Contacts of the helix formed by residues 188 - 203 (chain B) in PDB entry 2W27
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 TYR 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ASP* 3.2 32.3 + - - -
165A ALA* 5.9 0.9 - - + -
154B ILE 5.4 1.7 + - - -
174B ILE* 4.8 5.9 - - - +
175B ASP 4.6 5.0 + - - -
176B LEU* 4.7 1.8 - - + -
178B ALA* 3.7 26.1 - - + +
179B LEU* 3.3 39.0 - - + -
185B SER* 4.0 18.6 - - - +
186B PRO 3.0 5.3 + - - +
187B SER* 1.3 75.4 - - - +
189B GLU* 1.3 65.2 + - - +
190B HIS 3.0 2.5 - - - -
191B VAL* 3.0 42.2 + - + +
192B LEU* 3.0 28.1 + - + +
219B TYR* 6.1 2.0 - + + -
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO 4.4 3.6 + - - +
187B SER* 3.5 1.0 - - - +
188B TYR* 1.3 79.7 - - - +
190B HIS* 1.3 59.4 + - + +
192B LEU* 3.7 8.5 - - - -
193B TYR* 2.7 37.3 + - + +
219B TYR* 3.6 32.0 + - + +
222B ARG* 3.2 37.9 + - - -
223B ASN* 2.8 37.2 + - - +
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Residues in contact with HIS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.4 19.1 - - + -
201A LYS* 3.4 59.3 + - + +
202A ILE* 4.5 2.5 - - + -
187B SER* 3.1 31.6 + - - +
188B TYR 3.0 0.2 - - - -
189B GLU* 1.3 81.8 + - + +
191B VAL* 1.3 63.3 + - - +
193B TYR* 3.8 5.7 - - - +
194B SER* 2.6 35.9 + - - -
368B LEU* 6.1 0.4 - - + -
377B MET* 4.0 17.5 - - + +
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Residues in contact with VAL 191 (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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161A LEU* 3.7 19.5 - - + +
162A ASP* 3.5 20.0 - - - +
165A ALA* 3.7 30.5 - - + -
198A LEU* 4.2 3.8 - - + +
187B SER 4.3 0.9 - - - +
188B TYR* 3.0 39.7 + - + +
190B HIS* 1.3 80.2 - - - +
192B LEU* 1.3 67.2 + - + +
194B SER* 3.0 5.9 + - - -
195B ILE* 2.9 33.2 + - + +
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Residues in contact with LEU 192 (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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174B ILE* 4.2 24.7 - - + -
176B LEU* 4.3 16.6 - - + -
179B LEU* 4.6 0.2 - - + -
188B TYR* 3.0 40.4 + - + +
189B GLU* 3.7 7.9 - - - +
191B VAL* 1.3 79.6 - - + +
193B TYR* 1.3 65.1 + - - +
195B ILE* 2.9 18.1 + - + +
196B SER* 3.0 14.6 + - - -
208B TYR* 4.2 13.9 + - + +
219B TYR* 3.8 32.3 - - + +
223B ASN* 3.8 25.4 - - + +
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.5 20.2 - - + +
201A LYS* 3.9 32.8 - - + -
349A TYR* 4.8 8.5 + + - -
189B GLU* 2.7 23.3 + - + +
190B HIS* 3.8 5.6 - - - +
192B LEU* 1.3 70.8 - - - +
194B SER* 1.3 70.1 + - - +
196B SER* 3.0 23.7 + - - -
197B LEU* 3.2 42.0 + - + +
223B ASN* 3.5 13.5 + - - +
349B TYR* 4.9 7.8 + - - -
367B ASP* 4.6 9.2 + - - -
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Residues in contact with SER 194 (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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161A LEU* 3.7 20.6 - - - -
194A SER* 3.7 25.5 + - - -
197A LEU* 5.1 3.8 - - - -
198A LEU* 3.5 25.8 + - - +
190B HIS 2.6 29.8 + - - -
191B VAL* 3.3 4.5 - - - -
193B TYR* 1.3 81.7 - - - +
195B ILE* 1.3 66.2 + - - +
197B LEU* 3.3 4.4 + - - +
198B LEU 3.1 15.8 + - - -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.0 34.8 - - + -
154B ILE* 4.8 14.1 - - + -
161B LEU* 4.0 20.9 - - + -
172B LEU* 4.0 23.8 - - + -
174B ILE* 4.1 25.4 - - + -
191B VAL* 2.9 27.0 + - + +
192B LEU* 2.9 12.0 + - + +
194B SER* 1.3 75.7 - - - +
196B SER* 1.3 65.3 + - - +
198B LEU* 3.0 8.6 + - + +
199B ALA* 2.8 19.8 + - - +
206B LEU* 4.3 2.7 - - + -
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PRO* 4.3 8.1 - - - +
