Contacts of the helix formed by residues 184 - 200 (chain D) in PDB entry 6F0X
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 184 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 5.2 0.9 - - - -
141D TYR* 3.5 9.4 + - - -
183D THR* 1.3 73.0 - - - +
185D LYS* 1.3 50.3 + - - -
187D SER* 3.2 2.7 - - - -
188D LEU* 2.3 38.1 + - - +
901D AGS 2.3 55.6 + - - -
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Residues in contact with LYS 185 (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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141D TYR* 4.7 0.7 - - + -
177D LEU* 4.8 11.9 - - + -
178D HIS* 3.4 34.1 - - - +
179D GLY* 3.4 28.0 - - - +
180D PRO 3.5 14.5 + - - -
181D PRO* 4.2 2.6 - - - +
182D GLY 4.2 0.4 - - - +
183D THR* 2.9 14.5 + - - +
184D GLY* 1.3 58.0 - - - +
186D THR* 1.3 64.4 + - - +
188D LEU* 2.8 18.0 + - + +
189D CYS* 2.9 19.0 + - - -
298D THR* 3.5 21.1 - - + +
299D SER 3.5 14.8 + - - +
300D ASN* 5.3 0.6 - - - +
319D ILE* 5.0 6.5 - - + -
901D AGS 1.3 78.8 + - - +
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Residues in contact with THR 186 (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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185D LYS* 1.3 67.9 - - - +
187D SER* 1.3 62.2 + - - -
189D CYS* 3.3 4.8 + - - +
190D LYS* 3.0 52.6 + - + +
211D GLU* 5.4 3.4 - - - +
250D LEU* 4.9 11.0 - - + -
251D ILE 6.0 0.4 - - - +
252D ASP* 2.7 39.0 + - + +
298D THR* 3.9 8.9 - - - +
901D AGS 2.3 49.7 + - - -
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Residues in contact with SER 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU* 3.9 10.2 - - - +
139D LEU* 3.3 16.2 - - - +
184D GLY 3.2 5.2 - - - -
186D THR* 1.3 62.1 - - - +
188D LEU* 1.3 61.7 + - - +
190D LYS* 3.3 12.2 + - - +
191D ALA* 3.0 20.8 + - - +
901D AGS 1.3 90.8 + - - -
288E LYS* 5.7 1.0 + - - -
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D TRP* 4.6 17.9 - - + -
139D LEU* 3.6 16.5 - - + +
141D TYR* 3.0 53.6 - - + +
145D VAL* 4.8 7.4 - - + -
146D LYS* 4.8 5.6 - - + -
149D LEU* 4.5 14.1 - - + -
177D LEU* 3.5 29.2 - - + -
184D GLY 2.3 23.5 + - - +
185D LYS* 2.8 9.0 + - - +
187D SER* 1.3 70.0 - - - +
189D CYS* 1.3 57.5 + - - +
191D ALA* 3.8 0.3 - - - -
192D LEU* 2.8 32.3 + - + +
319D ILE* 5.6 0.4 - - + -
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Residues in contact with CYS 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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149D LEU* 5.9 1.6 - - - -
177D LEU* 4.5 23.1 - - - -
185D LYS 2.9 17.5 + - - -
186D THR* 3.8 5.2 - - - +
188D LEU* 1.3 75.7 - - - +
190D LYS* 1.3 66.5 + - - +
192D LEU* 3.3 7.1 + - - +
193D ALA* 3.0 17.5 + - - +
250D LEU* 3.5 15.2 - - + +
296D LEU* 3.4 46.3 - - + +
297D THR 4.7 0.7 - - - -
298D THR* 4.0 17.7 - - - -
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Residues in contact with LYS 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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125D TRP* 3.9 25.6 - - + -
132D PHE* 3.4 42.4 - - + -
135D LEU* 5.6 0.2 - - + -
186D THR* 3.0 39.8 + - - +
187D SER* 3.5 11.8 + - - +
189D CYS* 1.3 79.6 - - - +
191D ALA* 1.3 65.5 + - - +
193D ALA* 3.0 5.0 + - - +
194D GLN* 3.0 20.7 + - - +
209D LEU* 5.0 3.5 - - + +
211D GLU* 4.4 9.2 + - - -
250D LEU* 3.6 25.1 - - + +
285E ASP* 5.9 4.9 - - - +
289E ARG* 5.0 8.3 - - - +
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Residues in contact with ALA 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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132D PHE* 4.6 0.7 - - - -
135D LEU* 3.5 25.7 - - + +
136D TRP* 3.4 36.5 - - + +
139D LEU* 3.6 15.7 - - + -
187D SER 3.0 3.4 + - - -
188D LEU 4.0 0.2 - - - +
190D LYS* 1.3 77.6 - - - +
192D LEU* 1.3 66.4 + - - +
194D GLN* 3.2 9.8 - - - +
195D LYS* 3.0 22.0 + - - +
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Residues in contact with LEU 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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136D TRP* 3.4 33.8 - - + -
149D LEU* 3.5 38.8 - - + +
150D LEU* 4.1 12.6 - - + +
153D VAL* 5.5 2.9 - - + -
188D LEU* 2.8 20.7 + - + +
189D CYS* 3.3 6.5 - - - +
191D ALA* 1.3 79.1 - - - +
193D ALA* 1.3 66.8 + - - +
195D LYS* 3.0 1.4 + - - +
196D LEU* 2.8 52.6 + - + +
294D VAL* 6.0 0.2 - - + -
296D LEU* 4.4 20.2 - - + -
