Contacts of the strand formed by residues 187 - 199 (chain B) in PDB entry 4X3G
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 PHE 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B GLN 3.8 0.9 - - - +
183B SER* 3.6 4.7 + - - -
184B CYS 3.0 32.7 + - - +
185B PHE 3.3 21.8 - - - -
186B GLY* 1.3 81.4 - - - +
188B HIS* 1.3 66.0 + - - +
189B PHE* 3.9 7.5 - - + -
211B LEU* 3.5 30.3 - - + -
212B ILE 4.3 11.7 - - - -
217B GLN* 3.5 50.7 - - + -
221B PHE* 3.5 19.7 - + - -
281B MET* 5.0 5.4 - - + -
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Residues in contact with HIS 188 (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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145B MET* 3.5 50.5 - - + +
149B MET* 4.8 7.6 - - + -
157B THR* 3.9 19.7 - - + +
181B MET* 4.7 3.5 - - + -
182B GLN 3.5 2.9 - - - +
183B SER* 3.5 23.9 + - - -
186B GLY 5.4 2.7 - - - -
187B PHE* 1.3 81.5 - - - +
189B PHE* 1.3 62.1 + - - +
211B LEU* 4.0 2.9 - - - +
212B ILE* 3.0 36.4 + - + +
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Residues in contact with PHE 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B MET* 3.2 6.1 - - - -
182B GLN* 2.7 49.3 + - + +
184B CYS* 3.9 14.6 - - - -
187B PHE* 3.9 19.3 - - + -
188B HIS* 1.3 76.8 - - - +
190B MET* 1.3 59.8 + - - +
191B LEU* 3.7 0.6 + - + -
209B VAL* 3.9 22.2 - - + -
210B GLN 3.2 10.3 - - - +
211B LEU* 3.6 25.4 - - + -
212B ILE* 4.3 2.7 - - - -
221B PHE* 3.6 31.0 - + - -
240B PRO* 3.9 22.9 - - + -
279B ILE* 3.6 37.7 - - + -
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Residues in contact with MET 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO* 3.3 51.4 - - + +
130B CYS* 4.0 5.6 - - - +
148B LEU* 4.0 23.3 - - + -
155B ILE* 4.9 5.6 - - + -
179B VAL* 3.7 30.5 - - + -
180B MET 3.6 4.5 - - - +
181B MET* 4.3 13.0 - - + -
189B PHE* 1.3 71.6 - - - +
191B LEU* 1.3 60.8 + - - +
192B VAL* 3.8 13.1 + - + +
208B ILE 3.9 1.2 - - - +
209B VAL* 3.4 4.7 - - - -
210B GLN* 2.7 50.0 + - + +
212B ILE* 4.1 12.4 - - + +
243B ILE* 5.2 0.9 - - + -
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Residues in contact with LEU 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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163B ILE* 3.7 21.8 - - + -
165B PHE* 3.7 18.7 - - + -
178B TRP 3.8 0.5 - - - +
179B VAL* 3.4 4.9 - - - +
180B MET* 2.9 53.5 + - + +
182B GLN* 3.6 42.4 - - + +
189B PHE 4.1 1.3 - - - +
190B MET* 1.3 72.6 - - - +
192B VAL* 1.3 60.1 + - - +
208B ILE 3.9 4.3 - - - +
209B VAL* 3.7 35.0 - - + -
225B LEU* 6.4 0.2 - - + -
277B VAL* 3.8 16.6 - - + -
279B ILE* 4.4 0.7 - - + -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PRO 5.4 0.9 - - - +
131B PRO* 3.9 21.5 - - + -
165B PHE* 4.0 6.0 - - - -
177B ASP* 4.4 4.7 - - - +
178B TRP 3.3 8.5 - - - +
179B VAL* 4.0 9.9 - - + -
190B MET* 3.8 25.4 - - + +
191B LEU* 1.3 78.8 - - - +
193B LEU* 1.4 71.6 + - - +
194B GLU* 4.6 6.5 - - + +
206B PHE 3.8 1.2 - - - +
207B ALA* 3.4 3.8 - - - +
208B ILE* 3.0 40.2 + - + +
210B GLN* 4.8 4.5 - - + +
247B ILE* 4.1 26.9 - - + -
251B ILE* 6.0 0.2 - - + -