192B LEU 3.0 8.3 + - - -
193B TYR* 3.0 16.4 + - - -
195B ILE* 1.3 77.1 - - - +
197B LEU* 1.3 66.3 + - - +
199B ALA* 3.0 4.4 + - - +
200B ARG* 2.7 35.7 + - - +
206B LEU* 3.5 29.8 - - - +
223B ASN* 3.7 17.8 - - - -
224B GLY* 4.4 5.6 - - - -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TYR* 4.5 8.1 - - + +
197A LEU* 3.8 24.0 - - + -
348A PRO* 3.8 26.9 - - + -
349A TYR* 3.3 32.5 - - + +
193B TYR* 3.2 51.7 + - + +
194B SER 3.9 3.4 - - - +
195B ILE 3.1 1.0 - - - -
196B SER* 1.3 88.8 + - - +
198B LEU* 1.3 61.8 + - - +
200B ARG* 3.2 8.8 + - - +
201B LYS* 3.1 28.3 + - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS* 3.3 41.5 - - + +
191A VAL* 3.9 14.8 - - + +
193A TYR* 5.2 2.2 - - - -
194A SER* 3.8 20.3 - - - +
161B LEU* 3.3 46.4 - - + +
165B ALA* 4.9 2.7 - - + -
172B LEU* 5.9 3.8 - - + -
194B SER 3.1 6.5 + - - +
195B ILE* 3.0 12.3 + - + +
197B LEU* 1.3 76.2 - - - +
199B ALA* 1.3 62.9 + - - +
201B LYS* 3.5 4.5 + - - +
202B ILE* 3.3 35.4 + - + +
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Residues in contact with ALA 199 (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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172B LEU* 4.0 11.0 - - + -
195B ILE 2.8 12.3 + - - +
196B SER* 3.3 8.7 - - - +
198B LEU* 1.3 75.9 - - - +
200B ARG* 1.3 60.6 + - - +
202B ILE* 4.1 9.2 - - - -
203B GLY* 3.0 7.3 + - - -
204B ALA* 2.8 46.8 + - + +
206B LEU* 3.7 23.3 - - + -
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Residues in contact with ARG 200 (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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347A ARG* 4.7 7.6 - - - +
348A PRO* 3.6 36.5 + - + -
349A TYR* 3.3 36.0 - - - -
366A SER* 4.9 4.6 - - - -
367A ASP* 2.5 36.0 + - - -
369A TYR* 3.3 49.3 - - + +
370A SER 3.3 21.0 + - - +
196B SER 2.7 17.9 + - - +
197B LEU* 3.2 11.1 + - - +
199B ALA* 1.3 74.4 - - - +
201B LYS* 1.3 65.5 + - + +
203B GLY* 3.7 4.3 + - - -
204B ALA 5.1 0.2 - - - -
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Residues in contact with LYS 201 (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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190A HIS* 3.8 40.6 - - + +
193A TYR* 3.8 34.5 - - + -
367A ASP* 2.8 35.9 + - - +
368A LEU* 2.8 26.6 + - - +
369A TYR* 4.5 4.0 - - + +
370A SER* 3.2 18.0 - - - +
377A MET* 3.4 16.1 - - + +
197B LEU 3.1 15.4 + - - +
198B LEU* 3.5 5.1 + - - +
199B ALA 3.4 0.2 - - - -
200B ARG* 1.3 82.0 - - + +
202B ILE* 1.3 58.0 + - - +
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Residues in contact with ILE 202 (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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187A SER* 5.1 5.2 - - - +
190A HIS* 3.8 29.6 - - + +
370A SER* 3.5 12.1 + - - -
164B ILE* 5.8 2.0 - - + -
165B ALA* 4.4 31.0 - - + +
168B SER* 4.7 15.6 + - - +
169B PRO* 4.7 14.7 - - + +
172B LEU* 5.4 5.4 - - + -
198B LEU* 3.3 28.2 + - + +
199B ALA* 3.9 8.1 - - - +
201B LYS* 1.3 75.1 - - - +
203B GLY* 1.3 62.5 + - - +
204B ALA* 4.1 17.3 - - + +
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Residues in contact with GLY 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A SER* 3.4 26.8 - - - -
371A ASP 5.2 2.0 - - - -
372A LEU* 5.2 15.2 - - - +
169B PRO 4.1 6.1 - - - +
170B ASP* 4.3 5.0 - - - +
199B ALA 3.0 6.6 + - - -
200B ARG* 3.7 2.2 + - - -
201B LYS 3.4 2.4 - - - -
202B ILE* 1.3 80.6 - - - +
204B ALA* 1.3 60.4 + - - +
205B ALA 4.2 0.2 + - - -
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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