Contacts of the helix formed by residues 313 - 333 (chain A) in PDB entry 2NPG
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 ASP 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A VAL* 3.5 44.3 - - + +
302A LEU* 4.0 16.6 - - - +
303A LYS 3.6 16.6 - - - +
310A ASP* 2.9 41.2 + - - +
312A CYS* 1.3 75.9 - - - +
314A VAL* 1.3 55.9 + - + +
315A PHE 3.2 0.2 - - - -
316A GLY* 2.8 26.1 + - - -
317A VAL 3.5 3.3 + - - -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 5.9 0.2 - - + -
31A PHE* 3.7 29.2 - - + -
32A TYR* 3.4 26.2 - - + +
35A LEU* 4.1 12.8 - - + -
114A LEU* 6.0 0.2 - - + -
311A PRO* 3.2 19.7 - - + +
313A ASP* 1.3 75.3 - - + +
315A PHE* 1.3 59.2 + - + +
316A GLY 3.0 4.7 - - - -
317A VAL* 3.0 23.8 + - + +
318A PHE* 3.1 38.9 + - + -
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.9 5.2 - - - -
114A LEU* 3.3 28.0 - - + -
115A ILE* 3.9 8.7 - - + -
118A ALA* 3.3 33.7 - - + -
119A LEU* 4.7 2.0 - - + -
171A ALA* 3.8 18.4 - - + -
172A ALA* 3.5 16.1 - - - +
175A GLY* 3.5 34.1 - - - -
176A LEU* 3.6 26.0 - - + +
312A CYS* 2.9 37.7 + - + +
314A VAL* 1.3 78.9 - - + +
316A GLY* 1.3 56.8 + - - +
318A PHE* 4.4 5.6 - + + +
319A GLY* 2.9 27.3 + - - -
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Residues in contact with GLY 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A LEU* 5.2 2.2 - - - -
298A GLY* 4.9 1.6 - - - -
299A VAL* 4.8 10.5 - - - -
302A LEU* 3.7 21.0 - - - +
313A ASP 2.8 13.9 + - - -
315A PHE* 1.3 78.6 - - - +
317A VAL* 1.3 57.1 + - - +
320A VAL* 3.0 40.1 + - - +
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Residues in contact with VAL 317 (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 - - + -
263A SER* 4.5 7.2 - - - +
266A ILE* 4.0 20.0 - - + +
267A ALA* 3.9 29.6 - - + +
270A VAL* 4.9 0.9 - - + -
295A GLY* 4.4 3.8 - - - +
299A VAL* 3.5 25.1 - - + -
313A ASP 3.5 1.7 + - - +
314A VAL* 3.0 12.1 + - + +
316A GLY* 1.3 74.1 - - - +
318A PHE* 1.3 62.4 + - + +
321A CYS* 2.9 43.1 + - + +
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Residues in contact with PHE 318 (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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28A ILE* 5.0 5.4 - - + -
31A PHE* 5.6 3.4 - + - -
114A LEU* 3.7 41.1 - - + -
168A HIS* 3.5 38.3 - + + +
172A ALA* 4.0 8.5 - - + +
208A LEU* 5.9 2.2 - - + -
212A TRP* 4.1 11.7 - + - -
266A ILE* 3.6 28.9 - - + -
270A VAL* 3.5 29.4 - - + +
314A VAL* 3.1 40.2 + - + +
315A PHE* 4.3 5.6 - + + +
317A VAL* 1.3 80.5 - - + +
319A GLY* 1.3 57.9 + - - +
322A GLY* 3.1 24.1 + - - -
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Residues in contact with GLY 319 (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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168A HIS 4.8 0.7 - - - -
169A ILE* 4.3 5.7 - - - +
172A ALA* 3.4 19.5 - - - +
173A ILE* 6.2 1.8 - - - -
176A LEU* 5.8 2.0 - - - -
315A PHE 2.9 15.3 + - - -
318A PHE* 1.3 77.2 - - - +
320A VAL* 1.3 64.7 + - - +
322A GLY* 3.9 0.2 - - - -
323A ILE* 3.0 35.9 + - - +
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Residues in contact with VAL 320 (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* 3.4 40.8 - - + +
