Contacts of the helix formed by residues 273 - 284 (chain B) in PDB entry 1N1E
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 SER 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B PHE* 3.7 10.7 - - - -
267B THR* 3.1 33.4 - - - +
270B SER 3.0 9.6 + - - -
271B GLU 3.3 1.0 - - - +
272B LEU* 1.3 77.0 - - - +
274B ARG* 1.3 57.1 + - - +
276B PHE* 3.0 18.1 + - - +
277B THR* 3.0 31.2 + - - -
401B NDE 2.5 30.3 + - - -
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Residues in contact with ARG 274 (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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25B ALA* 4.6 4.6 - - - +
272B LEU 3.9 10.8 - - - -
273B SER* 1.3 72.1 - - - +
275B ASN* 1.3 58.1 + - - +
277B THR* 3.4 7.5 + - - +
278B VAL* 3.0 31.7 + - - +
297B ALA* 3.7 32.0 - - + +
298B VAL* 3.5 24.8 + - - +
299B ALA* 4.1 8.1 - - + -
401B NDE 2.7 116.2 + - - +
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Residues in contact with ASN 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASN* 3.1 41.1 + - - +
214B ALA* 4.0 5.4 - - + -
215B ILE* 3.5 19.6 - - + +
273B SER* 3.2 1.9 + - - +
274B ARG* 1.3 75.3 - - - +
276B PHE* 1.3 65.3 + - - +
278B VAL* 3.3 2.2 + - - +
279B GLY 3.0 18.2 + - - -
299B ALA* 3.4 14.1 - - - +
300B GLU 3.8 10.3 - - - +
301B GLY* 2.8 28.3 + - - -
302B VAL 3.9 1.4 + - - -
401B NDE 2.9 31.6 + - - +
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Residues in contact with PHE 276 (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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214B ALA 3.5 9.5 + - - -
217B SER* 3.6 12.1 - - - -
218B GLY* 3.3 19.7 - - - -
221B ASN* 3.7 26.5 - - + -
230B ARG* 3.7 24.7 - - - -
267B THR 3.7 4.7 - - - +
268B CYS 3.4 32.5 - - - -
270B SER* 3.4 27.4 - - - +
271B GLU* 3.7 29.4 - - + -
273B SER* 3.0 15.8 + - - +
275B ASN* 1.3 75.2 - - - +
277B THR* 1.3 60.2 + - - +
279B GLY 3.1 2.3 + - - -
280B LYS* 2.9 28.3 + - + -
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Residues in contact with THR 277 (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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271B GLU* 2.9 37.6 + - - +
273B SER 3.0 9.1 + - - -
274B ARG* 3.6 8.5 - - - -
275B ASN 3.2 0.2 - - - -
276B PHE* 1.3 77.2 - - - +
278B VAL* 1.3 64.6 + - + +
280B LYS* 3.3 9.7 + - + +
281B LYS* 3.1 49.8 + - + +
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ILE* 4.5 6.7 - - + -
274B ARG 3.0 17.7 + - - +
275B ASN* 3.5 9.6 - - - +
277B THR* 1.3 77.2 - - + +
279B GLY* 1.3 58.1 + - - +
281B LYS* 3.2 5.3 + - - +
282B LEU* 3.0 44.9 + - + +
288B ILE* 3.9 10.3 - - + -
291B ILE* 3.8 24.6 - - + +
292B GLN* 4.1 7.0 - - - +
295B SER* 5.2 3.4 - - - +
299B ALA* 3.7 20.4 - - + -
302B VAL* 3.9 19.5 - - + -
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Residues in contact with GLY 279 (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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215B ILE* 3.2 33.6 - - - +
218B GLY 3.2 6.3 - - - -
219B VAL* 3.2 13.1 - - - +
275B ASN 3.0 11.3 + - - -
276B PHE 3.5 3.1 - - - -
278B VAL* 1.3 74.6 - - - +
280B LYS* 1.3 65.5 + - - +
282B LEU* 3.2 2.0 + - - -
283B GLY 2.9 19.9 + - - -
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Residues in contact with LYS 280 (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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218B GLY* 3.1 14.9 - - - +
221B ASN* 3.5 25.2 + - - +
222B GLY* 3.8 7.3 - - - -
271B GLU* 3.2 42.5 + - + +
276B PHE* 2.9 15.5 + - + +
277B THR* 3.3 13.7 + - + +
279B GLY* 1.3 73.7 - - - +
281B LYS* 1.3 60.7 + - + +
283B GLY* 3.2 2.6 + - - -
284B LYS* 2.9 56.3 + - + +
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Residues in contact with LYS 281 (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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277B THR* 3.1 38.3 + - + +
278B VAL 3.6 4.9 - - - +
280B LYS* 1.3 80.0 - - + +
282B LEU* 1.3 61.4 + - - +
284B LYS* 3.3 6.6 + - - +
285B GLY 3.1 5.7 + - - -
286B LEU* 3.1 38.2 + - + +
291B ILE* 3.4 39.7 + - + +
294B THR* 5.2 9.1 + - - -
295B SER* 4.7 11.7 + - - -
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Residues in contact with LEU 282 (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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215B ILE* 4.1 17.5 - - + -
219B VAL* 4.2 6.5 - - + -
278B VAL* 3.0 34.9 + - + +
279B GLY 3.6 5.4 - - - +
281B LYS* 1.3 75.8 - - - +
283B GLY* 1.3 58.4 + - - +
285B GLY* 3.1 18.7 + - - -
286B LEU 3.5 19.9 - - - +
287B PRO 4.4 0.2 - - - -
288B ILE* 3.9 31.0 - - + +
291B ILE* 4.5 2.7 - - + -
328B ILE* 4.0 31.0 - - + +
329B VAL* 4.2 10.8 - - + -
335B PRO* 3.6 16.0 - - + +
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 4.1 24.1 - - - +
222B GLY 3.6 11.8 - - - +
223B LEU* 3.5 25.0 - - - +
279B GLY 2.9 13.9 + - - -
280B LYS 3.6 4.0 - - - -
282B LEU* 1.3 75.8 - - - +
284B LYS* 1.3 60.1 + - - +
285B GLY* 3.5 0.9 + - - -
335B PRO* 4.5 2.8 - - - +
336B ARG* 4.7 5.5 + - - -
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ASN 5.1 2.0 - - - -
222B GLY* 3.6 25.8 - - - +
280B LYS* 2.9 44.3 + - + +
281B LYS* 3.7 8.3 - - - +
282B LEU 3.2 0.2 - - - -
283B GLY* 1.3 75.0 - - - +
285B GLY* 1.3 57.7 + - - +
286B LEU* 3.7 12.2 - - + +
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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