Contacts of the strand formed by residues 211 - 219 (chain K) in PDB entry 7JOA
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 211 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207K SER* 3.2 32.8 + - - +
208K ALA* 3.2 24.0 + - + +
209K PRO 3.5 0.2 - - - -
210K ASN* 1.3 90.4 - - - +
212K PHE* 1.3 72.3 + - - +
213K ASP* 5.9 0.2 - - - -
305K SER* 3.5 22.9 + - - +
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Residues in contact with PHE 212 (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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164K ILE* 4.1 11.9 - - + -
167K ALA* 3.7 18.4 - - + -
168K ALA* 3.4 39.7 - - + -
171K VAL* 3.5 37.5 - - + -
199K SER* 5.7 10.5 - - - -
209K PRO 3.7 24.9 - - - -
210K ASN 4.0 7.0 - - - -
211K GLU* 1.3 80.9 - - - +
213K ASP* 1.3 69.3 + - - +
304K ILE* 4.1 3.1 - - + -
305K SER 2.9 7.6 + - - +
306K VAL* 3.2 10.2 - - + -
307K ASP 3.1 21.8 + - - -
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Residues in contact with ASP 213 (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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197K THR* 5.3 4.9 + - - -
205K LYS* 5.6 7.4 + - - +
207K SER* 5.6 4.3 + - - -
211K GLU 5.9 0.2 - - - -
212K PHE* 1.3 80.1 - - - +
214K VAL* 1.3 70.9 + - - +
306K VAL* 4.7 0.4 - - - -
307K ASP* 3.1 35.4 - - - +
309K ILE* 4.4 9.2 - - + +
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Residues in contact with VAL 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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171K VAL* 4.8 9.0 - - + -
172K ASN* 5.8 1.1 - - - +
175K VAL* 4.2 22.9 - - + -
194K GLN* 3.5 30.1 - - - +
195K LEU 5.7 0.4 - - - -
197K THR* 6.0 1.3 - - - -
212K PHE* 5.7 0.2 - - + -
213K ASP* 1.3 81.2 - - - +
215K MET* 1.3 58.6 + - - +
216K PHE* 3.9 22.4 + - + -
306K VAL* 4.3 8.5 - - + -
307K ASP 3.4 5.6 + - - +
308K ILE* 3.7 22.4 - - + -
309K ILE* 3.3 24.6 + - - +
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Residues in contact with MET 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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194K GLN* 3.5 1.7 - - - +
195K LEU* 2.9 68.5 + - + +
197K THR* 5.0 9.0 + - + +
214K VAL* 1.3 72.9 - - - +
216K PHE* 1.3 68.8 + - - +
217K LYS* 4.8 0.7 - - - +
309K ILE* 3.5 13.5 - - + +
311K ALA* 3.5 29.8 - - + -
346K TYR* 5.0 4.7 - - - -
348K VAL* 3.8 22.2 - - + -
366K SER* 4.1 16.6 - - - +
368K SER* 5.2 4.7 - - - +
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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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175K VAL* 3.9 31.9 - - + -
178K LEU* 5.1 11.2 - - + -
179K LEU* 4.9 14.6 - - + -
182K MET* 5.5 8.7 - - + -
192K VAL* 3.5 23.8 - - + -
193K GLU 3.4 2.9 - - - -
194K GLN* 4.1 18.8 - - + -
214K VAL* 3.9 22.6 + - + -
215K MET* 1.3 78.6 - - - +
217K LYS* 1.3 57.1 + - - +
266K PHE* 4.4 15.7 - + + -
270K ILE* 6.6 0.2 - - + -
308K ILE* 4.0 30.5 - - + -
309K ILE 3.1 10.5 + - - +
310K LEU* 3.3 10.6 - - + +
311K ALA 2.8 28.7 + - - -
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Residues in contact with LYS 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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191K GLY 4.1 15.7 + - - +
192K VAL* 3.1 10.4 - - - +
193K GLU* 2.8 64.1 + - - +
194K GLN 5.5 1.3 - - - +
195K LEU* 4.9 15.7 - - + +
215K MET* 3.9 2.2 + - + -
216K PHE* 1.3 72.1 - - - +
218K LEU* 1.3 60.9 + - - +
219K GLU* 4.7 12.5 + - - +
311K ALA* 3.0 12.1 - - + +
313K GLU* 4.5 16.2 + - + -
346K TYR* 4.1 36.1 - - + +
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Residues in contact with LEU 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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188K GLU 4.3 18.2 - - - +
189K PHE* 4.6 16.6 - - + -
191K GLY* 4.8 13.0 - - - +
192K VAL* 4.4 18.4 - - + +
217K LYS* 1.3 78.0 - - - +
219K GLU* 1.3 81.8 + - + +
220K VAL* 5.8 1.8 - - + -
248K LEU* 5.3 6.3 - - + -
262K MET* 4.5 22.7 - - + -
310K LEU* 4.4 10.1 - - + -
311K ALA 3.0 9.2 + - - +
312K LEU* 3.6 13.3 - - + +
313K GLU* 2.7 36.8 + - - +
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Residues in contact with GLU 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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191K GLY* 5.2 4.0 + - - +
217K LYS* 4.7 8.7 + - - +
218K LEU* 1.3 96.7 - - + +
220K VAL* 1.3 73.7 + - - +
221K PRO* 4.7 4.2 - - + +
248K LEU* 6.0 1.7 - - - +
313K GLU* 2.8 27.5 - - - +
315K LYS* 3.7 27.0 + - - +
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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