Contacts of the helix formed by residues 287 - 303 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LYS* 4.1 22.4 + - + -
251B SER* 6.0 4.7 - - - -
284B PRO* 3.7 9.0 - - + +
285B LYS 3.6 3.0 - - - +
286B THR* 1.3 81.4 - - - +
288B SER* 1.3 66.7 + - - +
289B PRO* 3.3 21.8 - - + +
290B LYS* 2.7 59.9 + - + +
291B GLU* 2.8 21.0 + - - +
293B MET* 5.8 1.3 - - - -
131C ASP* 3.3 3.1 - - - -
134C LEU* 5.3 0.4 - - - +
135C ARG* 5.3 6.7 - - - -
306C ASP* 4.3 13.9 - - + -
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Residues in contact with SER 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B HIS* 1.3 70.5 - - - +
289B PRO* 1.3 74.6 - - - +
291B GLU* 2.6 24.4 + - - +
292B VAL* 2.9 15.7 + - - +
329B HIS* 3.5 40.5 + - - -
332B VAL* 4.5 2.8 - - - +
125C GLN 5.0 0.2 - - - -
130C TYR* 3.6 10.2 - - - -
131C ASP* 2.6 28.7 + - - -
134C LEU* 5.2 1.6 - - - +
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Residues in contact with PRO 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B SER* 6.2 2.2 - - - -
287B HIS* 3.3 20.9 - - + +
288B SER* 1.3 95.6 - - - +
290B LYS* 1.3 64.6 + - - +
292B VAL* 2.9 7.9 + - + +
293B MET* 2.9 28.5 + - + +
329B HIS* 5.6 0.2 - - + -
331B GLN* 6.1 0.9 - - - +
125C GLN 5.9 0.9 - - - +
126C VAL 5.9 3.4 - - - +
131C ASP* 3.8 9.2 - - - +
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Residues in contact with LYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B HIS 2.8 29.5 + - - -
246B LYS* 2.8 19.6 + - - +
247B VAL 3.6 13.2 - - - +
248B LYS* 4.6 4.3 - - - +
250B LEU* 3.7 24.2 - - + -
251B SER 5.5 0.4 - - - +
282B TYR 5.0 1.0 + - - -
284B PRO* 3.6 9.4 - - + +
287B HIS* 2.7 49.0 + - + +
289B PRO* 1.3 71.5 - - - +
291B GLU* 1.3 56.4 + - - +
293B MET* 3.2 12.5 + - - +
294B PHE* 2.8 44.9 + - - -
306C ASP* 2.8 29.6 + - - +
307C TYR* 5.9 0.2 - - - -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TRP* 2.6 33.3 + - + +
284B PRO* 3.9 21.6 - - + +
285B LYS* 5.5 2.6 - - - -
287B HIS 2.8 11.0 + - - +
288B SER* 2.6 25.3 + - - +
290B LYS* 1.3 72.0 - - - +
292B VAL* 1.3 60.7 + - - -
294B PHE* 3.1 5.7 + - - +
295B LEU* 2.9 25.6 + - + +
320B GLN* 4.2 4.0 + - - -
324B CYS* 4.3 3.5 - - - +
332B VAL* 3.4 39.1 - - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B SER 2.9 15.8 + - - +
289B PRO* 3.6 8.1 - - + +
291B GLU* 1.3 74.8 - - - +
293B MET* 1.3 54.1 + - + +
295B LEU* 3.0 9.8 + - - +
296B ASN* 2.7 35.8 + - + +
329B HIS* 5.3 0.7 - - + +
331B GLN* 3.5 36.3 - - + +
332B VAL* 4.1 10.1 - - + +
335B ARG* 3.9 25.4 - - + +
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Residues in contact with MET 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU* 4.0 12.8 - - + -
251B SER* 3.2 40.2 - - - +
254B HIS* 3.1 62.1 + - + +
255B PRO* 5.4 0.4 - - + -
287B HIS* 5.8 0.4 - - - -
289B PRO* 2.9 21.4 + - + +
290B LYS* 3.3 19.7 - - - +
292B VAL* 1.3 77.3 - - + +
294B PHE* 1.3 64.3 + - - +
296B ASN* 3.0 6.6 + - - +
297B GLU 2.7 20.3 + - - -
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B HIS* 4.0 28.5 - + + -
250B LEU* 4.1 11.4 - - + -
254B HIS* 4.9 0.9 - + - -
279B LEU* 3.1 43.9 - - + +
282B TYR* 3.5 21.3 - - + -
283B TRP* 3.7 27.6 - + + -
284B PRO* 3.5 28.7 - - + -
290B LYS* 2.8 40.4 + - - +
291B GLU* 3.3 9.0 - - - +
293B MET* 1.3 71.4 - - - +
295B LEU* 1.3 66.4 + - - +
297B GLU* 2.7 11.9 + - - +
298B LEU* 2.7 23.8 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B TRP* 3.5 24.6 - - + -
291B GLU* 2.9 16.3 + - + +
292B VAL* 3.2 9.4 - - - +
294B PHE* 1.3 73.4 - - - +
296B ASN* 1.3 59.3 + - - +
298B LEU* 2.7 19.2 + - - -
299B GLU* 3.0 3.8 + - - +
321B LEU* 3.6 26.7 - - + -
324B CYS* 3.9 6.3 - - - -
332B VAL* 3.7 42.0 - - + +
335B ARG* 4.0 15.3 - - + -