295A GLY* 4.4 0.4 - - - +
297A TRP* 4.3 17.7 - - + -
298A GLY* 4.2 14.6 - - - -
316A GLY* 3.0 25.1 + - - +
317A VAL 4.4 0.2 - - - +
319A GLY* 1.3 75.3 - - - +
321A CYS* 1.3 60.8 + - - +
323A ILE* 3.3 10.6 + - + +
324A VAL* 3.0 31.9 + - + +
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Residues in contact with CYS 321 (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* 3.7 26.5 - - - +
270A VAL* 3.6 15.5 - - + -
271A GLY* 3.6 8.1 - - - +
291A ALA* 3.4 29.6 - - + -
294A ALA* 5.1 0.2 - - - -
295A GLY* 3.7 20.4 - - - -
317A VAL* 2.9 24.8 + - - +
320A VAL* 1.3 73.6 - - - +
322A GLY* 1.3 59.8 + - - +
324A VAL* 3.8 7.8 - - - +
325A GLY* 2.8 27.2 + - - -
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Residues in contact with GLY 322 (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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164A GLY* 4.5 8.5 - - - -
168A HIS* 4.6 0.7 - - - -
169A ILE* 3.6 15.3 - - - -
270A VAL* 3.5 12.7 - - - +
274A PRO* 4.8 0.7 - - - +
318A PHE 3.1 21.1 + - - -
319A GLY 3.9 0.4 - - - -
321A CYS* 1.3 73.8 - - - +
323A ILE* 1.3 65.7 + - - +
325A GLY* 5.2 0.4 - - - -
326A CYS* 3.0 28.9 + - - -
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Residues in contact with ILE 323 (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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169A ILE* 3.9 20.0 - - + -
173A ILE* 6.2 2.0 - - + -
319A GLY* 3.0 27.8 + - - +
320A VAL* 3.7 8.3 - - + +
322A GLY* 1.3 75.7 - - - +
324A VAL* 1.3 65.8 + - + +
326A CYS* 3.2 2.9 + - - +
327A ILE* 2.9 43.1 + - + +
359A ILE* 4.0 20.6 - - + -
363A ILE* 4.3 17.5 - - + -
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Residues in contact with VAL 324 (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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287A ILE* 5.3 0.7 - - + +
290A VAL* 3.9 16.2 - - + -
291A ALA* 4.5 14.8 - - + -
294A ALA* 3.9 21.1 - - + -
320A VAL* 3.0 23.8 + - + +
321A CYS* 3.8 6.7 - - - +
323A ILE* 1.3 79.4 - - + +
325A GLY* 1.3 57.7 + - - +
327A ILE* 3.3 7.5 + - + +
328A MET* 2.9 57.5 + - + +
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Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLY* 3.2 26.9 - - - +
274A PRO* 3.4 8.0 - - - +
275A ALA* 4.5 1.6 - - - +
287A ILE* 4.7 3.4 - - - -
321A CYS 2.8 19.4 + - - -
322A GLY 4.0 1.1 - - - -
324A VAL* 1.3 75.4 - - - +
326A CYS* 1.3 52.1 + - - +
328A MET* 3.4 5.0 + - - +
329A THR* 2.7 36.6 + - - -
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Residues in contact with CYS 326 (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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159A LEU 5.4 0.9 - - - -
160A ASP* 4.7 1.8 - - - -
164A GLY* 3.9 11.4 - - - -
165A THR* 3.9 27.6 - - - -
169A ILE* 4.0 3.8 - - - -
274A PRO* 3.8 23.6 - - - -
322A GLY 3.0 24.2 + - - +
323A ILE 3.6 3.6 - - - +
325A GLY* 1.3 72.4 - - - +
327A ILE* 1.3 66.0 + - - +
329A THR* 3.6 5.3 + - - -
355A GLN* 2.9 36.1 + - + +
359A ILE* 3.7 17.7 - - + -
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Residues in contact with ILE 327 (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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323A ILE* 2.9 38.7 + - + +
