Contacts of the helix formed by residues 167 - 184 (chain C) in PDB entry 3FIW
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 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C HIS* 1.3 76.3 + - + +
169C GLU* 3.0 8.0 - - - +
170C SER* 3.5 24.2 + - - +
171C ALA* 3.0 22.9 + - - +
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Residues in contact with HIS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ARG* 4.3 26.6 + - - -
167C ASP* 1.3 83.8 + - + +
169C GLU* 1.3 65.4 + - - +
171C ALA* 3.6 5.2 + - - +
172C PHE* 3.0 23.7 + - - +
87D ARG* 4.4 2.1 + - - -
143D CYS* 4.8 4.5 + - - +
146D GLU* 4.4 9.9 - - + -
147D GLU* 3.6 61.2 + - + +
150D GLU 4.2 19.1 - - - -
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Residues in contact with GLU 169 (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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167C ASP 4.3 7.9 - - - +
168C HIS* 1.3 80.1 - - - +
170C SER* 1.3 61.6 + - - +
172C PHE* 3.2 8.7 + - - +
173C GLU* 2.9 38.8 + - + +
87D ARG* 2.7 44.1 + - - +
147D GLU* 5.1 0.6 + - - +
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Residues in contact with SER 170 (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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127C ARG* 3.5 22.0 + - - -
131C MSE 4.5 0.5 - - - +
167C ASP* 3.4 21.3 + - - -
168C HIS 3.3 0.2 - - - -
169C GLU* 1.3 82.6 - - - +
171C ALA* 1.3 61.4 + - - +
173C GLU* 3.4 8.1 + - - +
174C ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 171 (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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131C MSE 3.7 24.2 - - + +
134C LEU* 4.5 8.4 - - + +
138C ARG* 3.5 28.3 - - - +
167C ASP* 3.0 14.5 + - - +
168C HIS* 3.8 5.8 - - - +
170C SER* 1.3 77.8 + - - +
172C PHE* 1.3 64.8 + - - +
174C ALA* 3.5 0.9 + - - +
175C GLY* 3.0 22.3 + - - -
139D PHE* 3.9 4.0 - - - -
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Residues in contact with PHE 172 (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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168C HIS 3.0 15.7 + - - +
169C GLU* 3.2 10.5 + - - +
171C ALA* 1.3 76.7 - - - +
173C GLU* 1.3 86.9 + - - +
176C LEU* 3.0 47.6 + - + +
83D THR* 3.9 19.1 - - + -
84D ARG* 3.8 13.0 - - + -
87D ARG* 3.5 43.5 - - + +
139D PHE* 3.4 24.7 - + - -
140D THR* 3.5 24.0 - - + -
143D CYS* 4.2 17.4 - - + -
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Residues in contact with GLU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C GLU* 2.9 35.3 + - + +
170C SER* 3.4 8.3 + - - +
171C ALA 3.3 0.2 - - - -
172C PHE* 1.3 90.8 - - + +
174C ALA* 1.3 57.1 + - - +
176C LEU* 3.5 7.1 + - - +
177C ALA* 3.0 27.9 + - - +
80D LEU* 5.7 1.7 - - - +
84D ARG* 2.7 50.2 + - - -
87D ARG* 5.5 0.2 + - - -
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Residues in contact with ALA 174 (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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127C ARG* 5.1 6.1 - - - +
131C MSE 3.6 32.3 - - + -
170C SER 3.0 16.7 + - - +
171C ALA 3.9 2.2 - - - +
173C GLU* 1.3 74.5 - - - +
175C GLY* 1.3 64.1 + - - +
177C ALA* 3.2 8.2 + - - +
178C LEU* 3.0 28.5 + - - +
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Residues in contact with GLY 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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131C MSE 5.0 1.9 + - - +
135C ALA* 3.8 19.9 - - - +
171C ALA 3.0 11.5 + - - -
174C ALA* 1.3 76.0 - - - +
176C LEU* 1.3 60.7 + - - +
178C LEU* 3.4 9.4 - - - +
179C ILE* 3.2 27.0 + - - +
139D PHE* 3.4 22.4 - - - -
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Residues in contact with LEU 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 PHE* 3.0 47.2 + - + +
173C GLU* 3.8 8.7 - - - +
175C GLY* 1.3 73.7 - - - +
177C ALA* 1.3 62.1 + - - +
179C ILE* 3.3 8.6 + - + +
180C THR* 3.0 38.4 + - - +
79D PHE* 4.1 10.5 - - + -
80D LEU* 3.6 35.0 - - + +
83D THR* 3.7 34.1 - - + +
84D ARG* 4.4 1.8 - - + -
136D ALA* 4.2 8.5 - - + -
139D PHE* 3.5 11.0 - - + -
