Contacts of the helix formed by residues 216 - 230 (chain B) in PDB entry 2OKC
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 THR 216 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 4.1 16.6 + - - +
214B ASP* 3.2 8.7 + - - -
215B ASN* 1.3 92.1 + - - +
217B PRO* 1.3 72.1 - - + +
218B LEU* 4.2 14.6 - - + -
219B VAL* 2.9 31.8 + - + +
220B VAL* 3.2 10.7 + - - +
241B CYS* 4.3 2.2 - - - -
500B SAM 3.2 10.6 + - - -
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Residues in contact with PRO 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 5.8 0.7 - - - +
98B THR* 3.6 31.3 - - + +
99B LYS* 4.0 24.7 - - + +
215B ASN 3.6 9.4 - - - +
216B THR* 1.3 86.9 - - + +
218B LEU* 1.3 62.1 + - - +
219B VAL 3.1 0.7 + - - -
220B VAL* 3.2 5.5 + - + +
221B THR* 3.2 22.4 + - - -
241B CYS* 4.0 13.7 - - - -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 3.5 35.0 - - + -
31B ASP* 4.3 13.7 - - - +
34B THR* 3.6 27.0 + - + +
38B TYR* 5.2 2.9 + - - +
103B LYS* 6.5 0.4 - - - -
152B TYR* 4.7 7.9 - - + +
216B THR* 3.2 12.0 + - + +
217B PRO* 1.3 78.7 - - - +
219B VAL* 1.3 79.1 + - + +
221B THR* 3.4 10.9 - - - -
222B LEU* 3.1 38.4 + - + +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.4 39.0 - - + -
180B GLY* 3.4 27.8 - - - +
181B THR* 6.0 0.7 - - + -
214B ASP* 3.4 26.2 - - + +
216B THR* 2.9 17.8 + - + +
218B LEU* 1.3 95.8 - - + +
220B VAL* 1.3 58.4 + - - +
222B LEU* 3.4 7.8 + - + +
223B ALA* 3.0 28.8 + - - +
500B SAM 3.8 1.6 - - - +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR* 3.8 18.2 - - + +
98B THR* 3.7 21.8 - - - +
214B ASP* 3.6 31.9 - - + +
216B THR 3.2 8.0 + - - +
217B PRO 3.2 8.7 + - - +
219B VAL* 1.3 74.7 - - - +
221B THR* 1.3 52.1 + - - +
223B ALA* 4.0 0.4 - - - +
224B SER* 2.8 36.9 + - - -
239B ILE* 3.8 16.9 - - + +
240B VAL* 3.9 6.3 - - - +
241B CYS* 3.7 24.0 - - + +
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Residues in contact with THR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 4.5 5.8 - - + -
37B THR* 3.7 25.5 - - + +
38B TYR* 3.7 25.3 + - + -
95B THR 4.1 2.9 + - - -
96B ILE* 2.6 31.0 + - + +
98B THR 4.3 5.2 + - - -
217B PRO 3.2 12.6 + - - -
218B LEU* 3.4 14.9 - - - +
220B VAL* 1.3 76.0 - - - +
222B LEU* 1.3 63.0 + - + +
224B SER* 3.1 6.4 + - - -
225B MSE 3.0 26.3 + - - +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 5.2 5.2 - - + -
33B ILE* 3.5 31.2 - - + +
34B THR* 4.1 14.1 - - - +
37B THR* 3.7 8.5 - - - +
134B TYR* 3.4 25.4 - - + +
138B LEU* 4.0 24.2 - - + -
141B ASN* 6.0 1.1 - - - +
152B TYR* 6.4 3.1 - - + -
181B THR* 4.8 11.7 - - + -
218B LEU* 3.1 31.9 + - + +
219B VAL* 3.4 8.7 + - + +
221B THR* 1.3 78.0 - - + +
223B ALA* 1.3 56.4 + - - +
226B ASN* 2.9 30.9 + - - +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B CYS* 4.6 0.9 - - - -
180B GLY 3.3 24.8 + - - +
181B THR* 3.6 17.2 - - - +
182B GLY* 4.2 2.9 - - - +
219B VAL 3.0 11.9 + - - +
220B VAL 4.0 2.5 - - - +
222B LEU* 1.3 73.6 - - - +
224B SER* 1.3 67.2 + - - +
226B ASN* 3.2 2.3 + - - +
227B LEU* 3.0 28.6 + - - +
239B ILE* 4.1 26.7 - - + -