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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
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165B PHE* 4.1 10.3 - - + -
167B ALA* 3.7 22.4 - - + -
170B ILE* 4.3 7.6 - - + -
177B ASP* 3.6 4.3 - - - +
178B TRP* 2.8 71.4 + - + +
192B VAL* 1.4 73.2 - - - +
194B GLU* 1.3 61.3 + - - +
205B PHE* 3.9 26.2 - - + -
206B PHE 3.4 15.5 - - - +
207B ALA* 4.1 7.0 - - + -
259B PHE* 4.0 18.8 - - + -
273B LEU* 4.6 3.6 - - + -
275B ILE* 4.1 11.7 - - + -
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Residues in contact with GLU 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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131B PRO* 5.2 3.1 - - - +
176B VAL 3.7 3.1 - - - +
177B ASP* 3.4 24.8 - - - +
192B VAL* 4.8 5.9 - - + +
193B LEU* 1.3 74.5 - - - +
195B LYS* 1.3 63.6 + - - +
196B GLN* 2.8 36.3 + - + +
204B GLN 3.6 1.4 - - - +
205B PHE* 3.3 7.8 - - - -
206B PHE* 2.9 45.5 + - + +
247B ILE* 5.1 4.2 - - - +
251B ILE* 3.8 24.8 - - + +
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Residues in contact with LYS 195 (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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170B ILE 3.7 15.3 + - - +
171B ASN* 4.9 5.1 + - - +
172B LEU 3.4 26.7 - - - +
173B PRO* 4.9 2.7 - - - -
174B GLY 3.9 11.0 - - - +
175B ALA* 3.4 10.8 - - - +
176B VAL* 2.7 41.4 + - + +
178B TRP* 4.2 4.3 - - + -
194B GLU* 1.3 75.2 - - - +
196B GLN* 1.3 63.5 + - - +
203B GLN* 3.5 41.0 + - + +
204B GLN 3.5 6.5 - - - +
205B PHE* 3.5 35.2 - - + -
261B THR* 3.5 13.3 - - - +
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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
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174B GLY 5.1 0.9 - - - -
175B ALA* 5.3 2.2 - - - +
194B GLU* 2.8 29.5 + - + +
195B LYS* 1.3 75.8 - - - +
197B GLU* 1.3 60.6 + - - +
198B LYS* 3.4 40.6 - - + +
202B HIS 4.1 0.2 - - - +
203B GLN* 3.2 8.1 - - - +
204B GLN* 2.8 40.2 + - + +
206B PHE* 3.3 31.1 - - + -
251B ILE* 3.5 15.9 - - - +
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO* 5.6 0.7 - - - +
174B GLY* 3.8 32.3 + - - +
175B ALA* 5.6 3.0 - - + +
196B GLN* 1.3 74.0 - - - +
198B LYS* 1.3 66.3 + - - +
199B TYR 3.3 17.2 - - - +
200B ASP* 4.1 2.9 - - - -
201B GLY* 3.1 26.6 + - - -
202B HIS 3.5 11.2 - - - +
203B GLN* 3.7 21.3 + - + +
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Residues in contact with LYS 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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196B GLN* 3.4 42.9 - - + +
197B GLU* 1.3 76.0 - - - +
199B TYR* 1.3 78.6 + - + +
200B ASP 4.4 0.2 + - - -
202B HIS 4.4 1.2 + - - -
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Residues in contact with TYR 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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199A TYR* 4.1 39.2 + - + -
197B GLU* 3.4 7.9 - - - +
198B LYS* 1.3 93.1 - - + +
200B ASP* 1.3 64.6 + - - +
201B GLY 3.4 0.7 + - - -
202B HIS* 3.0 44.5 + - + +
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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