Contacts of the helix formed by residues 214 - 222 (chain B) in PDB entry 3R2W
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 214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 5.5 3.6 - - - +
151B MET* 5.2 0.9 - - - -
179B GLN* 5.2 4.0 - - + +
180B SER* 3.0 20.1 + - - +
182B TYR* 4.1 12.1 + - - -
210B PRO* 3.8 33.3 - - + +
211B GLY 4.2 8.0 + - - +
212B HIS 2.5 8.1 + - - -
213B GLY* 1.3 73.2 - - - +
215B ILE* 1.3 55.1 + - - -
216B TYR 3.2 3.6 + - - -
217B ALA* 3.6 18.6 + - - +
218B SER* 2.5 34.0 + - - +
339B MET* 5.5 2.6 - - - +
359B THR* 4.2 6.6 + - - +
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Residues in contact with ILE 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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100B VAL* 3.9 13.5 - - + -
102B LEU* 3.8 14.1 - - + -
151B MET* 3.5 19.9 - - + -
177B PHE* 4.1 8.7 - - + -
212B HIS 2.7 9.5 + - - +
213B GLY 4.7 0.2 - - - -
214B ASP* 1.3 78.5 - - - +
216B TYR* 1.3 74.9 + - + +
218B SER* 3.3 6.8 + - - -
219B PHE* 2.6 46.4 + - + +
236B ILE* 5.5 7.6 - - + -
238B VAL* 3.6 30.5 - - + -
323B ILE* 5.9 1.1 - - + -
361B VAL* 3.6 26.9 - - + -
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Residues in contact with TYR 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLY 3.7 14.1 - - - -
214B ASP 3.2 0.6 - - - -
215B ILE* 1.3 89.8 - - + +
217B ALA* 1.3 69.4 + - - +
219B PHE* 2.8 5.3 + - - -
220B TYR* 2.8 29.7 + - - +
236B ILE* 5.8 4.0 - - + -
267B PHE* 4.0 10.1 - + - -
323B ILE* 4.0 20.6 - - + +
328B VAL* 4.7 25.9 - - + +
332B GLN* 3.8 14.6 - - - +
337B ILE* 4.1 14.8 - - + -
339B MET* 3.9 19.1 - - + -
361B VAL* 3.1 31.7 + - + +
364B ALA* 3.4 26.0 - - + +
368B PHE* 5.3 8.1 - + - -
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Residues in contact with ALA 217 (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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214B ASP* 3.6 24.5 + - - +
216B TYR* 1.3 77.7 - - - +
218B SER* 1.3 57.6 + - - +
220B TYR* 4.1 2.5 - - - +
221B ASN* 3.0 30.3 + - - +
332B GLN* 3.4 28.9 - - - +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B MET* 4.8 1.4 - - - -
177B PHE* 3.4 12.4 - - - -
178B ASN 4.1 18.4 - - - +
179B GLN* 4.3 12.4 - - - +
180B SER* 4.7 4.3 - - - -
214B ASP* 2.5 32.3 + - - +
215B ILE* 3.3 8.3 + - - -
217B ALA* 1.3 77.5 - - - +
219B PHE* 1.3 63.7 + - - +
221B ASN* 4.1 5.6 - - - +
222B SER* 3.3 20.8 + - - -
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Residues in contact with PHE 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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100B VAL* 4.7 12.3 - - + -
149B VAL* 4.3 9.9 - - + -
177B PHE* 3.7 20.2 - + + -
215B ILE* 2.6 30.9 + - + +
216B TYR* 3.7 3.8 - - - +
218B SER* 1.3 70.3 - - - +
220B TYR* 1.3 67.3 + - - +
222B SER* 2.4 22.6 + - - -
223B GLY 3.7 1.4 + - - -
224B LEU* 3.2 40.8 - - + -
225B LEU* 3.8 34.4 + - + -
228B PHE* 4.3 19.5 - + - -
236B ILE* 4.3 22.4 - - + -
325B LEU* 4.2 16.2 - - + -
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Residues in contact with TYR 220 (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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216B TYR 2.8 15.2 + - - +
217B ALA 4.1 3.4 - - - +
219B PHE* 1.3 80.1 - - - +
221B ASN* 1.3 74.0 + - - +
223B GLY* 3.2 13.0 + - - -
224B LEU 4.6 0.7 + - - -
225B LEU* 3.7 35.7 - - + +
226B ASP* 4.3 16.4 + - - -
328B VAL* 5.4 1.6 - - + -
329B LYS* 4.9 0.4 - - + -
332B GLN* 4.0 28.9 - - + -
333B GLU* 3.2 51.8 + - + +
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Residues in contact with ASN 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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39B HIS* 5.7 2.8 - - - +
42B LYS* 3.2 48.2 + - - +
217B ALA 3.0 20.9 + - - +
218B SER* 4.3 5.4 - - - -
220B TYR* 1.3 91.1 - - - +
222B SER* 1.3 60.4 + - - +
223B GLY* 3.1 2.1 + - - -
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Residues in contact with SER 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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177B PHE* 4.2 20.4 - - - -
218B SER 3.3 14.9 + - - -
219B PHE* 2.4 23.6 + - - -
220B TYR 3.2 0.2 - - - -
221B ASN* 1.3 78.4 - - - +
223B GLY* 1.3 63.1 + - - +
224B LEU* 3.5 20.7 - - - +
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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