Contacts of the helix formed by residues 188 - 203 (chain B) in PDB entry 6B5G
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 188 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 4.1 0.9 - - - -
130B LYS* 3.6 6.1 - - - +
138B VAL* 5.4 0.2 - - + -
139B ASP* 3.1 34.1 - - - -
186B TRP 4.8 0.2 - - - -
187B ASN* 1.3 94.8 + - - +
189B PRO* 1.3 59.1 - - - +
190B LEU 3.4 1.8 - - - -
191B LEU* 3.2 18.9 + - + -
192B MET* 2.7 42.9 + - + +
314B PHE* 3.6 31.4 - + - -
315B ASN* 3.2 23.6 - - + -
319B CYS* 3.6 6.5 - - - -
602B CQY 3.5 67.3 - + - -
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Residues in contact with PRO 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B GLU* 3.1 23.1 - - - +
128B GLY* 5.4 3.1 - - - -
130B LYS* 3.8 8.1 - - - -
184B ILE* 4.2 6.4 - - + +
185B PRO 4.5 10.5 - - - +
186B TRP 3.2 19.5 - - - +
187B ASN 3.6 2.2 - - - -
188B PHE* 1.3 87.9 - - - +
190B LEU* 1.3 57.5 + - - +
192B MET* 3.9 2.8 - - + +
193B PHE* 3.1 26.7 + - - +
215B THR* 3.3 36.6 - - + +
218B SER* 3.9 12.8 - - - +
219B ALA* 5.5 3.9 - - + +
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Residues in contact with LEU 190 (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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120B LEU* 3.8 28.0 - - + +
124B GLU* 2.9 27.6 + - + +
139B ASP* 6.0 2.7 - - + -
140B LEU* 3.8 31.0 - - + -
143B VAL* 3.7 19.5 - - + +
189B PRO* 1.3 72.8 - - - +
191B LEU* 1.3 61.9 + - - +
193B PHE* 3.2 11.6 + - + +
194B ALA* 3.0 23.0 + - - +
218B SER* 4.0 15.9 - - - +
222B MET* 3.4 34.3 - - + -
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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
----------------------------------------------------------
124B GLU* 4.5 0.8 + - - -
139B ASP* 4.3 15.8 + - - +
142B GLY* 3.5 35.4 - - - +
143B VAL* 3.7 12.5 - - + +
146B THR* 4.1 1.1 - - - +
188B PHE* 3.2 21.9 + - + +
190B LEU* 1.3 73.7 - - - +
192B MET* 1.3 62.3 + - - +
194B ALA* 3.3 1.0 + - + -
195B TRP* 2.8 53.6 + - + +
602B CQY 3.8 52.9 - - + -
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Residues in contact with MET 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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184B ILE* 3.7 23.6 - - + -
185B PRO* 4.1 16.4 - - + +
187B ASN* 4.8 1.1 - - - +
188B PHE* 2.7 37.1 + - + +
189B PRO* 3.9 4.0 - - + +
191B LEU* 1.3 72.0 - - - +
193B PHE* 1.3 62.1 + - - +
195B TRP* 3.4 5.6 + - + +
196B LYS* 3.1 43.6 + - - +
262B THR* 3.5 41.7 - - + +
494B GLU* 5.0 4.3 - - - +
601B NAD 4.5 4.5 - - - +
602B CQY 3.5 30.5 - - + -
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Residues in contact with PHE 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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147B PHE* 5.0 0.7 - + - -
184B ILE* 4.1 9.6 - - + +
189B PRO 3.1 16.1 + - - +
190B LEU* 3.3 14.6 - - + +
191B LEU 3.2 0.2 - - - -
192B MET* 1.3 77.5 - - - +
194B ALA* 1.3 64.6 + - - +
196B LYS* 3.2 2.4 + - - +
197B ILE* 3.1 52.8 + - + +
209B ILE* 3.8 39.3 - - + -
219B ALA* 3.8 28.9 - - + -
222B MET* 3.6 37.0 - - + -
226B ILE* 4.2 7.6 - - + -
236B ILE* 4.7 0.7 - - + -
238B ILE* 3.8 24.0 - - + -
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Residues in contact with ALA 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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143B VAL* 4.1 15.3 - - + -
146B THR* 4.1 20.6 - - + +
147B PHE* 3.9 33.4 - - + -
190B LEU 3.0 13.3 + - - +
191B LEU* 3.8 6.3 - - - +
193B PHE* 1.3 77.0 - - + +
195B TRP* 1.3 63.2 + - - +
196B LYS 2.9 1.6 + - - -
198B ALA* 3.0 28.9 + - - +
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Residues in contact with TRP 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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146B THR* 3.6 28.8 + - + -
191B LEU* 2.8 39.4 + - + +
192B MET* 3.7 11.4 - - + +
194B ALA* 1.3 72.0 - - - +
196B LYS* 1.3 57.9 + - - +
199B PRO* 3.2 22.3 - - - +
477B LEU* 4.6 17.9 - - + -
478B ASN 3.9 13.5 - - - -
479B ALA 4.8 3.6 - - - +
483B PHE* 4.1 32.8 - + + -
494B GLU* 3.6 17.5 - - + +
495B MET* 3.0 57.3 - - + +
503B TYR* 5.4 0.3 + - - -
601B NAD 5.4 0.9 - - - -
602B CQY 3.7 43.5 - + + -
