Contacts of the helix formed by residues 184 - 200 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F LEU* 3.3 20.9 - - - +
141F TYR* 2.7 17.7 + - - -
182F GLY 3.3 5.5 + - - -
183F THR* 1.3 76.7 - - - +
185F LYS* 1.3 54.9 + - - +
187F SER* 3.7 12.8 - - - -
188F LEU* 2.6 30.4 + - - +
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Residues in contact with LYS 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F TYR* 4.6 0.7 - - - -
177F LEU* 5.5 11.2 - - + -
178F HIS* 4.6 11.4 - - - +
179F GLY* 4.5 17.7 - - - +
180F PRO 3.1 29.2 - - - -
181F PRO* 3.5 6.0 - - - +
182F GLY* 2.8 25.4 - - - +
183F THR* 3.3 20.6 - - - +
184F GLY* 1.3 72.8 - - - +
186F THR* 1.3 67.2 + - - +
187F SER 3.1 1.3 - - - +
188F LEU* 3.1 6.2 + - - +
189F CYS* 2.9 34.3 + - - -
298F THR* 5.0 5.8 - - + -
300F ASN* 5.0 14.9 + - - +
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Residues in contact with THR 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F LYS* 1.3 81.1 + - - +
187F SER* 1.3 57.2 + - - +
189F CYS* 3.1 11.0 + - - +
190F LYS* 2.9 53.7 + - - +
250F LEU* 3.9 17.7 - - + -
252F ASP* 3.0 30.2 + - + +
298F THR* 3.8 14.6 - - + +
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Residues in contact with SER 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135F LEU* 3.4 25.1 - - - +
139F LEU* 3.5 22.0 - - - -
184F GLY* 3.7 11.8 - - - -
185F LYS 3.1 0.6 - - - -
186F THR* 1.3 79.5 - - - +
188F LEU* 1.3 57.7 + - - +
190F LYS* 3.3 7.3 + - - +
191F ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F TRP* 4.2 33.7 - - + +
139F LEU* 3.7 7.4 - - + +
141F TYR* 3.8 31.4 - - + +
145F VAL* 4.6 13.5 - - + +
146F LYS* 5.7 6.7 - - + -
149F LEU* 3.8 29.4 - - + -
177F LEU* 6.1 4.5 - - + -
184F GLY 2.6 22.9 + - - +
185F LYS* 3.6 6.3 - - - +
187F SER* 1.3 70.8 - - - +
189F CYS* 1.3 61.3 + - - +
191F ALA* 4.6 3.1 - - + +
192F LEU* 2.7 32.7 + - + +
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Residues in contact with CYS 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175F VAL* 4.6 17.3 - - - -
185F LYS 2.9 24.1 + - - -
186F THR 3.1 8.0 + - - +
188F LEU* 1.3 77.5 - - - +
190F LYS* 1.3 56.8 + - - +
192F LEU* 3.2 11.1 + - - +
193F ALA* 2.9 28.1 + - - +
250F LEU* 3.7 19.3 - - + -
296F LEU* 4.0 17.2 - - + +
297F THR 4.5 7.0 - - - -
298F THR* 3.7 25.1 - - - -
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Residues in contact with LYS 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125F TRP* 3.7 27.1 - - + -
132F PHE* 3.4 41.9 - - + -
135F LEU* 4.3 0.9 - - + -
186F THR* 2.9 39.4 + - - +
187F SER* 3.6 9.6 - - - +
188F LEU 3.2 0.2 - - - -
189F CYS* 1.3 71.3 - - - +
191F ALA* 1.3 63.2 + - - +
192F LEU 2.9 4.9 + - - -
193F ALA* 3.1 6.4 + - - +
194F GLN* 3.0 19.5 + - - +
209F LEU* 4.2 20.2 - - + +
211F GLU* 5.4 4.0 + - - -
250F LEU* 3.7 20.6 - - + -
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Residues in contact with ALA 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE* 5.5 1.8 - - - -
135F LEU* 3.5 20.3 - - + +
136F TRP* 3.1 46.9 - - + +
139F LEU* 5.9 0.2 - - + -
187F SER 3.0 17.2 + - - +
188F LEU* 4.3 5.6 - - + +
190F LYS* 1.3 75.5 - - - +
192F LEU* 1.3 56.2 + - - +
194F GLN* 3.1 11.9 - - + +
195F LYS* 2.9 22.3 + - - +
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F TRP* 3.7 26.7 - - + -
149F LEU* 3.8 45.8 - - + +
150F LEU* 5.0 2.0 - - + +
152F TYR* 5.9 0.2 - - + -
153F VAL* 5.1 2.7 - - + -
175F VAL* 4.6 21.1 - - + -
188F LEU* 2.7 21.8 + - + +
189F CYS* 3.2 11.9 - - - +
190F LYS 2.9 0.2 - - - -
191F ALA* 1.3 74.9 - - - +
