Contacts of the helix formed by residues 287 - 303 (chain E) in PDB entry 2NPP
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 287 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E LYS* 3.9 22.9 + - + -
251E SER* 6.1 4.5 - - - -
284E PRO* 3.6 10.5 - - + +
285E LYS 3.7 2.4 - - - +
286E THR* 1.3 80.8 - - - +
288E SER* 1.3 67.1 + - - +
289E PRO* 3.4 30.3 - - + +
290E LYS* 3.0 48.1 + - + +
291E GLU* 2.9 18.2 + - - +
293E MET* 6.0 0.4 - - - -
131F ASP* 3.5 3.8 - - - -
134F LEU* 5.3 0.4 - - - +
135F ARG* 5.3 6.7 - - - -
306F ASP* 4.2 17.7 - - + -
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Residues in contact with SER 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E HIS* 1.3 71.0 + - - +
289E PRO* 1.3 73.2 - - - +
291E GLU* 2.6 31.1 + - - +
292E VAL* 2.9 9.8 + - - +
329E HIS* 3.5 43.1 + - - +
332E VAL* 4.4 3.2 - - - +
130F TYR* 3.7 14.2 - - - -
131F ASP* 2.8 17.8 + - - -
134F LEU* 5.3 2.1 - - - +
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Residues in contact with PRO 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E SER* 6.1 3.4 - - - -
287E HIS* 3.4 22.0 - - + +
288E SER* 1.3 96.1 - - - +
290E LYS* 1.3 63.7 + - - +
292E VAL* 2.9 9.0 + - + +
293E MET* 2.9 28.5 + - + +
329E HIS* 5.8 0.2 - - + -
331E GLN* 5.9 4.3 - - - +
125F GLN 6.0 0.7 - - - +
131F ASP* 3.7 9.4 - - - +
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Residues in contact with LYS 290 (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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245E HIS 2.8 28.6 + - - -
246E LYS* 2.9 20.0 + - - +
247E VAL 3.1 14.9 + - - +
248E LYS* 4.3 4.0 - - - +
250E LEU* 4.0 19.1 - - + +
251E SER 5.4 0.7 - - - +
282E TYR 5.2 1.0 + - - -
284E PRO* 3.7 7.6 - - + +
287E HIS* 3.0 44.1 + - + +
289E PRO* 1.3 74.7 - - - +
291E GLU* 1.3 58.2 + - - +
293E MET* 3.0 13.1 + - - +
294E PHE* 2.8 49.3 + - + -
306F ASP* 2.7 29.6 + - - +
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Residues in contact with GLU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E TRP* 2.6 33.2 + - - +
284E PRO* 3.9 21.8 - - + +
285E LYS* 5.7 1.2 - - - -
287E HIS 2.9 13.4 + - - +
288E SER* 2.6 27.2 + - - +
290E LYS* 1.3 70.7 - - - +
292E VAL* 1.3 61.0 + - - +
294E PHE* 2.9 7.8 + - - +
295E LEU* 2.9 24.4 + - + +
320E GLN* 4.5 1.0 + - - -
324E CYS* 4.0 5.5 - - - -
327E SER* 5.3 1.6 + - - -
332E VAL* 3.6 38.1 - - + +
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Residues in contact with VAL 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E SER 2.9 15.2 + - - +
289E PRO* 3.5 8.1 - - + +
291E GLU* 1.3 74.5 - - - +
293E MET* 1.3 55.1 + - + +
295E LEU* 3.0 10.0 + - - +
296E ASN* 2.6 37.4 + - + +
329E HIS* 5.5 0.4 - - + +
331E GLN* 3.8 37.7 - - + +
332E VAL* 4.3 9.9 - - + +
335E ARG* 3.9 23.1 - - + -
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Residues in contact with MET 293 (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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250E LEU* 3.9 17.3 - - + -
251E SER* 3.4 33.9 - - - +
254E HIS* 2.8 64.3 + - + +
255E PRO* 5.5 0.7 - - + -
287E HIS* 6.0 0.2 - - - -
289E PRO* 2.9 18.0 + - + +
290E LYS* 3.2 20.4 - - - +
292E VAL* 1.3 77.6 - - + +
294E PHE* 1.3 57.9 + - - +
296E ASN* 3.2 5.0 + - - +
297E GLU* 2.7 25.3 + - - +
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Residues in contact with PHE 294 (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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245E HIS* 3.7 39.9 - + + -
250E LEU* 4.3 9.6 - - + -
279E LEU* 3.2 52.1 - - + +
282E TYR* 3.7 20.2 - - + -
283E TRP* 3.8 26.0 - + + -
284E PRO* 3.5 20.2 - - + -
290E LYS* 2.8 34.4 + - - +
291E GLU 3.2 8.3 - - - +
293E MET* 1.3 72.9 - - - +
295E LEU* 1.3 52.6 + - - +
297E GLU* 2.8 11.6 + - - +
298E LEU* 2.7 36.3 + - - +
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Residues in contact with LEU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E TRP* 3.7 24.0 - - + -
291E GLU 2.9 12.2 + - - +
292E VAL* 3.3 10.1 - - - +
294E PHE* 1.3 74.4 - - - +
296E ASN* 1.3 64.2 + - - +
298E LEU* 3.0 5.4 + - - -
299E GLU* 3.1 3.1 + - - +
321E LEU* 3.4 33.2 - - + -
324E CYS* 3.9 9.2 - - - -
332E VAL* 3.9 39.9 - - + +
