Contacts of the helix formed by residues 209 - 229 (chain B) in PDB entry 3K3B
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 GLU 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 5.5 0.5 - - - +
203B THR 3.2 10.2 - - - +
204B VAL* 3.9 3.5 - - + -
205B HIS* 2.8 51.2 + - - +
206B ASN* 2.9 26.8 + - - +
208B ASP* 1.3 79.8 - - - +
210B VAL* 1.3 61.7 + - - +
211B TYR 3.5 2.2 + - - -
212B GLN* 3.5 22.6 - - - +
213B ILE* 3.1 34.6 + - + +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 3.2 37.2 - - + -
137B PRO* 5.6 0.2 - - + -
140B LEU* 4.4 22.0 - - + +
144B PHE* 4.1 11.0 - - + -
204B VAL* 3.6 24.7 - - + -
207B LYS* 3.4 25.1 + - - +
209B GLU* 1.3 77.9 - - - +
211B TYR* 1.3 66.0 + - - +
213B ILE* 3.1 8.7 + - - +
214B LEU* 2.9 40.6 + - + +
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Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ARG* 3.2 30.6 + - - +
127B TRP* 3.3 46.9 - + + +
207B LYS 4.7 1.2 + - - -
208B ASP 5.2 2.0 - - - +
209B GLU 3.5 1.0 - - - +
210B VAL* 1.3 83.0 - - - +
212B GLN* 1.3 64.7 + - + +
214B LEU* 3.2 7.0 + - + +
215B GLU* 3.0 59.6 + - + +
372B L31 3.3 55.1 - + - +
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP 3.9 20.1 + - - +
209B GLU* 3.5 23.8 - - - +
210B VAL 3.4 0.2 - - - -
211B TYR* 1.3 76.8 - - + +
213B ILE* 1.3 58.3 + - - +
215B GLU* 3.2 15.4 + - - +
216B LYS* 2.9 56.8 + - - +
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Residues in contact with ILE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.9 23.1 - - + -
172B LEU* 3.8 22.5 - - + +
202B ILE* 3.7 24.5 - - + -
203B THR 4.6 0.2 - - - +
204B VAL* 3.5 35.0 - - + -
209B GLU* 3.1 29.4 - - + +
210B VAL* 3.1 7.8 + - - +
212B GLN* 1.3 77.2 - - - +
214B LEU* 1.3 65.4 + - + +
216B LYS* 3.6 18.3 + - + +
217B GLY 3.1 17.3 + - - -
239B PHE* 5.7 1.1 - - + -
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.8 8.3 - - + -
137B PRO* 4.3 13.9 - - + -
140B LEU* 4.2 5.2 - - + -
210B VAL* 2.9 32.1 + - + +
211B TYR* 3.2 7.8 + - - +
213B ILE* 1.3 75.3 - - + +
215B GLU* 1.3 60.1 + - - +
217B GLY* 3.4 0.9 + - - -
218B ALA* 3.0 24.9 + - - +
239B PHE* 3.4 39.7 - - + -
372B L31 3.2 68.8 - - + -
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Residues in contact with GLU 215 (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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211B TYR* 3.0 50.3 + - + +
212B GLN* 3.4 14.9 - - - +
214B LEU* 1.3 76.9 - - - +
216B LYS* 1.3 58.8 + - + +
218B ALA* 3.1 9.2 + - - +
219B ALA* 2.9 30.3 + - - +
372B L31 4.5 8.7 - - + +
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Residues in contact with LYS 216 (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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171B LEU 4.0 2.6 - - - +
172B LEU* 5.4 3.4 - - + -
212B GLN* 2.9 49.3 + - - +
213B ILE* 3.9 15.7 - - - +
215B GLU* 1.3 75.5 - - + +
217B GLY* 1.3 63.2 + - - +
219B ALA* 3.4 7.2 + - - +
220B LYS* 3.1 28.0 + - - +
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Residues in contact with GLY 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 3.8 13.9 - - - +
171B LEU* 3.5 11.1 - - - +
172B LEU* 3.5 26.8 - - - +
213B ILE 3.1 10.9 + - - -
214B LEU 3.8 3.4 - - - -
215B GLU 3.2 0.2 - - - -
216B LYS* 1.3 75.8 - - - +
218B ALA* 1.3 60.6 + - - +
220B LYS* 3.4 2.9 + - - +
221B ARG* 3.2 23.0 + - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 5.8 0.4 - - - +
214B LEU 3.0 17.6 + - - +
215B GLU* 3.5 7.6 - - - +
217B GLY* 1.3 73.5 - - - +
219B ALA* 1.3 64.9 + - - +
221B ARG* 3.3 20.7 + - - +
222B THR* 3.1 25.1 + - - -
372B L31 4.3 19.2 - - + +
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Residues in contact with ALA 219 (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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215B GLU 2.9 16.3 + - - +
216B LYS* 3.8 7.2 - - - +
218B ALA* 1.3 75.8 - - - +
220B LYS* 1.3 57.9 + - - +
222B THR* 3.3 10.7 + - - +
223B THR* 2.9 28.7 + - - -
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Residues in contact with LYS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ASP 4.5 4.7 - - - +
171B LEU* 3.5 34.6 - - + +
173B ASN* 3.1 20.5 + - + +
174B PRO* 5.4 0.2 - - - -
175B SER* 2.9 45.8 + - - +
176B SER 4.5 0.6 - - - +
