Contacts of the helix formed by residues 185 - 198 (chain F) in PDB entry 5NSS
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 ASP 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F GLU* 3.7 30.3 - - + +
12F ALA* 3.8 13.9 + - - -
13F ASN 4.9 1.1 - - - +
182F ARG* 3.0 14.7 + - - +
184F SER* 1.3 75.7 - - - +
186F ILE* 1.3 58.5 + - - +
187F MET 3.1 3.5 + - - -
188F LEU* 3.4 7.2 + - - +
189F MET* 2.9 29.9 + - - +
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Residues in contact with ILE 186 (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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182F ARG 3.3 6.4 + - - +
183F GLU* 3.3 20.9 + - - +
185F ASP* 1.3 78.9 - - - +
187F MET* 1.3 57.0 + - - +
189F MET* 3.8 6.6 - - - +
190F ALA* 2.9 29.5 + - - +
217F LEU* 3.7 31.2 - - + +
218F LEU* 3.8 7.0 - - - +
229F LEU* 5.7 8.0 - - + +
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Residues in contact with MET 187 (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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183F GLU 4.8 0.6 + - - -
184F SER 4.3 8.6 + - - +
185F ASP 3.1 0.8 - - - -
186F ILE* 1.3 76.2 - - - +
188F LEU* 1.3 60.3 + - - +
190F ALA* 3.1 6.5 + - - +
191F GLU* 2.9 28.5 + - - +
209F PHE* 4.5 8.0 - - + +
214F ARG* 4.0 30.6 + - + +
218F LEU* 5.5 0.6 - - - +
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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
----------------------------------------------------------
11F GLU* 3.7 27.1 - - + -
184F SER 5.3 0.2 + - - -
185F ASP* 3.4 6.2 + - - +
187F MET* 1.3 80.3 - - - +
189F MET* 1.3 57.3 + - - +
191F GLU* 4.0 5.3 - - - +
192F TYR* 2.9 32.6 + - - +
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Residues in contact with MET 189 (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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10F GLY* 3.7 22.8 - - - -
11F GLU 4.1 3.3 - - - +
12F ALA* 4.7 10.8 - - + +
185F ASP 2.9 19.5 + - - +
186F ILE* 4.0 7.0 - - - +
188F LEU* 1.3 76.8 - - - +
190F ALA* 1.3 51.0 + - - +
193F PHE* 2.6 40.6 + - + +
229F LEU* 4.6 18.2 - - + +
233F VAL* 4.5 0.4 - - - +
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Residues in contact with ALA 190 (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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186F ILE 2.9 20.0 + - - +
187F MET* 3.1 7.2 + - - +
189F MET* 1.3 76.8 - - - +
191F GLU* 1.3 58.4 + - - +
194F ALA* 2.9 31.0 + - - +
209F PHE* 5.0 9.4 - - + -
213F ALA* 5.5 4.9 - - + +
217F LEU* 4.9 12.8 - - + -
229F LEU* 5.3 2.0 - - + +
233F VAL* 3.8 16.8 - - + +
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Residues in contact with GLU 191 (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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187F MET 2.9 15.0 + - - +
188F LEU* 4.0 6.3 - - - +
190F ALA* 1.3 75.6 - - - +
192F TYR* 1.3 60.4 + - - +
194F ALA* 3.3 4.4 + - - +
195F ILE* 2.9 29.8 + - - +
206F PHE* 4.2 5.7 - - + +
208F GLY* 5.7 4.3 - - - -
209F PHE* 4.8 17.4 - - + +
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Residues in contact with TYR 192 (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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9F LEU* 4.1 7.0 - - + +
10F GLY* 3.7 22.0 - - - +
188F LEU 2.9 17.7 + - - +
191F GLU* 1.3 76.7 - - - +
193F PHE* 1.3 57.4 + - - +
195F ILE* 3.4 6.2 + - - +
196F GLN* 2.9 30.0 + - - +
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Residues in contact with PHE 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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9F LEU* 4.5 8.4 - - + +
10F GLY* 5.7 1.3 - - - +
189F MET* 2.6 24.7 + - + +
192F TYR* 1.3 77.2 - - - +
194F ALA* 1.3 56.7 + - - +
196F GLN* 3.9 5.6 - - - +
197F MET* 2.9 31.2 + - - +
229F LEU 4.2 7.9 - - - +
230F LYS* 4.4 13.6 - - + +
233F VAL* 3.7 16.7 - - + +
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Residues in contact with ALA 194 (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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190F ALA 2.9 22.1 + - - +
191F GLU* 3.7 5.6 - - - +
193F PHE* 1.3 76.7 - - - +
195F ILE* 1.3 61.0 + - - +
197F MET* 3.7 1.1 - - - +
198F CYS* 2.9 29.6 + - - +
206F PHE* 4.2 10.9 - - + +
207F PRO 6.0 0.4 - - - -
208F GLY 6.2 1.6 - - - +
233F VAL* 4.0 8.2 - - + +
237F VAL* 3.9 26.9 - - + +
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Residues in contact with ILE 195 (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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191F GLU 2.9 17.2 + - - +
192F TYR* 3.9 6.1 - - - +
194F ALA* 1.3 76.3 - - - +
196F GLN* 1.3 61.8 + - - +
198F CYS* 3.5 15.6 + - - +
199F ARG* 4.2 3.1 + - - +
206F PHE* 3.7 21.4 - - + +
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Residues in contact with GLN 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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9F LEU* 4.3 17.0 - - + -
192F TYR 2.9 18.7 + - - +
193F PHE* 3.9 4.0 - - - +
195F ILE* 1.3 79.0 - - - +
197F MET* 1.3 61.2 + - - +
198F CYS 3.4 0.7 + - - -
199F ARG* 3.6 16.6 + - - +
200F GLU 4.8 0.5 + - - -
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Residues in contact with MET 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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193F PHE 2.9 19.5 + - - +
194F ALA* 3.7 4.5 - - - +
196F GLN* 1.3 72.3 - - - +
198F CYS* 1.3 62.2 + - - +
199F ARG 3.2 4.0 + - - -
200F GLU* 3.6 8.3 + - - +
201F ILE* 3.5 18.2 + - - +
230F LYS 5.3 0.4 - - - +
233F VAL 4.9 0.2 - - - +
234F GLU* 3.7 35.7 - - + +
237F VAL* 5.2 3.8 - - + +
238F TYR* 5.6 3.0 + - + +
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Residues in contact with CYS 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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194F ALA 2.9 17.4 + - - +
195F ILE* 3.6 13.2 - - - +
196F GLN 3.2 1.0 - - - -
197F MET* 1.3 75.4 - - - +
199F ARG* 1.3 60.8 + - - +
200F GLU 3.5 0.2 - - - -
201F ILE* 3.8 4.9 - - - -
202F LYS 3.3 1.7 + - - -
203F LEU* 2.8 58.8 + - + +
205F LEU* 4.7 11.7 - - - -
206F PHE* 4.7 1.8 - - - +
237F VAL* 5.6 4.7 - - + -
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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