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Residues in contact with SER 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.7 3.3 - - - +
95B THR* 3.5 14.8 - - - +
96B ILE* 3.4 24.0 + - - +
220B VAL 2.8 24.5 + - - -
221B THR* 3.1 11.8 + - - -
223B ALA* 1.3 74.7 - - - +
225B MSE 1.3 55.2 + - - +
227B LEU* 3.6 3.2 + - - +
228B TYR* 3.0 28.8 + - - +
232B ILE 5.0 0.3 - - - +
233B GLY 5.3 0.5 - - - +
237B SER* 3.4 29.4 + - - -
239B ILE* 4.1 4.8 - - - +
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Residues in contact with MSE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 3.5 30.1 - - + +
40B LEU* 3.7 37.7 - - + -
41B PHE* 3.9 22.4 - - + +
44B MSE 4.4 7.6 - - - -
96B ILE* 3.7 6.9 - - + +
134B TYR* 3.4 31.6 - - + +
221B THR 3.0 19.6 + - - +
224B SER* 1.3 75.6 + - - +
226B ASN* 1.3 60.1 + - - +
228B TYR* 3.3 16.7 + - - +
229B LEU* 2.9 49.5 + - + +
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 3.7 18.3 - - + -
135B GLU* 2.9 27.3 + - - +
138B LEU* 4.0 11.2 - - + +
156B ARG* 4.2 1.8 - - - +
181B THR 3.0 22.2 + - - +
182B GLY 4.9 1.0 - - - -
186B LEU* 4.1 9.8 - - - +
222B LEU 2.9 22.9 + - - +
223B ALA 3.5 5.4 - - - +
225B MSE 1.3 72.7 - - - +
227B LEU* 1.3 63.9 + - - +
229B LEU* 3.6 1.1 + - - +
230B HIS* 2.5 59.0 + - - -
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY* 3.8 28.3 - - - +
185B LEU* 4.5 10.5 - - + -
186B LEU* 4.1 18.8 - - + +
210B LEU* 5.1 0.2 - - + -
223B ALA 3.0 15.5 + - - +
224B SER* 3.9 4.0 - - - +
226B ASN* 1.3 79.4 - - + +
228B TYR* 1.3 65.3 + - - +
230B HIS* 2.9 15.5 + - - -
231B GLY 3.0 0.7 + - - -
232B ILE* 3.0 47.0 + - + +
238B PRO* 3.5 34.5 - - + -
239B ILE* 3.9 21.8 - - + -
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Residues in contact with TYR 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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41B PHE* 3.8 24.0 - + - -
44B MSE 3.9 29.5 - - + +
92B LEU* 3.3 31.6 - - + -
96B ILE* 5.4 0.4 - - + -
123B LEU* 5.6 1.6 - - - +
224B SER 3.0 19.3 + - - +
225B MSE 3.3 23.8 + - - +
227B LEU* 1.3 74.3 - - - +
229B LEU* 1.3 62.3 + - + +
231B GLY* 3.0 19.6 + - - -
232B ILE 3.3 10.9 + - - +
233B GLY 4.6 1.6 - - - +
234B THR* 4.0 30.4 + - + -
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.5 4.7 - - + -
44B MSE 4.2 26.5 - - + -
127B GLY* 3.8 18.9 - - - +
130B LYS* 4.0 23.9 - - + +
131B GLY* 4.1 13.9 + - - +
134B TYR* 3.7 40.6 - - + -
225B MSE 2.9 45.6 + - + +
226B ASN 4.0 3.6 - - - +
228B TYR* 1.3 81.1 - - + +
230B HIS* 1.3 58.8 + - - +
231B GLY 3.3 1.3 - - - -
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Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLY* 3.2 39.8 + - - -
132B ALA* 5.1 0.4 - - - -
134B TYR* 5.4 0.4 - - + -
135B GLU* 3.6 15.1 - - + +
186B LEU* 3.5 36.6 - - + +
189B TYR* 5.7 1.0 - - - -
190B ASP* 5.3 5.4 - - - +
193B LYS* 5.4 4.3 + - - -
226B ASN* 2.5 48.8 + - - +
227B LEU 2.9 6.9 + - - +
229B LEU* 1.3 77.1 - - + +
231B GLY* 1.3 61.1 + - - +
232B ILE* 3.6 6.4 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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