Contacts of the helix formed by residues 280 - 301 (chain A) in PDB entry 2NPJ
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 GLY 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LEU* 4.7 4.5 - - - -
233A ASN* 3.7 2.8 - - - +
279A ILE* 1.3 79.0 - - - +
281A VAL* 1.3 60.5 + - - -
282A GLY 3.2 3.1 - - - -
283A GLY* 3.0 6.6 + - - +
284A ALA 3.0 22.3 + - - -
332A PHE 4.5 1.2 + - - -
337A LEU 4.9 1.2 + - - -
338A GLY* 3.2 29.9 + - - -
339A GLY* 3.9 0.2 - - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 5.0 6.8 - - + +
232A VAL* 3.5 32.3 - - + -
233A ASN* 3.5 14.8 - - - +
236A VAL* 3.8 13.3 - - + +
280A GLY* 1.3 71.5 - - - -
282A GLY* 1.3 58.6 + - - +
284A ALA* 3.3 3.7 + - - +
285A LEU* 3.0 28.1 + - - +
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY* 3.2 1.6 - - - -
281A VAL* 1.3 81.6 - - - +
283A GLY* 1.3 61.3 + - - +
285A LEU* 3.3 8.0 + - - +
286A ILE* 3.1 32.6 + - - +
332A PHE* 5.4 0.2 - - - -
337A LEU 5.8 0.9 - - - -
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 3.8 7.6 - - - -
280A GLY* 3.0 10.5 + - - -
282A GLY* 1.3 76.8 - - - +
284A ALA* 1.3 56.3 + - - +
286A ILE* 3.3 1.2 + - - +
287A ILE* 2.8 35.6 + - - +
332A PHE* 3.7 34.9 - - - -
337A LEU 4.8 6.1 + - - -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ASN* 3.5 50.7 - - + +
236A VAL* 4.0 8.7 - - + -
237A ALA* 3.5 14.7 - - + +
272A VAL* 4.6 0.2 - - + -
279A ILE* 3.5 12.2 - - + +
280A GLY 3.0 5.5 + - - -
281A VAL 3.5 7.4 - - - +
283A GLY* 1.3 76.8 - - - +
285A LEU* 1.3 56.7 + - - +
287A ILE* 3.9 2.0 - - - -
288A GLY 2.8 24.4 + - - -
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Residues in contact with LEU 285 (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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236A VAL* 3.7 18.1 - - + +
240A ALA* 3.4 18.1 - - + +
281A VAL 3.0 13.2 + - - +
282A GLY* 3.3 11.0 + - - +
284A ALA* 1.3 77.0 - - - +
286A ILE* 1.3 66.9 + - + +
288A GLY 3.4 0.5 + - - -
289A VAL* 3.0 38.9 + - + +
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Residues in contact with ILE 286 (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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282A GLY 3.1 20.0 + - - +
283A GLY 3.8 3.8 - - - +
285A LEU* 1.3 79.8 - - + +
287A ILE* 1.3 64.7 + - - +
289A VAL* 3.4 4.9 + - - +
290A VAL* 3.0 31.0 + - + +
328A MET* 3.8 19.3 - - + -
332A PHE* 3.8 30.7 - - + -
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Residues in contact with ILE 287 (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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271A GLY* 3.7 32.1 - - - +
272A VAL* 4.2 7.6 - - + +
275A ALA* 3.8 27.1 - - + -
279A ILE* 3.9 16.8 - - + -
283A GLY 2.8 19.9 + - - +
284A ALA* 4.0 4.7 - - - +
286A ILE* 1.3 71.3 - - - +
288A GLY* 1.3 58.7 + - - +
290A VAL* 3.7 0.7 - - - +
291A ALA* 2.8 34.3 + - + +
324A VAL* 5.3 0.6 - - + +
325A GLY* 4.8 4.9 - - - +
328A MET* 3.8 50.6 - - + +
329A THR 4.6 0.2 - - - +
332A PHE* 4.3 6.3 - - + -
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 3.4 27.8 - - - +
240A ALA* 3.9 1.3 - - - -
241A ALA* 3.2 19.1 - - - +
268A GLY* 4.8 1.3 - - - -
284A ALA 2.8 17.5 + - - -
285A LEU 3.7 1.3 - - - -
286A ILE 3.3 0.2 - - - -
287A ILE* 1.3 76.8 - - - +
289A VAL* 1.3 56.1 + - - +
291A ALA* 3.3 3.2 + - - +
292A GLY 2.9 25.3 + - - -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA* 3.7 24.9 - - + +
241A ALA* 4.7 0.4 - - - +
243A LEU* 6.2 0.4 - - + -
244A GLY* 4.5 9.3 - - - -
285A LEU* 3.0 28.4 + - + +
286A ILE* 3.4 5.1 + - - +
288A GLY* 1.3 73.8 - - - +
290A VAL* 1.3 66.1 + - + +
292A GLY* 3.4 2.1 + - - -
293A LEU* 3.1 42.3 + - + +
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Residues in contact with VAL 290 (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 ILE* 3.0 27.1 + - + +
287A ILE 3.9 2.7 - - - +
289A VAL* 1.3 78.2 - - + +
291A ALA* 1.3 58.3 + - - +
293A LEU* 3.4 8.5 + - + +
294A ALA* 2.8 30.8 + - + +
324A VAL* 3.9 11.2 - - + -
328A MET* 3.8 32.1 - - + -
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Residues in contact with ALA 291 (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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267A ALA* 3.4 27.1 - - - +
268A GLY* 4.4 2.0 - - - -
271A GLY* 4.3 14.4 - - - -
287A ILE* 2.8 22.4 + - + +