324A VAL* 3.8 7.0 - - + +
326A CYS* 1.3 77.2 - - - +
328A MET* 1.3 61.3 - - + +
330A GLY* 3.0 17.3 + - - -
331A ILE* 3.7 7.2 + - + -
352A LEU* 3.3 29.2 - - + +
355A GLN* 4.4 6.3 - - + -
356A LEU* 3.8 26.7 - - + -
359A ILE* 3.6 13.7 - - + -
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Residues in contact with MET 328 (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* 3.8 11.0 - - + -
287A ILE* 3.8 29.8 - - + -
290A VAL* 3.8 33.9 - - + -
324A VAL* 2.9 40.5 + - + +
325A GLY* 3.8 2.0 - - - +
327A ILE* 1.3 75.3 - - + +
329A THR* 1.3 59.6 + - - +
330A GLY 3.1 0.2 - - - -
331A ILE* 3.1 16.4 + - + +
332A PHE* 2.9 57.6 + - + +
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Residues in contact with THR 329 (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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159A LEU* 3.6 33.3 - - + +
274A PRO* 3.5 17.3 - - - +
275A ALA* 3.0 30.6 + - + +
278A TYR* 3.9 13.2 - - + -
279A ILE* 5.0 2.2 - - - -
325A GLY 2.7 23.6 + - - -
326A CYS* 3.6 8.5 - - - -
327A ILE 3.2 0.4 - - - -
328A MET* 1.3 76.7 - - - +
330A GLY* 1.3 60.6 + - - +
331A ILE 3.1 1.3 + - - -
333A ALA* 3.3 24.3 + - - +
355A GLN* 4.0 3.4 - - - -
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Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A CYS 3.8 2.4 + - - -
327A ILE 3.0 11.3 + - - -
329A THR* 1.3 78.7 - - - +
331A ILE* 1.3 59.6 + - - +
342A PHE* 3.1 23.1 - - - -
348A MET* 3.4 11.3 - - - +
351A GLN* 4.0 14.8 - - - +
352A LEU* 3.9 9.5 - - - +
355A GLN* 3.9 17.6 - - - +
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Residues in contact with ILE 331 (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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327A ILE* 4.0 7.0 - - + +
328A MET* 3.1 24.4 + - + +
329A THR 3.1 0.4 - - - -
330A GLY* 1.3 80.3 - - - +
332A PHE* 1.3 76.0 + - + +
333A ALA 3.4 0.7 - - - -
334A ALA* 3.3 15.9 + - - +
337A LEU* 3.6 18.9 - - + +
348A MET* 3.2 33.1 - - + +
352A LEU* 3.7 30.3 - - + -
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Residues in contact with PHE 332 (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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279A ILE* 3.7 24.9 - - + +
280A GLY 4.4 0.2 + - - -
283A GLY* 3.7 22.2 - - - -
286A ILE* 3.9 36.3 - - + -
287A ILE* 4.3 7.9 - - + -
328A MET* 2.9 49.8 + - + +
331A ILE* 1.3 90.5 - - + +
333A ALA* 1.3 56.9 + - - +
334A ALA 3.0 7.7 + - - +
337A LEU* 4.0 37.1 - - + +
339A GLY* 3.4 18.7 + - - -
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Residues in contact with ALA 333 (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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159A LEU* 3.8 22.7 - - + -
278A TYR* 3.4 27.6 - - + +
279A ILE* 4.1 0.4 - - - +
329A THR 3.3 19.9 + - - +
331A ILE 3.3 0.8 + - - -
332A PHE* 1.3 75.3 - - - +
334A ALA* 1.3 58.2 + - - +
339A GLY* 3.5 2.3 - - - -
341A GLY* 2.7 41.1 + - - +
342A PHE* 4.1 9.4 - - + -
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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