Contacts of the helix formed by residues 315 - 328 (chain A) in PDB entry 1N0U
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 GLU 315 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A PHE* 3.8 26.6 - - + +
313A ASP 3.6 11.4 - - - +
314A LEU* 1.3 81.8 - - - +
316A GLY* 1.3 70.5 + - - +
317A LYS 3.6 0.3 + - - -
318A ALA* 3.5 9.5 + - - +
319A LEU* 3.2 16.9 + - - -
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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
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288A ILE* 3.2 25.5 + - - +
289A MET* 3.8 11.4 - - - -
291A PHE* 3.5 22.8 - - - -
315A GLU* 1.3 75.2 - - - +
317A LYS* 1.3 64.4 + - - -
319A LEU* 3.0 4.2 + - - +
320A LEU 2.9 18.4 + - - -
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Residues in contact with LYS 317 (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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165A LEU* 6.2 5.4 - - + -
216A HIS* 6.4 1.6 - - + -
289A MET* 3.4 34.2 - - + +
315A GLU 3.6 0.2 + - - -
316A GLY* 1.3 70.3 - - - -
318A ALA* 1.3 58.0 + - - +
320A LEU* 3.1 5.3 + - + +
321A LYS* 2.8 51.8 + - - +
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Residues in contact with ALA 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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314A LEU* 4.4 21.8 - - + -
315A GLU 3.5 8.5 + - - +
316A GLY 3.3 0.6 - - - -
317A LYS* 1.3 79.3 - - - +
319A LEU* 1.3 61.7 + - - +
321A LYS* 3.9 9.2 - - - +
322A VAL* 3.3 27.5 + - - +
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Residues in contact with LEU 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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288A ILE* 3.8 19.5 - - + -
296A ILE* 4.1 28.0 - - + -
300A LEU* 5.5 0.2 - - + -
307A LEU* 3.8 27.1 - - + -
311A GLU 4.2 2.7 - - - +
314A LEU* 3.7 33.1 - - + +
315A GLU* 3.2 20.7 + - - +
316A GLY 3.0 8.4 + - - +
318A ALA* 1.3 76.8 - - - +
320A LEU* 1.3 55.4 + - - +
322A VAL* 3.1 3.9 + - + +
323A VAL* 2.7 56.3 + - + +
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Residues in contact with LEU 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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165A LEU* 5.4 2.9 - - + -
216A HIS* 3.5 25.8 - - + +
284A LEU 4.2 1.3 - - - +
285A PHE* 3.7 45.3 - - + +
288A ILE* 3.7 28.9 - - + +
289A MET* 4.0 18.4 - - + -
316A GLY 2.9 12.7 + - - +
317A LYS* 3.1 11.0 + - + +
319A LEU* 1.3 76.7 - - - +
321A LYS* 1.3 57.7 + - - +
323A VAL* 3.1 1.0 + - - +
324A MET* 2.8 54.0 + - + +
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Residues in contact with LYS 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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215A LEU* 5.7 10.4 + - - +
216A HIS* 4.5 46.4 - - + +
317A LYS* 2.8 40.4 + - - +
318A ALA* 3.9 8.1 - - - +
320A LEU* 1.3 71.7 - - - +
322A VAL* 1.3 64.5 + - + +
324A MET* 4.1 3.8 - - - +
325A ARG* 3.1 40.1 + - - +
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Residues in contact with VAL 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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307A LEU* 4.0 21.5 - - + -
311A GLU* 3.7 29.6 - - + +
314A LEU* 3.5 20.9 - - + -
318A ALA 3.3 14.1 + - - +
319A LEU* 3.1 8.6 + - + +
321A LYS* 1.3 78.9 - - + +
323A VAL* 1.3 61.4 + - - +
325A ARG* 3.6 9.1 + - - +
326A LYS* 3.3 27.5 + - - +
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Residues in contact with VAL 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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284A LEU* 4.1 13.9 - - + -
288A ILE* 3.6 27.4 - - + -
300A LEU* 4.6 12.6 - - + -
305A ILE* 4.3 21.1 - - + +
307A LEU* 4.2 11.0 - - + -
319A LEU* 2.7 39.6 + - + +
320A LEU 3.6 3.6 - - - +
322A VAL* 1.3 74.7 - - - +
324A MET* 1.3 74.6 + - + +
326A LYS* 3.3 4.2 + - - +
327A PHE* 2.9 25.9 + - + +
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Residues in contact with MET 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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216A HIS* 4.7 2.0 - - + +
218A TRP* 3.6 39.9 - - + +
281A ILE* 4.7 8.5 - - - -
284A LEU* 3.1 40.2 - - + -
285A PHE* 3.8 24.9 - - + -
320A LEU* 2.8 37.4 + - + +
321A LYS* 4.1 3.8 - - - +
323A VAL* 1.3 83.4 - - + +
325A ARG* 1.3 58.5 + - + +
327A PHE* 3.8 13.9 - - + -
328A LEU* 2.7 36.1 + - - +
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Residues in contact with ARG 325 (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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41A GLN* 5.5 4.9 + - - -
214A GLY 5.3 0.4 + - - -
215A LEU 3.7 13.5 + - - -
216A HIS 3.2 23.3 + - - +
217A GLY* 3.7 28.0 + - - +
321A LYS* 3.1 36.5 + - - +
322A VAL* 3.9 9.0 - - - +
323A VAL 3.3 0.2 - - - -
324A MET* 1.3 75.9 - - - +
326A LYS* 1.3 59.4 + - + +
329A PRO* 3.0 32.5 - - + +
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Residues in contact with LYS 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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305A ILE* 4.3 16.0 - - + +
306A VAL* 3.5 27.9 + - + +
307A LEU* 4.4 7.9 - - + +
308A LYS* 3.3 28.7 - - - +
311A GLU* 3.1 32.3 + - - -
322A VAL* 3.3 21.8 + - + +
323A VAL 3.7 3.1 - - - +
324A MET 3.2 0.2 - - - -
325A ARG* 1.3 78.5 - - + +
327A PHE* 1.3 65.3 + - - +
329A PRO* 4.1 6.6 - - - +
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Residues in contact with PHE 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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225A PHE* 4.1 20.2 - + - -
228A ARG* 3.2 57.7 + - - -
280A PRO* 4.8 5.6 - - + -
281A ILE* 4.1 13.9 - - + -
284A LEU* 3.7 27.6 - - + -
303A LEU* 4.2 24.9 - - + -
305A ILE* 3.6 26.4 - - + +
323A VAL 2.9 18.9 + - - +
324A MET* 3.7 14.8 - - + +
326A LYS* 1.3 81.7 - - - +
328A LEU* 1.3 79.9 + - + +
329A PRO* 3.8 3.3 - - - +
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Residues in contact with LEU 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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218A TRP* 3.0 15.5 - - + -
219A ALA 3.0 26.6 + - - +
220A PHE* 4.0 16.2 - - + -
224A GLN* 4.8 11.4 - - + +
225A PHE* 3.9 31.6 - - + -
228A ARG* 3.8 15.3 - - - +
281A ILE* 4.1 16.4 - - + -
324A MET* 2.7 16.0 + - - +
327A PHE* 1.3 110.3 - - + +
329A PRO* 1.3 70.7 - - - +
330A ALA 2.9 3.3 + - - -
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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
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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