Contacts of the helix formed by residues 222 - 233 (chain X) in PDB entry 3N5N
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 222 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204X TYR* 3.5 35.4 + - + -
220X VAL 4.2 0.2 - - - -
221X VAL* 1.3 75.2 - - - +
223X GLY* 1.3 66.9 + - - +
224X ASN* 2.8 30.7 + - - +
225X VAL* 2.9 20.7 + - - +
226X ALA* 3.0 21.8 + - - +
269X MET* 4.2 8.7 - - - +
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Residues in contact with GLY 223 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222X ASP* 1.3 76.5 - - - +
224X ASN* 1.3 56.3 + - - +
226X ALA* 3.3 6.7 + - - +
227X ARG* 3.0 36.6 + - - +
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Residues in contact with ASN 224 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222X ASP* 2.8 19.5 + - - +
223X GLY* 1.3 73.2 - - - +
225X VAL* 1.3 64.8 + - - +
227X ARG* 2.3 38.9 + - - +
228X VAL* 3.1 26.2 + - - +
268X ALA 4.7 0.2 - - - -
269X MET* 3.6 24.1 + - - +
272X GLY* 3.4 15.6 - - - +
273X ALA* 3.7 12.8 + - - +
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Residues in contact with VAL 225 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220X VAL* 3.6 28.0 - - + +
221X VAL* 4.1 6.7 - - + -
222X ASP* 2.9 24.7 + - - +
224X ASN* 1.3 73.4 - - - +
226X ALA* 1.3 57.1 + - - +
228X VAL* 3.2 7.0 + - + +
229X LEU* 2.8 52.0 + - + +
252X ALA* 5.0 2.7 - - + -
265X ASN* 4.7 2.7 - - - +
268X ALA* 3.6 30.7 - - + -
269X MET* 3.7 15.0 - - + +
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Residues in contact with ALA 226 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X VAL* 3.9 15.2 - - + +
222X ASP 3.0 17.4 + - - +
223X GLY* 3.5 8.1 - - - +
225X VAL* 1.3 74.9 - - - +
227X ARG* 1.3 65.7 + - - +
229X LEU* 4.2 2.6 - - - +
230X CYS* 2.9 32.4 + - - +
239X PRO* 5.9 4.3 - - + -
248X LEU* 4.0 18.2 - - + -
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Residues in contact with ARG 227 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223X GLY 3.0 18.9 + - - +
224X ASN* 2.3 37.8 + - - +
226X ALA* 1.3 79.2 - - - +
228X VAL* 1.3 62.0 + - - +
230X CYS* 3.7 4.6 - - - +
231X ARG* 3.2 54.1 + - - +
272X GLY 2.9 16.2 + - - -
273X ALA* 4.8 0.2 - - - +
276X CYS 2.7 22.1 + - - +
278X PRO* 3.6 39.3 - - - +
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Residues in contact with VAL 228 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X PHE* 4.8 11.2 - - + -
224X ASN 3.1 14.9 + - - +
225X VAL* 3.2 8.7 + - + +
227X ARG* 1.3 76.1 - - - +
229X LEU* 1.3 62.8 + - + +
231X ARG* 3.1 3.6 + - - +
232X VAL* 2.8 43.6 + - + +
268X ALA* 4.1 11.9 - - + +
271X LEU* 3.9 29.4 - - + -
272X GLY* 3.8 21.5 - - - +
276X CYS* 3.9 15.5 - - + +
400X SF4 4.5 2.2 - - - -
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Residues in contact with LEU 229 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73X PHE* 5.1 3.8 - - + -
82X PHE* 5.1 7.0 - - + -
221X VAL* 4.6 0.4 - - + -
225X VAL* 2.8 41.6 + - + +
226X ALA* 4.2 0.4 - - - +
228X VAL* 1.3 76.2 - - + +
230X CYS* 1.3 62.6 + - - +
232X VAL* 4.0 7.1 - - + +
233X ARG* 3.0 28.8 + - + +
235X ILE* 4.4 1.4 - - - +
248X LEU* 3.6 46.4 - - + +
251X LEU* 4.0 18.6 - - + -
252X ALA* 4.1 7.9 - - + +
255X LEU* 3.6 31.0 - - + -
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Residues in contact with CYS 230 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X ALA* 2.9 25.5 + - - +
227X ARG* 3.7 5.4 - - - +
229X LEU* 1.3 77.1 - - - +
231X ARG* 1.3 60.2 + - + +
234X ALA* 3.0 6.8 + - - -
235X ILE* 2.7 56.1 + - - +
237X ALA 5.7 1.3 - - - -
239X PRO* 4.9 14.6 - - - -
244X VAL* 5.0 1.6 - - - -
248X LEU* 4.1 23.8 - - - -
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Residues in contact with ARG 231 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227X ARG* 3.2 26.6 + - - +
228X VAL 3.1 6.5 + - - +
230X CYS* 1.3 80.7 - - + +
232X VAL* 1.3 65.1 + - - +
233X ARG 3.2 0.2 - - - -
234X ALA 3.1 6.4 + - - -
276X CYS* 3.4 31.5 - - - -
277X THR 2.9 21.0 + - - -
278X PRO 3.2 25.1 + - - -
281X PRO* 4.0 17.2 - - - +
292X CYS* 3.9 3.1 - - - -
294X ALA* 3.0 36.4 + - + +
400X SF4 3.7 25.1 - - - -
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Residues in contact with VAL 232 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X PHE* 3.6 33.4 - - + -
82X PHE* 4.0 11.7 - - + -
228X VAL* 2.8 31.3 + - + +
229X LEU* 3.4 8.5 + - + +
231X ARG* 1.3 72.8 - - - +
233X ARG* 1.3 72.0 + - + +
288X VAL* 3.9 16.2 - - + -
291X LEU 3.9 9.6 - - - +
292X CYS* 3.8 9.6 - - + -
293X ARG* 3.0 19.7 + - - +
400X SF4 3.8 22.2 - - - -
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Residues in contact with ARG 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X TYR 4.1 1.0 - - - +
71X HIS* 3.0 54.4 - - - +
72X LEU 3.0 20.6 + - - -
73X PHE* 3.7 27.1 - - + -
78X GLU* 3.4 28.1 + - - -
229X LEU* 3.0 14.2 + - - +
232X VAL* 1.3 96.6 + - + +
234X ALA* 1.3 73.4 + - - +
235X ILE* 3.3 9.0 + - + +
251X LEU* 3.8 17.7 - - + -
291X LEU 2.7 30.1 + - - -
293X ARG* 3.7 35.5 - - - +
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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
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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