335E ARG* 4.0 15.5 - - + -
336E ALA* 3.9 11.4 - - + +
339E TYR* 2.7 38.7 + - + +
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Residues in contact with ASN 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E HIS* 4.9 8.7 + - - -
292E VAL* 2.6 22.6 + - + +
293E MET* 3.5 8.0 + - - +
295E LEU* 1.3 75.4 - - - +
297E GLU* 1.3 61.5 + - - +
299E GLU* 3.8 3.1 + - - +
300E GLU* 3.6 36.0 + - - +
335E ARG* 3.1 35.2 + - - +
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Residues in contact with GLU 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E HIS* 2.7 43.2 + - - -
250E LEU* 5.4 0.2 - - - +
254E HIS* 3.0 21.6 - - + -
258E ALA* 3.7 24.7 - - + -
261E VAL* 3.6 14.7 - - + +
262E VAL* 6.1 0.4 - - + -
279E LEU* 3.8 19.7 - - - +
293E MET 2.7 19.6 + - - +
294E PHE* 2.8 7.8 + - - +
296E ASN* 1.3 72.3 - - - +
298E LEU* 1.3 63.3 + - - +
300E GLU* 3.6 11.2 - - + +
301E ILE* 3.0 33.3 + - + +
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Residues in contact with LEU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E VAL* 4.4 20.9 - - + -
279E LEU* 4.0 28.0 - - + +
280E LEU* 4.9 4.3 - - + -
283E TRP* 4.1 24.5 - - + -
294E PHE 2.7 11.9 + - - +
295E LEU* 3.0 3.3 + - - +
297E GLU* 1.3 75.5 - - - +
299E GLU* 1.3 67.0 + - - +
301E ILE* 2.8 21.2 + - + +
302E LEU* 2.9 12.4 + - + +
317E LEU* 3.3 40.4 - - + -
321E LEU* 4.8 1.3 - - + -
339E TYR* 2.9 21.5 - - + +
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Residues in contact with GLU 299 (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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295E LEU 3.1 1.2 + - - +
296E ASN 4.0 2.2 - - - +
297E GLU 3.5 0.2 - - - -
298E LEU* 1.3 73.3 - - - +
300E GLU* 1.3 55.1 + - + +
301E ILE 2.7 1.6 + - - -
302E LEU* 2.5 30.9 + - - +
303E ASP* 2.8 23.0 + - - +
335E ARG* 3.1 40.6 + - - +
338E TYR* 4.4 3.4 - - - +
339E TYR* 3.1 38.2 + - + -
342E ASN* 3.5 22.1 + - - +
345E ILE* 4.0 17.5 - - + -
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Residues in contact with GLU 300 (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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258E ALA* 4.3 18.6 - - - +
259E TYR* 5.3 1.6 + - - -
262E VAL* 4.2 19.9 - - + +
296E ASN* 3.6 30.5 + - - +
297E GLU* 3.6 15.0 - - + +
298E LEU 3.2 0.2 - - - -
299E GLU* 1.3 79.8 - - + +
301E ILE* 1.3 60.1 + - - +
303E ASP* 3.7 23.4 - - - +
304E VAL* 4.0 11.4 - - - +
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Residues in contact with ILE 301 (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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261E VAL* 4.5 5.2 - - + -
262E VAL* 4.6 14.1 - - + -
265E LEU* 3.2 30.4 - - + +
272E THR* 5.2 3.6 - - + -
275E VAL* 4.2 12.1 - - + -
276E VAL* 4.4 17.7 - - + -
279E LEU* 3.5 32.3 - - + -
297E GLU* 3.0 25.1 - - + +
298E LEU* 2.8 15.5 + - + +
299E GLU 2.7 4.0 + - - -
300E GLU* 1.3 73.4 - - - +
302E LEU* 1.3 65.5 + - + +
304E VAL* 3.1 7.5 + - - +
305E ILE* 2.9 21.7 + - + +
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Residues in contact with LEU 302 (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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276E VAL* 6.4 1.8 - - + -
298E LEU* 2.9 12.2 + - + +
299E GLU 2.5 13.2 + - - +
301E ILE* 1.3 68.2 - - + +
303E ASP* 1.3 53.9 + - - +
304E VAL 2.6 7.6 + - - -
305E ILE* 2.5 46.8 + - + +
310E PHE* 3.7 35.2 - - + -
313E ILE* 5.7 1.6 - - + -
317E LEU* 4.1 23.3 - - + -
318E PHE* 5.4 2.9 - - + -
321E LEU* 5.5 0.2 - - + -
339E TYR* 3.6 23.1 - - + -
344E TYR* 3.6 7.0 - - - -
345E ILE* 3.3 41.7 - - + -
348E LEU* 5.1 1.1 - - + -
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Residues in contact with ASP 303 (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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299E GLU* 2.8 22.2 + - - +
300E GLU* 3.7 20.1 - - - +
301E ILE 3.3 0.2 - - - -
302E LEU* 1.3 73.9 - - - +
304E VAL* 1.3 62.8 + - + +
342E ASN* 3.1 32.3 + - - +
344E TYR* 3.7 24.6 - - - +
345E ILE* 5.3 0.8 - - - +
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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
------------------------------------------------------------
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