Contacts of the strand formed by residues 220 - 228 (chain B) in PDB entry 3V4R
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 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B GLU* 3.2 41.0 - - + +
166B GLU* 4.3 5.4 - - + +
167B ILE 5.4 0.2 - - - -
216B PHE* 3.2 9.8 - - - +
217B PHE* 2.9 48.7 + - - +
219B ASP* 1.3 80.2 - - - +
221B ILE* 1.3 72.1 + - - +
222B GLU* 4.2 6.5 - - - +
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Residues in contact with ILE 221 (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 LEU* 3.8 29.2 - - + -
162B ARG 3.7 6.1 - - - +
163B THR* 2.4 40.9 - - - +
164B GLU 3.5 6.3 + - - -
165B MET* 3.7 15.0 - - + -
166B GLU 4.4 0.6 - - - +
167B ILE* 3.7 31.9 - - + +
172B LEU* 5.7 1.6 - - + -
214B VAL* 3.8 30.7 - - + -
215B GLU 3.8 5.2 - - - +
216B PHE* 4.5 3.1 - - + +
220B GLU* 1.3 79.2 - - - +
222B GLU* 1.4 61.4 + - - +
223B ARG* 4.1 14.1 - - - +
224B ILE* 4.7 9.4 - - + -
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Residues in contact with GLU 222 (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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163B THR* 5.4 7.0 - - - +
215B GLU* 2.8 20.8 + - + +
216B PHE 4.6 0.2 - - - -
217B PHE* 3.9 26.0 - - + +
220B GLU* 3.3 14.8 + - - +
221B ILE* 1.4 74.1 - - - +
223B ARG* 1.4 60.3 + - + +
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Residues in contact with ARG 223 (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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163B THR* 6.0 3.6 - - - +
213B ARG 3.6 1.4 - - - +
214B VAL* 3.6 2.1 - - - -
215B GLU* 2.8 39.4 + - + +
221B ILE* 3.5 6.5 - - - +
222B GLU* 1.4 80.6 - - + +
224B ILE* 1.3 60.3 + - - +
225B ARG* 4.2 3.1 - - + +
237B ASP* 4.8 15.0 - - - +
238B ARG 5.6 0.2 - - - -
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Residues in contact with ILE 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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161B LEU* 5.8 6.1 - - + +
162B ARG 6.1 2.9 - - - -
163B THR* 5.9 4.0 - - + +
212B VAL* 5.2 3.4 - - + -
213B ARG 3.4 5.6 - - - +
214B VAL* 4.8 10.5 - - + -
221B ILE* 4.7 12.3 - - + +
223B ARG* 1.3 73.6 - - - +
225B ARG* 1.4 52.8 + - - +
237B ASP* 3.3 3.1 + - - +
238B ARG* 2.9 54.3 + - + +
239B ASP 5.6 5.6 - - - +
240B HIS 5.9 0.2 - - - -
241B VAL* 5.2 14.4 - - + -
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Residues in contact with ARG 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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211B CYS 3.6 0.2 - - - +
212B VAL* 4.8 3.1 - - - +
213B ARG* 3.0 43.7 + - + +
223B ARG* 4.2 3.8 - - + -
224B ILE* 1.4 71.9 - - - +
226B GLU* 1.4 63.8 + - - +
227B VAL* 3.7 3.0 - - + +
234B ILE* 5.8 5.8 - - + -
236B GLY 3.6 12.3 - - - +
237B ASP* 4.1 15.3 - - - +
238B ARG* 4.3 0.7 - - - +
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Residues in contact with GLU 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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210B HIS* 4.3 15.9 - - + +
211B CYS 3.2 8.5 - - - +
212B VAL* 4.8 4.5 - - + +
225B ARG* 1.4 71.2 - - - +
227B VAL* 1.3 59.1 - - - +
234B ILE* 3.5 5.9 - - - +
235B LEU* 3.1 27.6 + - + -
236B GLY 2.9 16.6 + - - +
238B ARG* 5.1 5.9 - - + +
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Residues in contact with VAL 227 (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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105A THR* 6.4 1.1 - - - -
201B GLU* 5.7 5.8 - - - +
210B HIS* 3.2 10.2 - - - -
211B CYS* 2.6 51.3 + - + +
213B ARG* 4.1 16.6 - - + -
225B ARG* 3.7 13.9 - - + +
226B GLU* 1.3 78.6 - - - +
228B ASP* 1.3 67.9 + - - +
229B ALA* 3.3 1.5 + - - -
232B GLY* 3.7 21.8 - - - +
233B GLU 3.5 11.7 - - - +
234B ILE* 4.8 8.5 - - + +
235B LEU* 4.3 0.7 - - - +
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Residues in contact with ASP 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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209B GLU 4.0 6.6 - - - +
210B HIS* 4.8 10.9 + - + -
227B VAL* 1.3 69.6 - - - +
229B ALA* 1.4 58.0 + - - +
230B LEU* 3.4 19.8 + - - +
231B THR* 2.7 28.7 + - - +
232B GLY* 2.7 34.7 + - - -
233B GLU* 2.7 31.2 + - + +
235B LEU* 4.3 7.6 - - + +
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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