Contacts of the strand formed by residues 185 - 202 (chain B) in PDB entry 3AA6
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 GLY 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A HIS 3.5 8.1 - - - -
210A LYS* 4.0 15.1 - - - +
179B THR 3.7 0.3 - - - +
180B ASN* 3.3 13.8 - - - -
181B LYS 2.8 26.2 + - - -
183B GLY 3.6 1.6 - - - -
184B SER* 1.3 94.4 + - - +
186B THR* 1.3 59.8 + - - -
187B MET 3.7 0.7 + - - -
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL 5.2 2.0 - - - +
208A SER* 3.1 21.4 + - - -
209A HIS* 3.0 42.9 + - + +
178B GLN* 5.5 7.6 - - + +
179B THR 3.3 9.6 - - - +
180B ASN* 3.6 20.6 + - + +
185B GLY* 1.3 70.8 - - - -
187B MET* 1.3 67.8 + - - +
188B ASN* 4.9 6.7 - - + +
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.6 24.9 - - + -
207A VAL 3.8 2.9 - - - -
208A SER* 4.3 5.6 - - - +
243A ILE* 3.8 22.0 - - + +
246A ASN* 3.3 35.4 - - + +
247A TYR* 3.6 41.7 - - + -
250A MET* 4.4 20.7 - - + +
178B GLN* 3.2 4.7 - - - +
179B THR* 2.8 43.6 + - + +
184B SER* 4.7 1.8 - - - +
185B GLY 3.7 1.5 + - - +
186B THR* 1.3 77.8 - - - +
188B ASN* 1.3 61.4 + - - +
189B LEU* 4.2 0.9 - - + -
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 3.5 2.2 - - - -
207A VAL* 2.9 38.9 + - + +
19B GLN* 3.0 41.3 + - + +
176B TRP* 5.1 4.0 - - - -
177B LEU 3.4 9.7 + - - +
178B GLN* 3.6 30.2 + - + +
186B THR* 5.2 6.3 - - + -
187B MET* 1.3 75.1 - - - +
189B LEU* 1.3 64.3 + - - +
190B GLY* 3.9 2.3 + - - -
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.6 3.1 - - + -
205A GLN 3.5 5.4 - - - +
206A LEU* 3.8 29.6 - - + +
247A TYR* 3.8 25.6 - - + +
250A MET* 4.2 12.3 - - + -
175B LEU 3.9 1.4 - - - +
176B TRP* 3.7 0.7 - - - -
177B LEU* 2.8 47.1 + - + +
187B MET* 4.2 0.6 - - + -
188B ASN* 1.3 74.3 - - - +
190B GLY* 1.3 58.2 + - - +
232B TYR* 3.5 32.2 - - + -
233B PHE* 4.1 17.7 - - + -
236B THR* 3.6 24.5 - - + +
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Residues in contact with GLY 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 3.4 2.1 - - - +
205A GLN 2.9 34.0 + - - +
18B PRO* 3.4 9.2 - - - +
19B GLN* 3.5 6.8 - - - +
175B LEU 3.3 10.8 - - - -
176B TRP* 3.6 16.6 - - - -
188B ASN* 4.3 0.7 - - - -
189B LEU* 1.3 76.2 - - - +
191B GLY* 1.3 58.2 + - - -
232B TYR* 3.5 6.8 - - - -
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Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ASN 3.1 12.8 - - - -
204A VAL* 4.2 0.7 - - - -
18B PRO* 3.7 14.1 - - - -
21B ILE* 6.2 0.4 - - - -
174B MET* 3.2 7.6 - - - +
175B LEU 2.9 27.5 + - - -
176B TRP* 3.4 13.4 - - - -
190B GLY* 1.3 74.2 - - - -
192B SER* 1.3 62.5 + - - -
232B TYR* 3.3 8.4 + - - -
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLY* 3.3 2.9 - - - -
203A ASN* 3.0 36.5 + - - +
204A VAL* 3.7 3.8 - - - +
21B ILE* 5.2 6.7 - - - +
44B ASP* 6.1 0.2 - - - +
172B THR* 3.9 12.4 - - - +
173B VAL 3.1 13.5 - - - -
174B MET* 3.7 21.7 - - - +
175B LEU 4.9 0.2 - - - +
191B GLY* 1.3 75.8 - - - -
193B LEU* 1.3 69.9 + - - +
194B THR* 5.3 0.9 + - - -
228B LEU* 5.6 0.7 - - - -
232B TYR* 3.9 2.6 + - - -
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 4.3 14.4 - - + -
200A GLU 4.3 9.0 - - - +
201A ASP* 3.5 13.5 - - + +
202A GLY* 4.1 5.2 - - - -
204A VAL* 4.0 15.7 - - + -
171B SER 3.9 0.7 - - - +
172B THR* 3.2 3.6 - - - +
173B VAL* 3.0 30.9 + - - +
192B SER* 1.3 82.2 - - - +
194B THR* 1.3 63.9 + - - +
195B ARG* 6.0 3.6 - - + -
224B ILE* 4.7 12.3 - - + +
227B THR* 3.8 31.4 - - + -
228B LEU* 3.7 37.2 - - + +