336B ALA* 4.1 11.7 - - + +
339B TYR* 2.9 31.4 + - + +
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Residues in contact with ASN 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B HIS* 4.6 11.3 + - - -
292B VAL* 2.7 18.8 + - + +
293B MET* 3.3 11.1 + - - +
295B LEU* 1.3 73.7 - - - +
297B GLU* 1.3 62.0 + - - +
298B LEU 3.3 0.3 + - - -
299B GLU* 3.5 3.1 + - - +
300B GLU* 3.4 38.5 + - - +
335B ARG* 3.1 35.9 + - - +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B HIS* 2.7 39.6 + - - -
254B HIS* 2.9 35.0 + - + -
258B ALA* 3.9 21.3 - - + +
261B VAL* 3.4 20.0 - - + +
262B VAL* 6.1 0.7 - - + -
279B LEU* 4.0 14.5 - - + +
293B MET 2.7 4.6 + - - +
294B PHE* 2.7 16.3 + - - +
296B ASN* 1.3 75.7 - - - +
298B LEU* 1.3 58.5 + - - +
300B GLU* 3.6 10.4 - - + +
301B ILE* 2.9 29.2 + - + +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B VAL* 4.5 18.6 - - + -
279B LEU* 3.7 28.7 - - + -
280B LEU* 4.9 5.4 - - + -
283B TRP* 3.8 26.5 - - + -
294B PHE 2.7 15.0 + - - +
295B LEU* 2.7 6.0 + - - +
297B GLU* 1.3 70.8 - - - +
299B GLU* 1.3 65.0 + - - +
301B ILE* 2.8 22.5 + - + +
302B LEU* 2.9 12.1 + - + +
317B LEU* 3.3 40.2 - - + -
321B LEU* 5.0 0.4 - - + -
339B TYR* 3.1 20.0 - - + +
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Residues in contact with GLU 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 LEU 3.0 6.2 + - - +
296B ASN 3.9 7.4 - - - +
297B GLU 3.5 0.2 - - - -
298B LEU* 1.3 74.9 - - - +
300B GLU* 1.3 57.4 + - + +
302B LEU* 2.6 30.3 + - - +
303B ASP* 2.8 22.1 + - - +
335B ARG* 3.1 36.0 + - - +
338B TYR* 4.4 5.9 - - - +
339B TYR* 3.3 33.7 + - + -
342B ASN* 3.7 18.3 + - - +
345B ILE* 4.0 17.3 - - + -
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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
----------------------------------------------------------
258B ALA* 4.3 16.4 - - - +
259B TYR* 5.3 1.6 + - - -
262B VAL* 4.3 18.9 - - + +
296B ASN* 3.4 31.3 + - - +
297B GLU* 3.6 14.1 - - + +
299B GLU* 1.3 80.1 - - + +
301B ILE* 1.3 60.8 + - - +
303B ASP* 3.5 24.8 + - - +
304B VAL* 3.8 11.6 - - - +
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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
----------------------------------------------------------
261B VAL* 4.3 5.8 - - + -
262B VAL* 4.6 13.9 - - + -
265B LEU* 3.2 30.0 - - + +
272B THR* 5.2 3.6 - - + -
275B VAL* 4.1 14.4 - - + -
276B VAL* 4.5 16.6 - - + -
279B LEU* 3.5 31.4 - - + -
297B GLU* 2.9 26.9 - - + +
298B LEU* 2.8 19.2 + - + +
300B GLU* 1.3 70.9 - - - +
302B LEU* 1.3 68.1 + - + +
304B VAL* 3.1 7.8 + - - +
305B ILE* 3.0 19.7 + - + +
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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
----------------------------------------------------------
298B LEU* 2.9 11.8 + - + +
299B GLU* 2.6 14.9 + - - +
301B ILE* 1.3 68.4 - - + +
303B ASP* 1.3 51.2 + - - +
304B VAL 2.6 17.5 + - - -
305B ILE* 2.6 32.8 + - + +
310B PHE* 3.5 38.8 - - + -
313B ILE* 5.9 1.6 - - + -
317B LEU* 4.1 24.0 - - + -
318B PHE* 5.4 3.1 - - + -
339B TYR* 3.6 32.3 - - + -
344B TYR* 3.5 9.1 - - - -
345B ILE* 3.6 26.9 - - + -
348B LEU* 5.2 1.6 - - + -
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Residues in contact with ASP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLU* 2.8 23.3 + - - +
300B GLU* 3.5 20.2 - - - +
301B ILE 3.3 0.4 - - - -
302B LEU* 1.3 73.9 - - - +
304B VAL* 1.3 62.1 + - + +
342B ASN* 3.1 33.3 + - - +
344B TYR* 4.0 20.4 - - - +
345B ILE* 5.4 1.7 - - - +
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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
------------------------------------------------------------
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