Contacts of the strand formed by residues 208 - 216 (chain B) in PDB entry 4EE5
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 ASP 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ARG* 5.2 4.9 + - - -
167B TYR 3.2 6.1 - - - +
168B ALA* 3.7 22.9 - - + +
169B PRO* 4.9 0.4 - - + -
174B SER* 3.8 16.2 + - - +
176B HIS 3.0 15.3 + - - +
177B LYS* 3.4 12.1 - - + +
178B VAL 2.9 24.6 + - - -
207B LEU* 1.3 71.0 - - - +
209B TYR* 1.3 59.7 + - - +
239B TYR* 2.6 40.9 + - - -
241B TYR* 4.7 2.8 - - - -
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Residues in contact with TYR 209 (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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161B VAL* 4.0 1.2 - - - +
165B GLY 4.1 4.5 - - - -
166B ARG* 3.3 10.5 + - - -
167B TYR* 2.8 65.6 + + + +
178B VAL* 3.1 16.6 - - + +
180B ILE* 4.0 12.3 - - + -
199B HIS* 2.7 53.9 + + - -
202B LEU* 3.4 33.4 - - + -
203B GLN* 3.5 8.4 - - - +
207B LEU* 3.5 20.9 - - + -
208B ASP* 1.3 76.2 + - - +
210B GLY* 1.3 62.9 + - - +
211B ILE* 3.7 20.4 - - + -
241B TYR* 4.4 2.0 - - - -
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Residues in contact with GLY 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLY 3.4 7.4 - - - -
166B ARG* 3.7 6.7 - - - -
178B VAL 3.0 8.1 + - - -
179B ALA* 3.6 0.9 - - - -
180B ILE* 2.8 28.6 + - - +
209B TYR* 1.3 74.1 - - - +
211B ILE* 1.3 68.2 + - - +
212B TYR* 3.6 9.1 - - - -
241B TYR* 3.6 18.7 + - - -
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Residues in contact with ILE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLY 3.5 4.0 + - - +
165B GLY 3.2 8.7 + - - +
180B ILE* 3.6 37.0 - - + +
182B ILE* 4.1 15.0 - - + -
194B TRP* 3.9 28.5 - - + -
195B LEU* 4.3 2.7 - - + -
199B HIS* 3.8 28.3 - - + +
202B LEU* 3.9 3.6 - - + -
209B TYR* 3.7 11.0 - - + -
210B GLY* 1.3 73.8 - - - -
212B TYR* 1.3 70.0 + - - +
213B VAL* 4.6 0.9 - - + -
386B LEU 3.8 9.6 - - - +
387B TYR* 3.8 15.5 - - + -
388B THR* 3.0 23.7 + - - -
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Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLY 5.8 0.9 - - - -
166B ARG* 4.4 3.3 + - - -
179B ALA* 4.2 5.4 - - + -
180B ILE 2.8 15.7 + - - +
181B ILE* 3.4 12.0 - - + -
182B ILE* 2.9 26.9 + - - +
210B GLY* 3.6 20.2 - - - -
211B ILE* 1.3 76.3 - - - +
213B VAL* 1.3 63.9 + - - +
214B ILE* 3.8 12.4 + - + +
231B GLY 5.4 0.2 - - - +
234B GLU 5.2 0.4 - - - -
235B ALA* 3.8 30.5 - - + -
238B ASP* 2.5 32.7 + - - +
241B TYR* 2.8 41.2 + + - -
388B THR* 3.3 27.1 - - + +
390B ILE* 4.1 17.9 - - + -
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Residues in contact with VAL 213 (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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182B ILE* 3.7 13.7 - - + +
184B PHE* 3.5 37.2 - - + -
191B LEU* 3.8 26.7 - - + -
211B ILE* 4.6 0.4 - - + -
212B TYR* 1.3 74.0 - - - +
214B ILE* 1.3 62.0 + - - +
215B ASN 3.6 1.1 + - - +
387B TYR* 3.6 31.0 - - + -
388B THR 2.7 10.5 + - - +
389B GLN* 3.2 21.1 - - + +
390B ILE 2.9 26.7 + - - +
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ILE* 3.8 15.0 - - + -
182B ILE 2.9 11.2 + - - +
183B PRO* 3.8 0.6 - - + +
184B PHE* 2.8 32.0 + - - +
212B TYR* 4.1 12.3 - - + +
213B VAL* 1.3 75.1 - - - +
215B ASN* 1.3 57.1 + - - +
216B GLN 3.6 0.9 + - - -
227B LEU* 3.4 43.8 - - + +
230B VAL* 3.7 18.2 - - + -
231B GLY* 3.5 31.0 - - - +
390B ILE* 3.4 27.8 - - + +
392B VAL* 3.9 6.5 - - + -
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Residues in contact with ASN 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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184B PHE* 3.2 21.9 - - + +
185B ARG* 3.9 0.9 - - - -
213B VAL* 3.6 0.4 + - + -
214B ILE* 1.3 71.2 - - - +
216B GLN* 1.3 69.6 + - - +
217B ALA 3.4 0.2 + - - -
227B LEU* 4.6 1.3 - - - -
389B GLN* 3.6 26.6 - - + +
390B ILE 2.8 10.6 + - - +
391B THR* 3.0 34.5 + - - +
392B VAL* 2.8 30.0 + - - +
407B GOL 2.5 45.2 + - - -
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE 2.7 16.5 + - - +
185B ARG* 3.4 41.9 - - + +
214B ILE 3.6 2.2 + - - -
215B ASN* 1.3 76.6 + - - +
217B ALA* 1.3 73.5 + - - +
218B GLY 3.9 0.3 + - - -
220B THR* 3.6 8.3 + - - -
221B ILE 3.1 24.2 + - - -
222B PHE* 3.5 13.0 - - + +
223B ASN 3.1 23.2 + - - -
227B LEU* 3.7 21.1 - - + +
392B VAL 3.8 4.0 - - - +
394B ILE* 3.6 27.7 - - + +
395B GLY 5.0 0.2 + - - -
407B GOL 4.8 1.2 + - - -
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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
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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