Contacts of the helix formed by residues 220 - 230 (chain B) in PDB entry 1NUS
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 PRO 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE 4.3 7.0 - - - +
20B ASN* 3.4 10.5 - - - +
23B LEU* 3.7 28.3 - - + -
70B LEU 5.5 0.2 - - - +
71B ALA* 3.9 21.3 - - + +
219B ILE* 1.3 91.8 - - + +
221B ASP* 1.3 66.9 + - - +
222B ALA* 4.4 3.4 - - + +
223B VAL* 3.0 33.6 + - + +
224B ILE* 3.1 11.8 + - - +
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LYS* 2.6 41.9 + - - +
217B TYR* 5.1 6.0 + - - -
219B ILE 3.6 2.5 + - - +
220B PRO* 1.3 70.5 - - - +
222B ALA* 1.3 58.0 + - - +
224B ILE* 3.2 11.3 + - - +
225B THR* 3.0 30.5 + - - +
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Residues in contact with ALA 222 (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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70B LEU* 3.8 38.5 - - + +
73B GLN* 5.2 3.1 - - - +
220B PRO* 3.2 3.8 - - + +
221B ASP* 1.3 80.1 - - - +
223B VAL* 1.3 57.4 + - - +
225B THR* 3.4 8.5 + - - -
226B TYR* 3.0 28.1 + - - +
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 4.4 6.7 - - + -
18B ILE* 4.0 7.4 - - + +
67B MET* 3.4 52.7 - - + +
70B LEU* 4.6 2.0 - - + -
71B ALA* 3.8 13.2 - - + +
219B ILE* 3.9 17.5 - - + -
220B PRO* 3.0 33.2 + - + +
222B ALA* 1.3 75.5 - - - +
224B ILE* 1.3 60.9 + - - +
226B TYR* 3.4 5.4 + - - +
227B ILE* 2.9 36.2 + - + +
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Residues in contact with ILE 224 (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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209B LEU* 5.6 5.4 - - + -
215B VAL* 3.8 15.7 - - + +
216B LYS* 3.4 45.8 - - + +
219B ILE* 3.4 33.7 - - + +
220B PRO 3.1 4.2 + - - +
221B ASP* 3.4 12.6 - - - +
223B VAL* 1.3 78.3 - - - +
225B THR* 1.3 64.0 + - - +
227B ILE* 3.2 9.1 + - + +
228B LYS* 3.0 24.4 + - + +
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Residues in contact with THR 225 (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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221B ASP* 3.0 14.8 + - - +
222B ALA* 3.7 11.1 - - - -
223B VAL 3.3 0.2 - - - -
224B ILE* 1.3 77.2 - - - +
226B TYR* 1.3 57.0 + - - +
228B LYS* 3.2 8.8 + - + +
229B ASP* 2.9 47.8 + - - +
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Residues in contact with TYR 226 (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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62B HIS* 4.3 4.5 + - - -
63B HIS* 2.5 44.7 + - - -
66B ALA* 3.7 22.6 - - + +
67B MET* 3.6 23.6 - - + -
70B LEU* 3.5 25.6 - - + -
222B ALA 3.0 17.9 + - - +
223B VAL* 3.7 6.1 - - - +
225B THR* 1.3 78.2 - - - +
227B ILE* 1.3 62.1 + - - +
229B ASP* 4.5 3.1 - - - -
230B HIS* 2.9 65.1 + + - +
232B LEU* 4.0 10.8 - - + -
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Residues in contact with ILE 227 (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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17B PRO* 4.3 3.4 - - + -
67B MET* 3.7 18.6 - - - -
209B LEU* 3.8 38.1 - - + -
219B ILE* 3.9 20.9 - - + -
223B VAL* 2.9 30.9 + - + +
224B ILE* 3.4 7.4 - - - +
226B TYR* 1.3 80.6 - - - +
228B LYS* 1.3 63.1 + - - +
230B HIS 3.5 0.3 + - - -
231B GLY* 3.1 3.5 + - - -
232B LEU* 2.9 54.7 + - + +
233B TYR* 4.0 14.8 - - + -
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Residues in contact with LYS 228 (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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224B ILE* 3.0 14.8 + - + +
225B THR* 3.5 11.0 - - + +
227B ILE* 1.3 76.6 - - - +
229B ASP* 1.3 72.7 + - - +
231B GLY* 3.0 14.3 + - - -
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Residues in contact with ASP 229 (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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225B THR* 2.9 40.6 + - - +
226B TYR* 3.8 5.4 - - - +
228B LYS* 1.3 79.9 - - - +
230B HIS* 1.3 72.3 + - + +
231B GLY 3.7 0.5 + - - -
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Residues in contact with HIS 230 (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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63B HIS* 3.7 23.5 + + + -
226B TYR* 2.9 69.4 + + + +
229B ASP* 1.3 87.2 + - + +
231B GLY* 1.3 64.5 + - - +
232B LEU* 3.2 18.2 + - + +
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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