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Residues in contact with ALA 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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127D LEU* 5.2 9.4 - - + -
189D CYS 3.0 9.2 + - - +
190D LYS* 3.7 7.0 - - - +
192D LEU* 1.3 78.4 - - - +
194D GLN* 1.3 64.0 + - - +
196D LEU* 3.3 12.7 - - - +
197D THR* 2.9 30.2 + - - -
209D LEU* 5.2 5.8 - - + -
248D PHE* 3.5 38.1 - - + -
250D LEU* 6.1 0.2 - - + -
296D LEU* 4.5 2.9 - - + -
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Residues in contact with GLN 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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102D LEU* 4.6 6.7 - - - +
127D LEU* 4.9 7.9 - - - +
128D PRO* 3.1 44.8 - - - +
129D ALA 3.3 20.6 + - - +
132D PHE* 3.6 38.5 - - + +
133D HIS* 4.5 7.8 + - - +
136D TRP* 6.1 2.2 - - + +
190D LYS 3.0 11.1 + - - +
191D ALA* 3.2 14.6 - - + +
193D ALA* 1.3 79.0 - - - +
195D LYS* 1.3 65.0 + - - +
197D THR* 3.8 3.8 - - - -
198D ILE* 3.0 33.4 + - + +
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Residues in contact with LYS 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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24D GLU* 2.6 42.7 + - - +
136D TRP* 3.4 51.6 - - + +
137D ASP* 4.9 4.7 + - - -
150D LEU* 4.5 12.1 - - + -
191D ALA 3.0 7.7 + - - +
192D LEU 3.0 8.4 + - - +
194D GLN* 1.3 81.0 - - - +
196D LEU* 1.3 63.4 + - - +
198D ILE* 3.1 28.7 - - + +
199D ARG* 2.9 44.3 + - + +
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Residues in contact with LEU 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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150D LEU* 3.6 39.5 - - + +
153D VAL* 4.1 22.7 - - + -
154D MET 5.7 0.4 - - - +
192D LEU* 2.8 43.2 + - + +
193D ALA* 3.3 8.3 - - - +
194D GLN 3.1 0.2 - - - -
195D LYS* 1.3 74.5 - - - +
197D THR* 1.3 57.2 + - - +
199D ARG* 2.7 29.5 + - + +
200D LEU* 3.1 22.6 + - + +
246D LEU* 5.3 0.7 - - + -
248D PHE* 3.5 35.9 - - + -
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Residues in contact with THR 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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127D LEU* 3.3 20.2 - - + +
128D PRO* 3.5 29.7 - - + +
193D ALA 2.9 17.9 + - - -
194D GLN 3.9 3.1 - - - -
196D LEU* 1.3 73.1 - - - +
198D ILE* 1.3 64.6 + - - +
200D LEU* 3.5 10.0 + - - +
201D SER* 3.9 9.2 + - - -
204D TYR* 5.7 4.5 - - + +
206D TYR* 4.3 8.7 - - - -
207D GLY* 4.0 20.9 - - - +
246D LEU* 4.3 11.9 - - + +
248D PHE* 3.7 8.5 - - - -
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Residues in contact with ILE 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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24D GLU* 5.2 6.7 - - + -
98D HIS* 3.9 27.0 + - + +
100D PHE* 4.2 44.2 - - + +
128D PRO* 4.2 15.0 - - + +
133D HIS* 6.0 0.9 - - - +
194D GLN* 3.0 30.4 + - + +
195D LYS* 3.1 41.5 - - + +
196D LEU 3.0 0.2 - - - -
197D THR* 1.3 78.5 - - - +
199D ARG* 1.3 68.5 + - + +
200D LEU 2.9 1.7 + - - -
201D SER* 3.7 10.0 + - - -
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Residues in contact with ARG 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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22D HIS* 3.6 47.6 + - + +
23D VAL 5.6 0.2 - - - +
24D GLU* 4.9 13.3 + - - +
76D ILE* 4.4 19.8 + - - +
77D ASP 4.9 8.1 + - - -
98D HIS* 3.1 32.8 + - - -
136D TRP* 5.5 2.6 - - - +
150D LEU* 4.5 28.0 - - + +
154D MET* 5.7 2.7 - - - -
195D LYS* 2.9 38.5 + - + +
196D LEU* 2.7 16.2 + - + +
198D ILE* 1.3 76.7 - - - +
200D LEU* 1.3 72.3 + - + +
201D SER 3.6 1.4 + - - -
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Residues in contact with LEU 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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153D VAL* 4.4 32.1 - - + +
154D MET* 3.7 31.0 - - + +
157D LEU* 4.6 18.8 - - + -
196D LEU* 3.1 21.8 + - + +
197D THR* 3.5 7.3 + - - +
198D ILE 2.9 2.6 + - - -
199D ARG* 1.3 93.2 - - + +
201D SER* 1.3 65.3 + - - +
202D SER* 3.6 3.1 - - - -
203D ARG* 3.9 2.4 + - + -
204D TYR* 3.2 34.6 - - + +
246D LEU* 4.9 10.3 - - + -
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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
------------------------------------------------------------
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