Contacts of the helix formed by residues 224 - 240 (chain B) in PDB entry 3SKU
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 ILE 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 5.5 0.4 - - + -
29B THR* 3.8 8.3 - - - +
30B ASP* 3.2 37.7 - - - +
36B ARG* 3.1 40.4 - - + +
132B GLN* 5.5 2.0 - - + -
133B PRO* 4.0 5.8 - - + -
222B ARG 3.8 1.1 + - - +
223B PHE* 1.3 76.5 - - - +
225B PRO* 1.3 81.1 - - + +
226B GLU* 3.1 6.8 + - + +
227B ASN* 3.0 39.8 + - - +
228B GLN* 3.4 4.5 + - - +
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Residues in contact with PRO 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ARG* 3.7 14.1 - - - +
113B MET* 4.5 14.8 - - - -
115B TYR* 5.6 1.6 - - - +
133B PRO* 4.1 9.6 - - + -
143B ALA* 4.9 1.0 - - - +
144B VAL* 3.9 12.8 - - + -
148B ASN* 3.6 28.9 - - - +
223B PHE 3.8 0.8 - - - +
224B ILE* 1.3 90.9 - - + +
226B GLU* 1.3 62.4 + - - +
228B GLN* 3.2 20.3 - - + +
229B ARG* 3.3 22.5 + - - +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.6 31.8 - - + +
146B GLU* 3.0 24.8 - - - +
224B ILE* 3.1 7.9 + - + +
225B PRO* 1.3 77.0 - - - +
227B ASN* 1.3 64.7 + - - +
229B ARG* 2.6 55.0 + - - +
230B THR* 3.4 11.3 + - - -
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Residues in contact with ASN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 2.8 45.2 + - + +
223B PHE* 3.7 29.2 - - + -
224B ILE* 3.0 36.2 + - - +
226B GLU* 1.3 73.5 - - - +
228B GLN* 1.3 65.1 + - - +
230B THR* 3.0 19.6 + - - -
231B VAL* 3.1 18.2 + - + +
129F PHE* 5.0 12.7 - - + +
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 3.4 31.9 - - - +
139B ASP* 3.5 31.0 + - - +
142B SER 3.6 10.7 + - - +
143B ALA* 3.2 22.2 - - + -
144B VAL* 6.2 0.2 - - + -
222B ARG* 4.4 3.5 - - - +
223B PHE* 3.7 34.4 + - + +
224B ILE 3.4 9.1 + - - +
225B PRO* 3.2 14.5 + - + +
227B ASN* 1.3 76.5 - - - +
229B ARG* 1.3 54.5 + - - +
230B THR 2.9 0.7 + - - -
231B VAL* 3.1 5.0 + - - +
232B ALA* 2.7 37.3 + - - +
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 4.1 14.6 - - + -
144B VAL* 3.5 32.9 + - - +
145B SER* 2.8 33.9 + - - +
146B GLU* 3.6 20.5 + - - +
148B ASN* 4.4 1.6 - - - +
152B LEU* 5.6 8.7 - - + -
154B HIS* 4.5 2.5 + - - -
225B PRO* 3.3 13.3 + - - +
226B GLU* 2.6 64.1 + - - +
227B ASN 3.2 0.4 - - - -
228B GLN* 1.3 78.2 - - - +
230B THR* 1.3 56.5 + - - +
232B ALA* 4.3 3.4 - - - +
233B VAL* 3.0 27.0 + - - +
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Residues in contact with THR 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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28B LEU* 5.0 6.6 - - - +
226B GLU* 3.4 11.3 + - - -
227B ASN* 3.0 13.5 + - - -
228B GLN 2.9 0.6 + - - -
229B ARG* 1.3 74.9 - - - +
231B VAL* 1.3 58.9 + - + -
232B ALA 3.1 1.1 - - - -
233B VAL* 2.7 36.9 + - + +
234B TYR* 2.8 17.2 + - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER 5.1 2.6 - - - +
223B PHE* 4.8 15.0 - - + -
227B ASN* 3.1 15.6 + - + +
228B GLN* 4.2 4.5 - - - +
230B THR* 1.3 76.8 - - - +
232B ALA* 1.3 57.9 + - - +
233B VAL 3.1 4.5 + - - -
234B TYR* 3.2 13.0 + - + -
235B SER* 3.8 9.7 + - - -
236B LEU 5.2 0.3 + - - -
128F THR 4.3 7.6 - - - +
129F PHE 3.4 16.6 - - - +
130F PRO 2.5 37.2 - - - +
131F THR* 3.9 18.8 + - - +
133F ASN* 5.9 6.1 - - + +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP 5.1 4.5 - - - +