178B VAL* 3.5 28.9 - - + +
216B LYS* 3.1 18.0 + - - +
217B GLY 3.9 0.9 - - - +
218B ALA 3.2 0.2 - - - -
219B ALA* 1.3 74.3 - - - +
221B ARG* 1.3 60.2 + - - +
223B THR* 3.5 7.8 - - - +
224B ALA* 3.0 26.0 + - - +
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Residues in contact with ARG 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 2.6 36.8 + - - -
160B LEU* 4.4 7.5 - - - +
162B GLU* 3.3 26.2 - - - +
171B LEU* 3.8 20.2 - - + +
217B GLY 3.2 13.0 + - - +
218B ALA* 3.7 20.9 + - - +
219B ALA 3.3 0.2 - - - -
220B LYS* 1.3 74.6 - - - +
222B THR* 1.3 65.8 + - - +
224B ALA* 3.4 3.9 + - - +
225B ALA* 3.1 22.9 + - - +
230B ALA 4.6 1.2 - - - +
232B SER* 4.1 22.0 - - - -
237B SER* 2.9 35.2 + - - -
265B ASP* 5.5 1.0 + - - -
372B L31 3.9 16.3 - - - +
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Residues in contact with THR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 5.5 0.2 - - - -
218B ALA 3.1 15.2 + - - -
219B ALA* 3.3 13.5 - - - +
221B ARG* 1.3 75.1 - - - +
223B THR* 1.3 64.9 + - - +
225B ALA* 3.4 7.7 + - - +
226B THR* 3.2 26.0 + - - +
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B VAL* 3.5 31.0 - - + -
219B ALA 2.9 17.7 + - - -
220B LYS* 3.5 13.2 - - - -
221B ARG 3.3 0.2 - - - -
222B THR* 1.3 76.6 - - - +
224B ALA* 1.3 53.1 + - - +
226B THR* 3.1 7.2 + - - -
227B LEU* 2.8 50.2 + - + +
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Residues in contact with ALA 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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162B GLU* 4.0 16.8 - - - +
169B PHE* 5.7 3.8 - - + -
171B LEU* 4.6 5.4 - - + -
178B VAL* 3.9 26.7 - - + +
220B LYS 3.0 18.1 + - - +
221B ARG* 3.7 6.3 - - - +
222B THR 3.3 0.4 - - - -
223B THR* 1.3 73.5 - - - +
225B ALA* 1.3 61.3 + - - +
227B LEU 4.5 0.2 - - - +
228B MET* 2.9 35.2 + - + +
230B ALA* 3.4 10.0 + - + -
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Residues in contact with ALA 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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36A SER* 6.4 1.3 - - - -
38A HIS* 3.7 23.6 - - + +
221B ARG 3.1 12.7 + - - +
222B THR* 3.5 11.4 - - - +
224B ALA* 1.3 75.4 - - - +
226B THR* 1.3 58.8 - - - +
229B ASN* 3.0 27.7 + - - +
230B ALA 3.3 24.1 + - - +
231B TYR* 3.6 12.7 - - + -
232B SER* 4.7 5.2 - - - +
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Residues in contact with THR 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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38A HIS* 4.3 15.2 + - - -
53A ARG* 5.8 0.5 + - - -
222B THR* 3.2 15.2 + - - +
223B THR* 3.1 10.5 + - - -
225B ALA* 1.3 81.1 - - - +
227B LEU* 1.3 78.0 + - + +
229B ASN* 4.1 8.1 - - - +
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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
----------------------------------------------------------
59A ASP* 5.9 2.9 - - - +
178B VAL* 4.4 9.9 - - + -
179B SER* 6.2 1.1 - - - -
223B THR* 2.8 40.9 + - + +
226B THR* 1.3 93.4 - - + +
228B MET* 1.3 66.7 + - + +
229B ASN* 3.6 1.4 - - - -
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Residues in contact with MET 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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57A LEU* 3.4 34.8 - - + +
169B PHE* 3.1 37.0 - - + -
178B VAL* 3.0 33.0 - - + +
179B SER* 3.1 30.3 - - - +
181B ARG* 5.0 3.8 - - - -
224B ALA* 2.9 16.2 + - - +
227B LEU* 1.3 85.4 - - + +
229B ASN* 1.3 72.7 + - - +
230B ALA* 3.1 7.9 + - + +
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Residues in contact with ASN 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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53A ARG* 3.6 8.2 + - - -
55A GLY* 3.0 32.3 - - - +
56A GLY 3.6 0.6 - - - +
57A LEU 3.6 12.7 - - - +
58A ALA 3.4 6.7 + - - +
59A ASP* 2.4 33.0 + - - +
164B TYR* 3.0 19.0 + - - -
225B ALA 3.0 17.7 + - - +
226B THR 4.1 7.4 - - - +
227B LEU 5.6 1.1 - - - -
228B MET* 1.3 80.2 - - - +
230B ALA* 1.3 58.1 - - - +
231B TYR* 3.0 33.2 + - + -
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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
------------------------------------------------------------
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