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Residues in contact with ALA 177 (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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173C GLU 3.0 18.2 + - - +
174C ALA* 3.2 8.5 + - - +
176C LEU* 1.3 73.9 - - - +
178C LEU* 1.3 55.2 + - - +
180C THR* 4.5 4.3 - - - +
181C ASP* 2.7 52.4 + - - +
76D HIS* 5.9 1.8 - - + -
80D LEU* 4.9 6.9 - - + +
186D HIS* 6.4 0.7 - - + -
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Residues in contact with LEU 178 (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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128C HIS* 4.7 2.9 - - - +
131C MSE 4.0 10.5 - - + +
132C ALA* 3.5 37.2 - - + +
135C ALA* 4.3 3.8 - - + -
174C ALA* 3.0 18.3 + - + +
175C GLY* 3.4 13.7 - - - +
176C LEU 3.3 0.2 - - - -
177C ALA* 1.3 74.4 - - - +
179C ILE* 1.4 53.5 + - - +
181C ASP* 4.5 1.3 - - - -
182C GLY 2.8 29.6 + - - -
178D LEU 3.5 4.4 - - - +
179D ILE* 3.8 15.9 - - + +
182D GLY* 3.3 16.2 - - - +
183D LEU* 3.4 40.2 - - + +
186D HIS* 4.3 14.1 - - + +
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Residues in contact with ILE 179 (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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175C GLY 3.2 16.2 + - - +
176C LEU* 3.6 8.5 - - + +
178C LEU* 1.4 77.2 - - - +
180C THR* 1.3 68.5 + - - +
182C GLY* 3.3 10.7 + - - -
183C LEU* 3.3 12.5 + - - +
79D PHE* 4.7 8.7 - - + -
132D ALA* 4.3 17.0 - - + +
135D ALA* 4.4 10.8 - - + +
136D ALA* 4.4 11.9 - - + +
139D PHE* 3.9 36.6 - - + -
178D LEU* 3.9 29.8 - - + +
179D ILE* 3.7 26.0 - - + +
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Residues in contact with THR 180 (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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176C LEU* 3.0 17.4 + - - +
177C ALA* 4.0 2.0 - - - -
179C ILE* 1.3 77.0 - - - +
181C ASP* 1.3 59.9 + - - +
183C LEU* 3.1 26.3 + - + +
184C VAL* 3.6 9.9 + - - +
75D TRP* 3.7 23.2 - - + -
76D HIS* 3.2 36.8 - - + +
79D PHE* 3.5 28.9 - - + -
80D LEU* 3.7 9.8 - - + +
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Residues in contact with ASP 181 (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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177C ALA* 2.7 34.4 + - - +
178C LEU* 3.7 2.9 - - - +
180C THR* 1.3 70.8 - - - +
182C GLY* 1.3 65.6 + - - +
183C LEU 3.0 2.6 + - - -
184C VAL* 3.3 8.9 + - - +
185C ARG* 4.6 1.4 + - - +
76D HIS* 3.7 18.0 + - - -
182D GLY* 4.3 12.1 - - - +
185D ARG* 3.0 46.4 + - - +
186D HIS* 4.6 15.5 + - + -
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Residues in contact with GLY 182 (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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178C LEU 2.8 14.8 + - - -
179C ILE 3.3 2.6 + - - -
181C ASP* 1.3 71.8 - - - +
183C LEU* 1.3 59.2 + - - +
184C VAL 3.5 0.2 - - - -
185C ARG* 4.3 8.0 + - - +
186C HIS* 4.4 8.5 + - - -
178D LEU* 3.2 37.5 - - - +
181D ASP* 4.2 13.1 - - - +
182D GLY* 3.6 10.6 - - - -
185D ARG* 5.4 0.2 - - - -
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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
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179C ILE 3.3 7.9 + - - +
180C THR* 3.1 15.8 + - - +
181C ASP 3.0 1.8 - - - -
182C GLY* 1.3 75.7 - - - +
184C VAL* 1.3 53.5 + - - +
185C ARG 3.2 2.2 - - - -
186C HIS* 2.7 35.2 + - + +
187C VAL* 3.6 5.4 + - + +
75D TRP* 3.7 30.3 - - + -
79D PHE* 4.9 6.7 - - + -
119D LEU* 6.4 0.7 - - + -
124D VAL* 4.4 15.9 - - + -
128D HIS* 3.6 41.3 - - + +
132D ALA* 3.6 21.5 - - + -
178D LEU* 3.8 17.7 - - + -
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Residues in contact with VAL 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 THR 3.6 13.9 - - - +
181C ASP* 3.3 4.2 + - - +
183C LEU* 1.3 76.6 - - - +
185C ARG* 1.3 63.9 + - - +
187C VAL* 3.0 31.5 + - + +
75D TRP* 4.5 5.6 - - + -
76D HIS* 4.2 20.6 - - + +
185D ARG* 3.5 32.8 - - - +
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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