Contacts of the helix formed by residues 213 - 227 (chain K) in PDB entry 6T9L
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 GLN 213 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138K GLY 2.4 31.7 + - - -
139K LEU* 3.4 16.7 - - - +
140K ILE* 3.3 46.4 + - + +
142K MET* 4.7 6.3 - - + +
193K GLU* 2.9 1.1 + - - -
209K SER 5.1 0.7 - - - +
210K THR* 5.3 2.9 - - - -
211K ASN 3.1 21.0 + - - +
212K ARG* 1.3 84.1 + - - +
214K THR* 1.3 66.8 + - + +
215K GLY 3.4 1.8 - - - -
216K PHE* 3.5 21.7 + - - +
217K ILE* 3.3 21.0 + - + +
71M ILE* 5.4 7.6 - - + -
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Residues in contact with THR 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LYS* 5.2 2.9 - - - +
193K GLU* 2.6 29.3 + - - +
198K LEU* 3.3 18.6 - - + +
210K THR 5.4 8.3 - - - +
211K ASN* 6.0 0.4 - - - -
212K ARG 5.5 1.3 - - - +
213K GLN* 1.3 72.9 - - + +
215K GLY* 1.3 64.7 + - - -
217K ILE* 3.1 26.4 + - + +
218K TYR* 3.2 25.3 - - - -
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Residues in contact with GLY 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K ALA 4.5 2.4 - - - +
189K LYS* 4.0 24.2 - - - -
190K ILE* 3.6 23.1 - - - +
193K GLU* 2.7 22.6 + - - -
214K THR* 1.3 74.9 + - - +
216K PHE* 1.3 59.7 + - - +
218K TYR* 3.4 15.2 + - - +
219K LEU 3.6 7.4 + - - -
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Residues in contact with PHE 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K LEU* 3.6 36.6 - - + -
140K ILE 4.1 17.7 - - - -
142K MET* 4.4 17.9 - - + -
145K THR* 4.7 17.5 - - - -
148K MET* 4.9 7.6 - - + -
149K SER* 4.9 7.0 - - - -
152K LEU* 3.7 26.2 - - + -
190K ILE* 4.3 10.8 - - + +
193K GLU* 4.2 2.0 + - - -
213K GLN* 3.5 27.4 + - - +
214K THR 3.2 1.0 - - - -
215K GLY* 1.3 74.4 - - - +
217K ILE* 1.3 66.0 + - + +
219K LEU* 3.4 15.4 + - + +
220K LEU* 3.5 39.3 + - + +
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Residues in contact with ILE 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K MET* 5.3 5.4 - - + -
213K GLN* 3.3 19.7 - - + +
214K THR* 3.1 18.3 + - + +
216K PHE* 1.3 78.3 - - + +
218K TYR* 1.3 65.9 + - + +
220K LEU* 3.2 9.1 + - + +
221K THR* 3.0 29.7 + - - +
71M ILE* 3.7 30.1 - - + -
72M HIS 5.1 5.2 - - - +
73M CYS* 6.2 6.5 - - - -
74M GLU* 6.4 2.2 - - + -
85M LEU* 4.6 25.6 - - + -
89M LEU* 4.9 12.1 - - + +
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Residues in contact with TYR 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K PRO* 4.5 25.8 - - + +
180K ASP* 4.4 25.4 - - + -
186K ALA* 4.6 7.6 - - + -
189K LYS* 4.8 15.7 - - + -
214K THR* 3.2 34.8 - - - -
215K GLY* 3.8 13.7 - - - +
216K PHE 3.3 0.4 - - - -
217K ILE* 1.3 79.3 - - + +
219K LEU* 1.3 57.6 + - - +
221K THR* 3.3 8.6 + - - -
222K CYS* 2.9 36.4 + - - -
74M GLU* 4.4 22.6 - - + +
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Residues in contact with LEU 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K MET* 3.8 27.1 - - + -
152K LEU* 3.8 34.3 - - + -
183K PHE* 5.1 5.7 - - + -
186K ALA* 4.7 10.0 - - + +
187K LEU* 4.0 17.0 - - + -
190K ILE* 3.8 17.9 - - + -
215K GLY 3.6 8.4 + - - +
216K PHE* 3.4 11.8 + - + +
217K ILE 3.2 0.2 - - - -
218K TYR* 1.3 80.1 - - - +
220K LEU* 1.3 59.1 + - + +
222K CYS* 4.0 4.5 - - - +
223K ALA* 3.1 29.4 + - + +
241K PHE* 4.6 10.5 - - + -
245K ILE* 5.0 6.3 - - + -