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Residues in contact with LYS 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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182B GLN* 2.8 38.3 + - + +
183B ILE 4.1 1.3 - - - -
184B ILE* 3.6 20.0 - - + -
192B MET* 3.1 26.2 + - + +
193B PHE 3.7 3.4 - - - +
194B ALA 3.0 1.0 - - - -
195B TRP* 1.3 78.3 - - - +
197B ILE* 1.3 64.9 + - - +
198B ALA 3.4 0.4 - - - -
199B PRO* 3.8 2.4 - - - +
200B ALA* 3.4 10.9 + - - +
209B ILE* 4.0 6.7 - - + -
260B ALA* 3.5 41.3 - - + -
261B PHE 4.8 0.2 - - - -
262B THR* 2.6 29.2 + - - -
494B GLU* 2.6 28.3 + - - +
503B TYR* 3.8 6.9 + - - +
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Residues in contact with ILE 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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109B LEU* 4.2 9.0 - - + -
147B PHE* 3.8 26.0 - - + -
182B GLN* 3.6 15.9 - - - +
193B PHE* 3.1 47.7 + - + +
196B LYS* 1.3 75.1 - - - +
198B ALA* 1.3 58.9 + - - +
200B ALA* 3.2 4.0 + - - -
201B LEU* 2.7 62.1 + - + +
207B VAL* 4.2 12.6 - - + -
209B ILE* 4.1 12.6 - - + -
226B ILE* 4.4 9.2 - - + -
236B ILE* 4.5 5.4 - - + -
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Residues in contact with ALA 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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106B LEU* 3.8 13.2 - - + +
146B THR* 4.0 7.2 - - + +
147B PHE* 3.9 21.3 - - + -
150B TYR* 3.9 24.0 - - + -
194B ALA 3.0 18.9 + - - +
197B ILE* 1.3 78.8 - - - +
199B PRO* 1.3 61.0 - - + +
202B CYS* 2.9 31.5 + - - +
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Residues in contact with PRO 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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150B TYR* 3.7 43.7 - - + +
194B ALA 3.9 0.2 - - - +
195B TRP 3.2 30.1 - - - +
196B LYS 3.8 4.7 - - - +
198B ALA* 1.3 90.4 - - + +
200B ALA* 1.3 62.3 - - - +
202B CYS* 3.7 0.9 - - + +
203B CYS* 3.2 28.9 + - - -
495B MET* 5.1 4.7 - - + +
499B GLY 5.0 5.2 - - - +
500B LEU* 4.5 4.3 - - + -
502B GLU* 6.0 0.2 - - - +
503B TYR* 4.0 21.8 - - + +
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Residues in contact with ALA 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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180B CYS* 5.0 0.2 - - + -
182B GLN* 3.5 7.6 - - - +
196B LYS 3.4 16.8 + - - +
197B ILE 3.2 4.3 + - - +
199B PRO* 1.3 81.7 - - - +
201B LEU* 1.3 60.3 + - - +
203B CYS 3.4 4.0 + - - -
205B ASN* 3.1 34.7 + - + +
207B VAL* 3.8 17.0 - - + -
503B TYR* 3.5 32.3 - - + -
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Residues in contact with LEU 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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94B TRP* 3.6 13.5 - - + -
102B ARG* 3.3 15.7 - - - +
106B LEU* 4.4 13.2 - - + -
197B ILE* 2.7 44.6 + - + +
198B ALA 4.2 1.3 - - - +
200B ALA* 1.3 67.7 - - - +
202B CYS* 1.3 65.8 + - - +
203B CYS 3.1 1.8 - - - -
204B GLY* 2.9 12.7 + - - +
205B ASN 3.7 10.8 - - - +
207B VAL* 4.3 7.9 - - + -
231B PHE* 3.9 17.3 - - + -
235B VAL* 3.5 33.9 - - + +
236B ILE* 3.6 31.6 - - + -
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Residues in contact with CYS 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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102B ARG* 2.7 26.5 + - - +
106B LEU* 3.9 9.9 - - + +
150B TYR* 3.3 28.7 - - + +
153B TRP* 3.5 24.5 - - - -
154B ALA* 3.6 20.6 - - - +
157B ILE* 3.9 5.0 - - - +
198B ALA 2.9 19.7 + - - +
199B PRO* 3.7 6.7 - - + +
201B LEU* 1.3 76.1 - - - +
203B CYS* 1.3 51.6 + - - +
500B LEU* 3.8 15.7 - - - -
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Residues in contact with CYS 203 (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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102B ARG* 3.6 7.1 + - - +
157B ILE* 4.0 15.0 - - - -
174B HIS 5.6 0.2 - - - +
175B GLU 4.6 0.5 - - - -
176B PRO* 3.3 25.7 - - - +
199B PRO 3.2 17.2 + - - +
201B LEU 3.1 1.0 - - - -
202B CYS* 1.3 78.0 - - - +
204B GLY* 1.3 58.5 + - - +
205B ASN* 3.5 5.8 - - - +
500B LEU* 3.6 43.7 - - - -
503B TYR* 3.5 24.7 - - + +
504B SER* 4.7 7.4 - - - +
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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