Contacts of the helix formed by residues 188 - 203 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D GLU* 4.3 0.2 - - - -
130D LYS* 3.2 9.2 - - - +
134D GLN* 5.8 0.2 - - - -
139D ASP* 2.9 35.0 - - - -
187D ASN* 1.3 98.4 + - - +
189D PRO* 1.3 68.0 - - - +
190D LEU 3.5 1.8 - - - -
191D LEU* 4.0 17.3 - - + -
192D MET* 2.9 33.8 + - + +
314D PHE* 3.4 32.8 - + - -
315D ASN* 3.4 21.3 - - + -
318D GLN 4.4 0.4 - - - -
319D CYS* 3.8 3.8 - - - -
602D CQY 3.3 57.7 - + + -
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Residues in contact with PRO 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLU* 3.1 29.2 - - - +
128D GLY* 5.3 4.0 - - - -
130D LYS* 3.7 11.0 - - - -
184D ILE* 4.1 7.8 - - + +
185D PRO 4.4 10.8 - - - +
186D TRP 3.3 19.1 - - - +
187D ASN 3.6 2.0 - - - -
188D PHE* 1.3 86.8 - - - +
190D LEU* 1.3 60.5 + - - +
192D MET* 4.9 0.4 - - + -
193D PHE* 3.1 22.9 + - - +
215D THR* 3.5 38.8 - - + +
218D SER* 4.1 4.5 - - - +
219D ALA* 5.7 3.0 - - + +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 3.7 39.9 - - + -
124D GLU* 2.9 25.6 + - + +
139D ASP* 6.1 1.6 - - + -
140D LEU* 3.9 22.4 - - + -
143D VAL* 3.7 18.6 - - + -
189D PRO* 1.3 71.3 - - - +
191D LEU* 1.3 67.6 + - - +
193D PHE* 3.2 12.2 + - + +
194D ALA* 3.0 20.3 + - - +
218D SER* 3.7 15.9 + - - +
219D ALA 5.7 0.2 - - - +
222D MET* 3.5 35.2 - - + -
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLU* 4.6 0.8 + - - -
139D ASP* 4.4 13.3 + - - +
142D GLY* 3.6 33.2 - - - +
143D VAL* 3.7 12.3 - - + +
146D THR* 4.0 0.7 - - - +
188D PHE* 3.4 21.4 + - + +
189D PRO 3.4 0.4 - - - -
190D LEU* 1.3 78.8 - - - +
192D MET* 1.3 57.7 + - - +
194D ALA* 2.9 6.5 + - + +
195D TRP* 2.8 51.4 + - + +
602D CQY 3.5 52.3 - - + +
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Residues in contact with MET 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ILE* 4.2 15.7 - - + -
185D PRO* 3.6 41.3 - - + +
187D ASN* 3.2 23.3 - - - +
188D PHE* 2.9 33.4 + - + +
189D PRO 4.4 0.9 - - - +
191D LEU* 1.3 75.4 - - - +
193D PHE* 1.3 65.0 + - - +
195D TRP* 3.8 9.1 - - + +
196D LYS* 3.1 30.7 + - - +
262D THR* 3.9 10.1 - - + +
494D GLU* 5.8 1.3 - - - +
601D NAD 3.9 17.5 - - - -
602D CQY 3.7 24.7 - - + -
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Residues in contact with PHE 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D PHE* 4.8 0.2 - + - -
184D ILE* 3.8 11.7 - - + +
189D PRO 3.1 16.1 + - - +
190D LEU* 3.2 15.3 - - + +
192D MET* 1.3 75.7 - - - +
194D ALA* 1.3 63.4 + - - +
196D LYS* 3.3 3.6 + - - +
197D ILE* 3.1 57.6 + - + +
209D ILE* 3.8 37.9 - - + -
211D PRO* 5.8 0.2 - - + -
219D ALA* 3.9 24.2 - - + -
222D MET* 3.5 39.9 - - + -
226D ILE* 4.2 5.8 - - + -
236D ILE* 4.8 0.7 - - + -
238D ILE* 3.8 28.5 - - + -
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Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D VAL* 4.0 20.2 - - + -
146D THR* 3.5 19.2 - - + +
147D PHE* 3.9 27.4 - - + -
190D LEU 3.0 11.1 + - - +
191D LEU* 2.9 10.3 + - + +
193D PHE* 1.3 73.9 - - + +
195D TRP* 1.3 66.5 + - - +
196D LYS 3.2 0.7 + - - -
198D ALA* 3.2 29.8 + - - +
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Residues in contact with TRP 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D THR* 3.7 8.8 + - - -
191D LEU* 2.8 45.4 + - + +
192D MET* 3.8 10.5 - - + +
194D ALA* 1.3 76.6 - - - +
196D LYS* 1.3 59.2 + - + +
199D PRO* 3.2 21.6 - - - +
477D LEU* 4.6 21.3 - - + -
478D ASN 4.6 8.3 - - - -
483D PHE* 3.6 33.7 - + + -
494D GLU* 3.2 38.9 - - + +
495D MET* 3.2 57.2 + - + +
503D TYR* 5.4 0.2 + - - -
602D CQY 3.5 40.2 - + - -