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Residues in contact with LEU 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142K MET* 4.7 23.8 - - + -
145K THR* 4.8 6.7 - - + -
148K MET* 3.9 19.7 - - + -
216K PHE* 3.5 40.8 - - + +
217K ILE* 3.2 10.6 + - - +
219K LEU* 1.3 78.0 - - + +
221K THR* 1.3 63.7 + - - +
223K ALA* 4.0 4.5 - - - +
224K TRP* 3.1 25.1 + - - +
231K ALA* 4.0 27.6 - - + +
85M LEU* 5.3 4.3 - - + -
86M ALA* 5.3 7.2 - - + -
89M LEU* 4.1 23.8 - - + +
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Residues in contact with THR 221 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K ASP* 5.2 8.7 - - + -
217K ILE* 3.0 18.9 + - - +
218K TYR* 3.3 13.9 + - + -
220K LEU* 1.3 77.5 - - - +
222K CYS* 1.3 61.2 + - - +
224K TRP* 3.5 7.8 + - - +
225K LYS* 3.3 34.2 + - - +
89M LEU* 4.5 8.8 - - - +
93M LEU* 3.7 38.6 - - + +
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Residues in contact with CYS 222 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K PRO 3.2 26.2 - - - -
180K ASP* 3.4 26.2 - - - -
181K LYS* 3.9 6.1 - - - +
182K CYS 4.2 8.5 - - - -
183K PHE* 3.5 23.1 - - + -
186K ALA* 4.3 3.8 - - + -
218K TYR 2.9 24.6 + - - +
219K LEU* 4.0 4.7 - - - +
221K THR* 1.3 74.8 - - - +
223K ALA* 1.3 64.2 + - - +
225K LYS* 3.1 16.1 + - - +
226K ILE* 3.2 18.8 - - - +
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Residues in contact with ALA 223 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K MET* 5.4 2.7 - - + -
183K PHE* 3.9 18.6 - - + -
219K LEU* 3.1 25.5 + - + +
220K LEU* 4.1 4.9 - - - +
222K CYS* 1.3 77.1 - - - +
224K TRP* 1.3 57.2 + - - +
225K LYS 3.4 0.2 + - - -
226K ILE* 3.4 2.2 + - - +
227K ASN* 2.8 35.0 + - - +
230K LEU* 4.3 17.7 - - + +
231K ALA* 5.1 2.2 - - - -
241K PHE* 5.7 3.4 - - + -
244K PHE* 4.9 10.3 - - + -
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Residues in contact with TRP 224 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220K LEU 3.1 19.3 + - - +
221K THR* 3.8 5.6 - - - +
222K CYS 3.2 0.6 - - - -
223K ALA* 1.3 77.0 - - - +
225K LYS* 1.3 77.3 + - + +
226K ILE 3.5 0.9 + - - -
227K ASN 4.2 5.2 - - - -
228K GLN* 3.6 39.8 + - + +
231K ALA* 4.3 15.4 - - + +
89M LEU* 4.5 9.6 - - + -
90M GLN* 4.4 24.3 + - + +
93M LEU* 3.6 51.4 - - + -
94M SER* 3.6 24.2 - - - -
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Residues in contact with LYS 225 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K ASP* 2.8 41.0 + - - +
181K LYS* 4.6 11.2 - - - +
221K THR* 3.3 29.5 - - - +
222K CYS* 3.1 10.4 + - - +
224K TRP* 1.3 94.9 - - + +
226K ILE* 1.3 65.3 - - + +
93M LEU* 6.0 2.0 - - - -
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Residues in contact with ILE 226 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K LYS 5.4 7.4 - - - +
183K PHE* 4.2 19.7 - - + -
222K CYS* 3.2 24.9 - - - +
223K ALA 3.4 2.8 + - - +
224K TRP 3.3 0.4 - - - -
225K LYS* 1.3 86.7 - - + +
227K ASN* 1.3 62.3 + - + +
228K GLN 4.2 0.4 - - - -
244K PHE* 4.2 25.4 - - + -
248K GLN* 4.5 17.5 - - - +
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Residues in contact with ASN 227 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223K ALA 2.8 22.0 + - - +
224K TRP 4.2 0.2 - - - -
226K ILE* 1.3 84.5 - - + +
228K GLN* 1.3 64.1 + - - +
229K ASN* 2.9 32.6 + - - +
230K LEU* 3.4 44.3 + - + +
231K ALA 4.1 0.2 + - - -
244K PHE* 4.7 14.8 - - + -
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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