Contacts of the helix formed by residues 228 - 241 (chain B) in PDB entry 3K5N
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 PHE 228 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B ASP* 5.5 0.2 - - - -
157B ILE* 3.7 24.0 - - + -
159B THR* 3.5 28.9 - - + -
223B TRP 5.8 0.9 - - - -
224B ASN* 3.3 26.3 + - + +
227B GLN* 1.3 78.5 - - - +
229B ASP* 1.3 100.4 + - - +
230B LEU 3.0 0.7 - - - -
231B ARG* 4.6 1.6 - - - +
232B MET* 2.8 53.4 + - + +
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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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155B ILE* 3.5 25.4 - - + +
156B ASP* 4.0 10.7 - - - +
157B ILE* 3.6 26.8 + - + +
223B TRP 3.9 11.8 + - - +
224B ASN 3.5 1.7 + - - -
225B VAL* 3.5 27.9 + - + +
228B PHE* 1.3 108.4 - - - +
230B LEU* 1.3 56.7 + - + +
232B MET* 3.8 0.2 - - - +
233B LEU* 2.0 38.2 + - + +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 5.2 9.4 - - + -
220B ILE* 5.1 10.5 - - + -
225B VAL* 2.3 46.7 + - + +
226B VAL* 3.3 21.5 - - + +
229B ASP* 1.3 73.2 - - - +
231B ARG* 1.3 61.9 + - - +
233B LEU* 3.6 13.8 + - + +
234B GLN* 3.7 6.2 + - - +
244B LEU* 5.1 1.1 - - + +
246B LEU* 4.4 22.9 - - + -
253B LEU* 4.3 19.4 - - + +
255B TRP* 3.5 12.0 - - + -
267B ALA* 4.6 4.7 - - + -
274B ILE* 3.9 37.7 - - + -
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Residues in contact with ARG 231 (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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226B VAL 3.0 9.1 + - - +
227B GLN* 2.5 58.5 + - - +
228B PHE* 3.1 4.4 + - - +
230B LEU* 1.3 73.3 - - - +
232B MET* 1.3 98.7 + - - +
234B GLN* 3.3 6.8 + - - +
235B LYS* 3.2 32.7 + - - +
255B TRP* 3.7 13.5 - - + -
265B PHE* 2.2 55.9 - - + -
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Residues in contact with MET 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 3.9 13.5 - - + -
159B THR* 5.1 0.9 - - - -
163B GLY* 4.3 28.5 - - - +
228B PHE* 2.8 49.1 + - + +
229B ASP 3.8 2.5 - - - +
231B ARG* 1.3 110.3 - - - +
233B LEU* 1.3 57.1 + - - +
235B LYS* 3.2 35.2 + - + +
236B HIS* 2.5 35.3 - - + +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 4.4 14.8 - - + -
157B ILE* 4.0 22.0 - - + -
165B LEU* 5.2 10.1 - - + -
168B ILE* 5.0 3.1 - - + -
205B LEU* 4.6 7.3 - - + +
208B LEU* 3.5 31.2 - - + -
229B ASP* 2.0 44.0 - - + +
230B LEU* 3.7 9.9 - - + +
231B ARG 3.3 0.2 - - - -
232B MET* 1.3 74.9 - - - +
234B GLN* 1.3 51.4 + - - +
236B HIS* 2.9 13.5 + - - +
237B ALA* 2.7 31.5 + - - +
244B LEU* 4.3 17.2 - - + +
246B LEU* 5.3 4.9 - - + -
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Residues in contact with GLN 234 (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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230B LEU 3.7 5.8 + - - +
231B ARG 3.3 10.5 + - - +
232B MET 3.1 0.6 - - - -
233B LEU* 1.3 74.8 - - - +
235B LYS* 1.3 68.6 + - - +
236B HIS 2.9 1.3 - - - -
237B ALA* 2.9 17.9 + - - +
238B GLU* 2.8 48.1 + - - +
244B LEU* 4.2 10.3 - - + +
253B LEU* 4.2 9.5 + - - +
255B TRP* 2.2 52.2 + - + +
265B PHE* 5.1 7.6 - - + -
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Residues in contact with LYS 235 (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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231B ARG* 3.2 22.4 + - - +
232B MET* 3.2 37.9 + - + +
234B GLN* 1.3 82.0 - - - +
236B HIS* 1.3 65.4 + - + +
238B GLU* 3.1 12.3 + - - +
239B ARG* 3.0 43.9 + - - +
265B PHE* 6.2 1.8 - - + -
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Residues in contact with HIS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 6.2 0.2 - - - +
163B GLY 3.0 24.3 + - - -
164B GLU* 4.1 1.3 - - + -
165B LEU* 3.3 45.5 - - + +
205B LEU* 4.1 9.2 - - + -
232B MET* 2.5 39.0 + - - +
233B LEU* 2.9 8.7 + - - +
235B LYS* 1.3 79.0 - - + +
237B ALA* 1.3 67.1 + - - +
239B ARG* 2.9 38.7 + - - +
240B TYR* 3.1 47.0 + - + -
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Residues in contact with ALA 237 (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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205B LEU* 3.8 12.3 - - + +
233B LEU 2.7 16.2 + - - +
234B GLN* 2.9 19.9 + - + +
236B HIS* 1.3 71.9 - - - +
238B GLU* 1.3 58.9 + - + +
241B ARG* 3.0 7.1 + - - -
242B LEU 2.8 44.4 + - - +
243B PRO* 5.1 0.2 - - + -
244B LEU* 4.0 23.3 - - + +
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Residues in contact with GLU 238 (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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234B GLN* 2.8 45.4 + - + +
235B LYS* 3.4 9.6 - - - +
237B ALA* 1.3 75.9 - - + +
239B ARG* 1.3 66.2 + - - +
241B ARG* 3.3 18.7 + - - +
265B PHE* 5.6 3.6 - - - -
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Residues in contact with ARG 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS 5.9 0.2 + - - -
163B GLY 4.5 4.9 + - - -
164B GLU* 4.9 9.7 + - - +
235B LYS* 3.0 43.8 + - - +
236B HIS* 2.9 45.9 + - - +
238B GLU* 1.3 80.1 - - - +
240B TYR* 1.3 80.7 + - + +
241B ARG* 3.9 6.1 - - - +
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Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLU* 5.6 1.2 - - - +
201B ARG* 3.2 34.6 + - + +
202B PRO* 3.6 40.2 - - + -
205B LEU* 4.3 4.9 - - + -
236B HIS* 3.1 49.3 + - + +
239B ARG* 1.3 95.6 + - + +
241B ARG* 1.3 74.9 + - - +
242B LEU* 3.2 24.6 + - + +
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Residues in contact with ARG 241 (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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237B ALA 3.0 9.0 + - - -
238B GLU* 3.3 15.6 + - - +
239B ARG 3.9 6.1 - - - +
240B TYR* 1.3 83.2 - - - +
242B LEU* 1.3 59.1 + - - +
243B PRO* 3.9 6.0 - - - +
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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