Contacts of the helix formed by residues 174 - 188 (chain C) in PDB entry 5FI6
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 LEU 174 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C LEU* 3.8 31.4 - - + -
167C LEU* 4.1 17.5 - - + -
168C ARG 4.0 16.4 - - - +
169C THR* 5.3 0.9 - - - -
171C ASP* 2.7 27.5 + - + +
173C ARG* 1.3 84.4 - - - +
175C LYS* 1.3 57.0 + - - +
177C CYS* 3.3 3.9 + - + +
178C MET* 2.9 39.9 + - + +
206C ASN* 3.4 24.0 - - + +
209C LEU* 3.7 19.7 - - + -
210C LEU* 4.3 15.5 - - + -
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ASP 3.5 3.5 + - - +
172C PRO* 3.4 18.8 + - + +
174C LEU* 1.3 77.0 - - - +
176C GLU* 1.3 61.8 + - + +
178C MET* 3.0 6.0 + - - +
179C ASP* 2.7 71.0 + - - +
182C ARG* 5.6 2.8 - - - +
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Residues in contact with GLU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PRO 4.2 5.5 - - - +
173C ARG 4.3 1.0 - - - +
175C LYS* 1.3 87.5 + - + +
177C CYS* 1.3 63.4 + - - +
179C ASP* 3.4 8.2 + - - +
180C MET* 3.0 24.6 + - - +
202C CYS 4.7 0.2 - - - -
205C SER* 3.5 23.3 - - - +
206C ASN* 3.6 18.5 + - - -
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Residues in contact with CYS 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 4.2 12.1 - - - -
174C LEU* 3.6 5.2 - - + +
175C LYS 3.2 0.2 - - - -
176C GLU* 1.3 75.9 - - - +
178C MET* 1.3 80.7 + - + +
180C MET* 3.4 3.5 + - - +
181C LEU* 3.1 28.1 + - - +
202C CYS 3.1 29.7 - - - +
203C VAL* 4.3 2.0 - - - -
205C SER* 3.3 3.0 + - - +
206C ASN* 2.9 28.9 + - + +
210C LEU* 4.2 16.6 - - + -
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Residues in contact with MET 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 3.9 2.9 - - + -
159C ILE* 4.2 9.6 - - + -
162C LEU* 3.7 26.5 - - + -
169C THR* 3.3 43.5 - - + +
174C LEU* 2.9 25.5 + - + +
175C LYS* 3.8 3.6 - - - +
177C CYS* 1.3 105.0 - - + +
179C ASP* 1.3 59.9 + - - +
181C LEU* 3.4 18.6 + - + +
182C ARG* 3.0 54.4 + - - +
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Residues in contact with ASP 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C LYS* 2.7 61.4 + - - +
176C GLU* 3.8 7.2 + - - +
178C MET* 1.3 72.1 - - - +
180C MET* 1.3 57.7 + - - +
182C ARG* 3.3 24.8 + - - +
183C LEU* 2.9 30.5 + - - +
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Residues in contact with MET 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLU 3.0 16.8 + - - +
177C CYS 3.7 4.7 - - - +
179C ASP* 1.3 75.2 - - - +
181C LEU* 1.3 59.9 + - - +
183C LEU* 3.7 32.2 - - + +
184C THR* 2.8 36.3 + - - +
201C LYS* 3.5 57.7 - - + +
202C CYS* 3.8 20.2 - - - +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 4.8 11.4 - - + -
158C PHE* 3.6 35.9 - - + -
159C ILE* 4.0 11.9 - - + -
177C CYS* 3.1 17.9 + - - +
178C MET* 3.8 21.8 - - + +
180C MET* 1.3 77.1 - - - +
182C ARG* 1.3 61.6 + - - +
184C THR* 3.5 2.6 + - + -
185C LEU* 3.0 35.4 + - + +
194C LEU* 3.7 27.6 - - + -
202C CYS* 3.5 28.5 - - + -
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Residues in contact with ARG 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C THR* 5.6 8.3 + - - +
175C LYS* 4.9 3.8 + - - +
178C MET* 3.0 40.7 + - - +
179C ASP* 3.3 29.0 + - - +
181C LEU* 1.3 76.1 - - - +
183C LEU* 1.3 63.0 + - - +
185C LEU* 3.2 11.7 + - + +
186C GLN* 3.2 25.4 + - - +
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASP 2.9 18.2 + - - +
180C MET* 3.7 28.5 - - + +
182C ARG* 1.3 75.8 - - - +
184C THR* 1.3 64.1 + - - +
186C GLN* 2.9 35.8 + - + +
187C THR* 3.0 28.5 + - + +
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Residues in contact with THR 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C MET* 2.8 22.0 + - - +
181C LEU* 3.8 5.2 - - - +
183C LEU* 1.3 75.3 - - - +
185C LEU* 1.3 66.4 + - + +
187C THR* 3.3 9.1 + - - -
188C THR* 2.7 46.9 + - + +
194C LEU* 4.3 11.7 - - + -
198C LEU* 3.9 28.8 - - + +
201C LYS* 3.9 21.6 + - - +
202C CYS* 4.0 10.8 - - - -
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 3.7 42.0 - - + -
181C LEU* 3.0 22.2 + - + +
182C ARG* 3.7 8.3 - - + +
183C LEU 3.2 0.4 - - - -
184C THR* 1.3 86.0 - - + +
186C GLN* 1.3 63.6 + - - +
188C THR* 3.4 19.1 - - - +
189C SER* 3.4 12.8 + - - -
192C VAL* 4.6 19.7 - - + -
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Residues in contact with GLN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ARG 3.2 14.0 + - - +
183C LEU* 2.9 32.3 + - - +
185C LEU* 1.3 78.4 - - - +
187C THR* 1.3 63.4 + - + +
188C THR 3.2 1.5 + - - -
189C SER* 3.8 10.0 + - - -
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Residues in contact with THR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C LEU* 3.0 31.8 + - + +
184C THR* 3.3 12.3 + - - -
186C GLN* 1.3 74.7 - - + +
188C THR* 1.3 68.5 + - - +
189C SER 4.1 0.2 - - - -
190C ASP* 4.3 2.3 - - - +
201C LYS* 5.1 6.4 + - - -
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Residues in contact with THR 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C THR* 2.7 33.4 + - + +
185C LEU* 3.4 16.7 - - - +
187C THR* 1.3 90.8 - - - +
189C SER* 1.3 60.4 + - - +
190C ASP* 2.9 27.3 + - - +
191C GLY* 4.0 8.5 + - - -
192C VAL* 5.2 2.8 - - - +
198C LEU* 5.1 13.0 - - + +
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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