193F ALA* 1.3 61.2 + - - +
194F GLN 3.1 0.9 - - - -
195F LYS* 3.1 1.4 + - + -
196F LEU* 2.8 58.9 + - + +
296F LEU* 4.9 4.3 - - + -
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Residues in contact with ALA 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F LEU* 3.3 10.8 - - + +
189F CYS 2.9 13.2 + - - +
190F LYS 3.1 8.3 + - - +
192F LEU* 1.3 74.1 - - - +
194F GLN* 1.3 65.6 + - - +
196F LEU* 3.2 2.1 + - - +
197F THR* 3.0 25.1 + - - -
209F LEU* 4.3 15.0 - - + -
248F PHE* 3.5 45.9 - - + -
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Residues in contact with GLN 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F VAL 5.4 0.9 - - - +
127F LEU* 4.0 7.6 - - - +
128F PRO* 3.2 50.8 + - - +
129F ALA 4.1 4.7 - - - +
132F PHE* 4.5 17.6 + - + +
133F HIS* 4.0 20.7 + - - -
134F GLY 5.1 4.9 - - - +
136F TRP* 5.3 5.8 - - + +
190F LYS 3.0 9.2 + - - +
191F ALA* 3.1 19.7 - - + +
193F ALA* 1.3 77.8 - - - +
195F LYS* 1.3 64.1 + - - +
197F THR* 3.1 4.8 + - - -
198F ILE* 2.9 44.2 + - + +
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Residues in contact with LYS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F TRP* 3.3 73.6 - - + +
150F LEU* 5.6 4.0 - - + -
191F ALA 2.9 9.3 + - - +
192F LEU* 3.1 2.7 + - + +
194F GLN* 1.3 73.1 - - - +
196F LEU* 1.3 58.2 + - + +
198F ILE* 3.4 39.9 - - + +
199F ARG* 2.8 56.3 + - + +
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F LEU* 4.2 24.9 - - + +
153F VAL* 3.6 42.8 - - + -
154F MET 4.5 1.8 - - - +
192F LEU* 2.8 46.1 + - + +
193F ALA 3.5 4.0 - - - +
194F GLN 3.1 0.2 - - - -
195F LYS* 1.3 74.7 - - + +
197F THR* 1.3 60.6 + - - +
199F ARG* 3.5 1.7 + - - -
200F LEU* 2.9 42.3 + - + +
246F LEU* 4.1 7.6 - - + -
248F PHE* 3.5 34.1 - - + -
296F LEU* 5.6 0.2 - - + -
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Residues in contact with THR 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F LEU* 2.9 36.4 - - + +
128F PRO* 3.4 31.9 - - + -
193F ALA 3.0 9.8 + - - -
194F GLN 3.6 6.3 - - - -
196F LEU* 1.3 76.5 - - - +
198F ILE* 1.3 57.5 + - - +
200F LEU 4.2 5.6 - - - +
201F SER* 2.7 37.1 + - - -
204F TYR 4.3 17.9 - - - +
205F ARG 5.8 0.2 - - - -
206F TYR* 5.2 5.4 - - - +
246F LEU* 4.0 5.6 - - + +
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Residues in contact with ILE 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PRO* 4.8 7.6 - - + -
133F HIS* 6.0 3.6 - - + -
136F TRP* 5.6 1.3 - - + -
194F GLN* 2.9 41.7 + - + +
195F LYS* 3.3 55.6 - - + +
196F LEU 3.2 0.2 - - - -
197F THR* 1.3 77.9 - - - +
199F ARG* 1.3 67.8 + - - +
201F SER* 4.1 6.1 + - - -
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F TRP* 5.3 7.3 - - - +
147F SER* 5.5 7.3 + - - +
150F LEU* 2.9 49.0 - - + +
154F MET* 5.2 3.3 - - - -
195F LYS* 2.8 49.3 + - + +
196F LEU* 3.9 1.8 - - - +
198F ILE* 1.3 76.2 - - - +
200F LEU* 1.3 79.5 + - + +
201F SER 3.8 0.9 + - - -
202F SER* 5.2 1.2 + - - -
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Residues in contact with LEU 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E PRO* 6.4 0.2 - - + -
154F MET* 3.6 50.3 - - + +
157F LEU* 4.5 20.6 - - + -
196F LEU* 2.9 26.4 + - + +
197F THR* 3.0 6.3 + - - -
199F ARG* 1.3 94.0 - - + +
201F SER* 1.3 65.1 + - - +
202F SER* 3.1 13.4 + - - +
203F ARG* 3.8 14.4 + - + +
204F TYR* 3.5 28.6 + - + +
246F LEU* 5.1 1.5 - - + +
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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
------------------------------------------------------------
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