288A GLY* 3.7 4.0 - - - +
290A VAL* 1.3 75.1 - - - +
292A GLY* 1.3 52.1 + - - +
294A ALA* 3.7 5.3 - - - -
295A GLY* 2.8 30.0 + - - -
321A CYS* 3.4 16.3 - - + -
324A VAL* 4.5 10.0 - - + +
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Residues in contact with GLY 292 (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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241A ALA* 3.7 23.9 - - - +
245A TRP* 3.3 22.4 - - - +
267A ALA* 4.0 12.3 - - - -
288A GLY 2.9 13.8 + - - -
289A VAL 3.8 2.2 - - - -
290A VAL 3.3 0.2 - - - -
291A ALA* 1.3 75.1 - - - +
293A LEU* 1.3 56.7 + - - +
296A LEU* 3.1 23.2 + - - +
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Residues in contact with LEU 293 (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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244A GLY* 3.4 26.7 - - - +
245A TRP* 5.2 0.2 - - - -
247A PHE* 5.0 7.6 - - + -
248A GLY* 4.4 14.8 - - - +
289A VAL* 3.1 33.3 + - + +
290A VAL* 3.9 6.7 - - + +
292A GLY* 1.3 74.2 - - - +
294A ALA* 1.3 59.1 + - - +
296A LEU* 3.3 8.4 + - + +
297A TRP* 3.0 27.8 + - - +
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Residues in contact with ALA 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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290A VAL* 2.8 21.9 + - + +
291A ALA* 3.8 4.0 - - - +
293A LEU* 1.3 74.0 - - - +
295A GLY* 1.3 56.0 + - - +
297A TRP* 3.3 8.9 + - + +
298A GLY 2.8 29.3 + - - -
320A VAL* 3.5 27.0 - - + +
321A CYS* 5.1 1.1 - - - -
324A VAL* 3.9 18.8 - - + -
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Residues in contact with GLY 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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245A TRP* 3.3 15.5 - - - -
291A ALA 2.8 17.5 + - - -
294A ALA* 1.3 74.4 - - - +
296A LEU* 1.3 63.1 + - - +
298A GLY* 3.3 1.3 + - - -
299A VAL* 3.0 29.8 + - - +
317A VAL* 4.3 6.9 - - - +
320A VAL* 4.9 2.2 - - - -
321A CYS* 3.7 17.0 - - - -
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Residues in contact with LEU 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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245A TRP* 3.4 41.8 - - + +
248A GLY* 3.6 37.7 - - - +
249A GLU* 3.7 11.2 - - + +
252A LEU* 4.2 16.2 - - + -
253A ARG* 5.5 10.8 - - - +
292A GLY 3.1 14.1 + - - +
293A LEU* 3.3 11.4 + - + +
295A GLY* 1.3 71.5 - - - +
297A TRP* 1.3 62.0 + - - +
299A VAL* 3.3 6.4 - - + +
300A THR* 2.6 43.9 + - - +
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Residues in contact with TRP 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 LEU 3.0 13.8 + - - +
294A ALA* 3.6 14.6 - - + +
296A LEU* 1.3 78.2 - - - +
298A GLY* 1.3 76.2 - - - +
300A THR* 3.3 6.2 + - - -
301A MET* 3.0 79.7 + - + +
320A VAL* 4.4 19.3 - - + -
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Residues in contact with GLY 298 (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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294A ALA 2.8 16.5 + - - -
295A GLY 3.3 2.4 + - - -
297A TRP* 1.3 88.6 - - - +
299A VAL* 1.3 62.5 + - - +
301A MET* 3.2 20.8 + - - +
302A LEU* 3.4 10.4 + - - +
316A GLY* 4.8 7.6 - - - -
320A VAL* 4.2 16.8 - - - -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TRP* 3.8 20.6 - - + -
295A GLY 3.0 8.8 + - - +
296A LEU* 3.3 14.8 - - + +
298A GLY* 1.3 71.4 - - - +
300A THR* 1.3 64.8 + - - +
301A MET 2.8 18.9 - - - +
302A LEU* 4.4 5.3 - - - +
313A ASP* 3.8 34.1 - - + +
316A GLY* 5.1 0.2 - - - -
317A VAL* 3.4 33.2 - - + +
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Residues in contact with THR 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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252A LEU* 5.8 3.0 - - + +
296A LEU* 2.6 36.8 + - - +
297A TRP* 3.3 8.7 + - - -
299A VAL* 1.3 77.2 - - - +
301A MET* 1.3 76.8 + - + +
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Residues in contact with MET 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 TRP* 3.0 65.0 + - + +
298A GLY* 3.3 5.2 - - - +
299A VAL 2.8 14.9 - - - +
300A THR* 1.3 97.2 - - + +
302A LEU* 1.3 73.5 + - - +
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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
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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