140B SER 4.5 7.0 - - - +
141B PHE* 3.8 16.9 - - - +
142B SER 3.0 41.3 - - - +
143B ALA* 4.7 0.2 - - + -
154B HIS* 3.4 17.4 - - + +
228B GLN* 2.7 23.9 + - + +
229B ARG* 4.3 6.1 - - - +
231B VAL* 1.3 70.7 - - - +
233B VAL* 1.3 57.7 + - + +
236B LEU* 4.5 6.5 - - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B HIS* 3.1 31.6 - - + +
229B ARG 3.0 19.5 - - - +
230B THR* 2.7 32.9 + - + +
232B ALA* 1.3 74.2 - - - +
234B TYR* 1.3 61.2 + - + +
235B SER 3.7 1.1 - - - -
236B LEU* 3.4 10.2 - - - +
237B LYS* 2.8 50.3 + - + +
241B TRP* 4.8 7.2 - - + -
244B PRO* 4.9 15.5 - - + -
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Residues in contact with TYR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 2.8 20.4 + - + +
231B VAL* 3.2 10.3 + - - -
233B VAL* 1.3 77.8 - - + +
235B SER* 1.3 57.9 + - - +
236B LEU 3.0 4.5 - - - -
237B LYS* 3.0 25.3 + - + +
238B ILE* 3.1 38.1 + - + +
130F PRO* 3.7 29.0 - - + +
131F THR* 3.5 31.2 - - + -
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Residues in contact with SER 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B VAL* 3.8 7.4 + - - -
234B TYR* 1.3 73.2 - - - +
236B LEU* 1.3 58.6 + - - +
238B ILE* 3.1 30.4 - - - +
239B ALA* 3.7 8.5 + - - +
131F THR* 2.6 41.8 + - - +
132F GLY* 5.1 1.2 - - - -
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER 5.7 0.9 - - - +
141B PHE* 4.6 6.1 - - + -
154B HIS* 4.3 23.8 - - + -
155B ALA* 4.4 15.3 - - + +
191B TYR* 3.4 27.8 - - + +
192B ALA* 5.4 0.4 - - - -
193B LEU* 3.4 38.7 - - + +
231B VAL 5.2 0.4 + - - -
232B ALA 4.5 8.7 - - - +
233B VAL* 3.4 12.5 - - - +
234B TYR 3.0 0.2 - - - -
235B SER* 1.3 76.8 - - - +
237B LYS* 1.3 68.3 + - - +
239B ALA* 3.1 16.6 + - + +
240B GLY 3.3 7.3 + - - -
241B TRP* 3.4 28.7 + - + +
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Residues in contact with LYS 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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233B VAL* 2.8 41.4 + - + +
234B TYR* 3.0 15.0 + - + +
236B LEU* 1.3 72.4 - - - +
238B ILE* 1.3 55.5 + - + +
240B GLY* 2.7 30.0 + - - -
241B TRP* 3.3 22.1 + - + +
243B GLY 2.6 33.9 + - - +
244B PRO* 3.3 13.7 - - - +
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Residues in contact with ILE 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 TYR* 3.1 34.9 + - + +
235B SER* 3.1 43.3 - - - +
237B LYS* 1.3 76.9 - - + +
239B ALA* 1.3 62.0 + - + +
240B GLY* 3.4 0.9 + - - -
131F THR* 4.4 11.9 - - + -
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Residues in contact with ALA 239 (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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191B TYR* 3.5 24.6 + - + -
193B LEU* 6.4 1.1 - - + -
235B SER 3.9 10.1 - - - +
236B LEU* 3.1 15.2 + - + +
237B LYS 3.1 0.8 - - - -
238B ILE* 1.3 82.0 - - + +
240B GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 240 (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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191B TYR* 3.2 28.8 + - - -
236B LEU 3.3 1.8 + - - -
237B LYS 2.7 16.5 + - - -
238B ILE 3.2 1.8 - - - -
239B ALA* 1.3 74.5 - - - +
241B TRP* 1.3 64.2 + - - +
242B HIS* 3.8 6.8 + - - -
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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