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Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D GLN* 2.8 36.2 + - + +
183D ILE 4.2 0.9 - - - -
184D ILE* 3.5 21.2 - - + +
192D MET* 3.1 22.7 + - - +
193D PHE 3.7 4.0 - - - +
194D ALA 3.1 0.8 - - - -
195D TRP* 1.3 79.9 - - - +
197D ILE* 1.3 64.4 + - - +
199D PRO* 3.5 12.7 - - - +
200D ALA* 3.6 3.1 - - - +
209D ILE* 4.0 7.9 - - + -
260D ALA* 3.6 42.4 - - + -
261D PHE 4.5 1.2 + - - -
262D THR* 2.6 29.5 + - - -
284D THR* 6.0 0.2 - - - +
286D GLU* 4.9 0.4 - - - +
494D GLU* 2.5 32.3 + - - +
503D TYR* 3.9 3.3 + - - +
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Residues in contact with ILE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 4.2 9.6 - - + -
147D PHE* 3.7 24.5 - - + -
182D GLN* 3.7 17.5 - - - +
193D PHE* 3.1 48.6 + - + +
196D LYS* 1.3 75.5 - - - +
198D ALA* 1.3 70.7 + - - +
200D ALA* 3.1 3.6 + - - -
201D LEU* 2.8 49.2 + - + +
207D VAL* 4.0 16.2 - - + -
209D ILE* 4.1 11.9 - - + -
226D ILE* 4.5 7.6 - - + -
236D ILE* 4.7 3.8 - - + -
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 3.9 16.3 - - + +
146D THR* 3.9 6.1 - - + +
147D PHE* 3.7 20.0 - - + -
150D TYR* 3.8 26.0 - - + -
194D ALA 3.2 16.7 + - - +
197D ILE* 1.3 81.0 - - - +
199D PRO* 1.3 61.4 - - + +
202D CYS* 2.9 29.8 + - - +
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Residues in contact with PRO 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D TYR* 4.1 21.7 - - + +
195D TRP 3.2 26.5 - - - +
196D LYS 3.5 7.9 - - - +
198D ALA* 1.3 94.5 - - + +
200D ALA* 1.3 62.6 + - - +
202D CYS* 3.4 2.2 + - + +
203D CYS* 3.1 30.3 + - - -
494D GLU* 6.6 0.2 - - + -
495D MET 5.9 2.7 - - - +
499D GLY 4.4 5.8 - - - +
500D LEU* 4.0 20.4 - - + -
503D TYR* 3.9 23.8 - - + -
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Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D CYS* 5.0 0.7 - - - -
182D GLN* 3.7 8.1 - - - +
196D LYS 3.6 16.2 - - - +
197D ILE 3.1 3.9 + - - +
199D PRO* 1.3 82.2 - - - +
201D LEU* 1.3 60.5 + - - +
204D GLY 3.4 2.1 + - - -
205D ASN* 2.9 35.8 + - + +
207D VAL* 3.7 17.5 - - + -
503D TYR* 3.6 31.6 - - + -
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Residues in contact with LEU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D TRP* 3.6 13.7 - - + -
102D ARG* 3.6 12.9 - - - +
106D LEU* 4.1 21.8 - - + -
109D LEU* 5.5 0.2 - - + -
197D ILE* 2.8 39.0 + - + +
198D ALA 4.2 1.1 - - - +
200D ALA* 1.3 67.5 - - - +
202D CYS* 1.3 62.1 + - - +
203D CYS 3.1 2.0 - - - -
204D GLY* 2.8 20.7 + - - +
205D ASN 3.9 9.4 - - - +
207D VAL* 4.2 10.5 - - + -
231D PHE* 4.0 12.6 - - + -
235D VAL* 3.6 33.0 - - + +
236D ILE* 3.6 31.9 - - + -
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Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ARG* 2.8 21.2 + - - +
106D LEU* 4.0 9.8 - - + +
150D TYR* 3.5 18.8 - - + +
153D TRP* 3.5 33.0 - - - -
154D ALA* 3.5 21.4 - - - +
157D ILE* 3.8 6.4 - - - +
198D ALA 2.9 20.5 + - - +
199D PRO* 3.6 7.0 - - + +
201D LEU* 1.3 75.7 - - - +
203D CYS* 1.3 55.9 + - - +
500D LEU* 3.6 16.6 - - + -
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Residues in contact with CYS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ARG* 3.7 7.8 + - - +
157D ILE* 4.1 15.0 - - - -
174D HIS 5.4 1.0 - - - +
175D GLU 4.8 0.2 - - - -
176D PRO* 3.4 23.7 - - - +
199D PRO 3.1 16.7 + - - +
201D LEU 3.1 0.6 - - - -
202D CYS* 1.3 75.9 - - - +
204D GLY* 1.3 58.1 + - - +
205D ASN* 3.6 8.5 - - - +
500D LEU* 3.6 42.4 - - - -
503D TYR* 3.5 23.3 - - - +
504D SER* 3.9 12.7 + - - +
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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