231B ILE* 4.3 6.7 - - + -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 3.0 31.1 + - - +
202A GLY* 4.7 0.6 - - - -
44B ASP* 4.5 0.3 + - - -
170B THR* 3.9 24.5 - - + -
171B SER 3.1 10.5 - - - +
172B THR* 2.8 26.4 + - - +
192B SER* 5.3 1.0 + - - -
193B LEU* 1.3 75.5 + - - +
195B ARG* 1.3 71.0 + - - +
224B ILE* 5.3 0.2 - - - -
489C LEU* 3.7 23.8 - - + +
490C THR* 4.2 11.7 - - + +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 5.5 6.2 + - + -
170B THR* 3.5 4.7 - - - +
171B SER 2.9 30.3 + - - -
193B LEU* 5.8 3.6 - - + -
194B THR* 1.3 80.0 - - - +
196B GLN* 1.3 64.0 + - - +
220B MET* 3.6 22.2 - - - +
223B LYS* 3.7 41.5 - - - +
224B ILE* 3.8 23.3 - - + +
227B THR* 4.8 14.2 + - - +
489C LEU* 4.3 5.8 - - - -
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Residues in contact with GLN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 3.9 30.5 + - + +
169B LEU 3.1 13.5 - - - +
170B THR* 2.6 28.9 + - + +
195B ARG* 1.3 79.0 - - - +
197B MET* 1.3 73.4 + - - +
198B GLU* 5.4 2.5 - - - +
220B MET* 3.9 2.8 - - - +
489C LEU* 3.7 40.1 + - + +
492C ASN* 4.8 7.7 + - - +
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Residues in contact with MET 197 (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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168B LYS* 3.4 2.9 - - - +
169B LEU* 2.7 39.7 + - + +
196B GLN* 1.3 81.5 - - - +
198B GLU* 1.3 72.0 + - - +
199B LYS* 4.8 7.9 - - + -
216B LEU* 3.9 40.4 - - + +
219B ASP* 6.1 4.7 - - + -
220B MET* 3.8 20.2 - - + -
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Residues in contact with GLU 198 (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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166B HIS* 2.8 38.2 + - + +
167B TYR 3.2 9.9 - - - +
168B LYS* 3.4 37.5 + - + +
196B GLN* 5.4 2.5 - - + +
197B MET* 1.3 84.4 - - - +
199B LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 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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166B HIS* 3.8 7.1 - - - -
167B TYR* 2.8 43.8 + - + +
197B MET* 4.8 8.3 - - + -
198B GLU* 1.3 80.4 - - - +
200B ASP* 1.3 68.8 + - - +
201B GLU* 2.5 38.1 + - + +
215B ARG* 6.4 0.2 - - - +
216B LEU* 3.7 27.0 - - + +
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Residues in contact with ASP 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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159B LYS* 4.4 6.4 + - - -
164B THR* 4.5 12.1 - - + +
165B ALA 3.5 5.7 - - - +
166B HIS* 2.9 36.9 + - - +
199B LYS* 1.3 87.4 - - - +
201B GLU* 1.3 62.1 - - - +
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Residues in contact with GLU 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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164B THR* 3.4 7.1 - - - -
165B ALA 3.0 32.1 + - - -
167B TYR* 3.5 27.4 - - + -
199B LYS* 2.5 47.0 + - + +
200B ASP* 1.3 77.6 - - - +
202B THR* 1.3 69.9 + - - +
203B VAL* 3.9 1.2 - - - +
212B ASN* 3.9 18.6 - - + +
215B ARG* 5.4 7.7 + - - +
216B LEU* 4.3 7.5 - - + +
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Residues in contact with THR 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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163B ARG 3.6 11.9 + - - +
164B THR* 4.4 4.3 + - - -
201B GLU* 1.3 75.1 + - - +
203B VAL* 1.3 65.0 + - - +
204B SER* 3.7 24.0 - - - +
207B SER* 3.4 13.7 + - - +
212B ASN* 3.0 22.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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