3 72.8 + - - +
299B ASN* 3.2 23.0 + - + +
300B VAL* 3.2 16.9 + - + +
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Residues in contact with ILE 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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223B ARG 4.2 6.5 - - - +
225B PRO* 4.3 14.1 - - + -
228B ILE* 4.0 24.5 - - + -
241B TRP* 3.9 36.3 - - + +
268B PHE* 3.6 26.1 - - + -
293B GLN* 2.9 26.3 + - + +
294B LEU* 2.9 13.0 + - + +
296B ILE* 1.3 76.9 - - - +
298B PHE* 1.3 66.9 + - + +
300B VAL* 3.1 5.9 + - - +
301B ILE* 3.0 37.8 + - + +
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Residues in contact with PHE 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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294B LEU* 2.6 48.3 + - + +
295B ASN* 3.7 4.0 - - - +
297B ILE* 1.3 79.4 - - + +
299B ASN* 1.3 57.2 + - - +
301B ILE* 5.1 0.9 - - + -
302B GLY* 2.6 47.4 + - - +
303B THR* 4.0 13.9 - - + +
304B PRO* 3.9 14.1 - - + -
321B ILE* 4.1 21.8 - - + -
324B PHE* 3.7 49.6 - + + -
327B ARG* 3.8 18.3 - - - +
353B PHE* 3.9 23.3 - + - -
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Residues in contact with ASN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASN* 2.8 32.8 + - - +
296B ILE* 3.2 18.9 + - + +
298B PHE* 1.3 75.5 - - - +
300B VAL* 1.3 60.4 + - + +
327B ARG* 3.1 33.1 + - - +
329B GLY* 3.5 14.4 - - - -
330B ILE* 3.6 13.0 - - - +
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Residues in contact with VAL 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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267B LEU* 3.9 32.3 - - + +
268B PHE* 3.6 21.1 - - + -
296B ILE* 3.2 14.5 + - + +
297B ILE 3.1 2.4 + - - -
299B ASN* 1.3 82.8 - - + +
301B ILE* 1.3 70.6 + - + +
302B GLY 3.5 0.4 - - - -
330B ILE* 2.8 50.7 + - + +
332B LEU* 4.2 19.4 - - + +
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Residues in contact with ILE 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 TRP* 4.2 4.3 - - + -
268B PHE* 4.6 9.9 - - + -
297B ILE* 3.0 34.1 + - + +
298B PHE* 4.7 1.3 - - + -
300B VAL* 1.3 88.7 - - + +
302B GLY* 1.3 73.9 + - - +
303B THR 4.7 0.9 - - - +
328B ASP 4.2 4.2 - - - +
329B GLY* 4.1 2.9 - - - -
332B LEU* 5.2 8.1 - - + -
351B LEU* 3.6 32.8 - - + +
353B PHE* 4.0 27.6 - - + +
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Residues in contact with GLY 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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298B PHE* 2.6 32.3 + - - -
301B ILE* 1.3 88.4 - - - +
303B THR* 1.3 69.9 + - - +
304B PRO* 4.6 0.2 - - - +
327B ARG 3.1 14.8 - - - -
328B ASP 3.6 2.7 - - - -
329B GLY* 3.4 14.7 - - - -
353B PHE* 6.0 0.7 - - - +
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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
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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