Contacts of the helix formed by residues 176 - 189 (chain D) in PDB entry 3FTN
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D GLY 3.6 3.0 - - - -
175D ILE* 1.3 78.4 - - - +
177D ALA* 1.3 55.3 + - - -
178D VAL* 3.4 2.2 - - - -
179D GLY 3.1 3.8 + - - +
180D LEU* 2.8 35.8 + - - +
203D CYS* 4.6 9.0 - - - -
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Residues in contact with ALA 177 (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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147D MET* 5.7 3.8 - - - -
151D MET* 3.5 30.3 - - + -
176D GLY* 1.3 68.3 - - - -
178D VAL* 1.3 62.8 - - - +
180D LEU* 3.0 23.6 + - - +
181D MET* 3.0 18.4 + - + +
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Residues in contact with VAL 178 (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 ASP* 5.2 0.4 - - - +
151D MET* 3.9 35.7 - - + -
154D THR* 3.6 37.0 - - + -
155D GLY* 3.5 6.4 - - - +
176D GLY 3.4 0.6 - - - -
177D ALA* 1.3 77.5 - - - +
179D GLY* 1.3 64.1 + - - +
181D MET 3.1 2.1 + - - -
182D GLY* 2.9 18.9 + - - -
242D ALA* 4.1 13.5 - - + +
265D ILE* 3.6 24.4 - - + +
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Residues in contact with GLY 179 (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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172D VAL* 3.5 6.8 - - - +
174D GLY 3.1 26.9 - - - -
175D ILE* 4.5 1.8 - - - -
176D GLY 3.1 7.8 + - - +
178D VAL* 1.3 79.2 - - - +
180D LEU* 1.3 58.5 + - - +
182D GLY* 3.2 1.2 + - - -
183D ILE* 3.1 30.4 + - - +
242D ALA* 3.4 17.6 + - - +
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Residues in contact with LEU 180 (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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175D ILE* 3.5 19.5 - - + +
176D GLY* 2.8 22.2 + - - +
177D ALA* 3.0 11.0 + - - +
179D GLY* 1.3 75.6 - - - +
181D MET* 1.3 64.0 + - + +
183D ILE* 3.4 7.4 + - + +
184D ALA* 3.1 23.4 + - - +
203D CYS* 3.7 13.2 - - + +
206D ALA* 3.7 21.8 - - + +
207D ALA* 3.4 42.0 - - + +
210D TYR* 3.9 19.9 - - + +
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Residues in contact with MET 181 (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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147D MET* 5.8 2.5 - - - +
151D MET* 3.6 34.1 - - + +
152D MET* 3.9 28.0 - - - +
155D GLY* 3.7 7.2 - - - -
156D PHE* 3.1 32.1 - - + -
177D ALA* 3.0 14.5 + - + +
178D VAL 3.1 5.4 + - - +
180D LEU* 1.3 76.3 - - + +
182D GLY* 1.3 58.6 + - - +
184D ALA* 3.7 6.1 - - + -
185D GLY 2.8 23.2 + - - -
210D TYR* 3.6 46.0 - - + +
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Residues in contact with GLY 182 (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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155D GLY* 3.4 18.6 - - - -
159D ALA* 4.3 0.5 - - - +
172D VAL* 4.4 8.5 - - - -
178D VAL 2.9 12.2 + - - -
179D GLY* 3.2 6.5 + - - -
180D LEU 3.2 0.4 - - - -
181D MET* 1.3 77.8 - - - +
183D ILE* 1.3 57.4 + - - +
185D GLY* 3.8 0.5 - - - -
186D ALA* 2.9 30.5 + - - +
240D ILE* 3.9 17.1 - - - +
265D ILE* 5.3 0.4 - - - -
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Residues in contact with ILE 183 (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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172D VAL* 3.7 22.7 - - + -
175D ILE* 3.9 18.4 - - + -
179D GLY 3.1 11.6 + - - +
180D LEU* 3.5 10.5 - - + +
182D GLY* 1.3 77.1 - - - +
184D ALA* 1.3 61.2 + - - +
186D ALA* 3.4 5.0 + - - +
187D LYS* 3.1 21.7 + - - +
194D ILE* 3.8 13.9 - - + +
196D GLY* 4.4 7.2 - - - -
207D ALA* 3.8 32.8 - - + +
210D TYR* 3.8 13.7 - - + +
211D GLY 4.1 0.9 - - - -
212D ALA* 3.7 31.4 - - + +
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Residues in contact with ALA 184 (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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156D PHE* 3.9 15.3 - - + -
180D LEU 3.1 13.6 + - - +
181D MET* 3.7 13.0 - - + +
182D GLY 3.4 0.2 - - - -
183D ILE* 1.3 78.1 - - - +
185D GLY* 1.3 57.2 + - - +
187D LYS* 3.2 3.9 + - - +
188D LEU* 2.8 36.1 + - + +
210D TYR* 3.8 33.0 + - + +
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Residues in contact with GLY 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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166C MET* 4.4 2.7 - - - -
156D PHE* 3.5 18.5 - - - -
159D ALA* 3.4 15.0 - - - -
181D MET 2.8 20.3 + - - -
182D GLY 3.8 1.3 - - - -
183D ILE 3.4 0.2 - - - -
184D ALA* 1.3 70.5 - - - +
186D ALA* 1.3 60.2 + - - +
188D LEU* 3.1 7.8 + - - +
189D ARG* 2.8 34.0 + - - +
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Residues in contact with ALA 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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159D ALA* 3.5 1.4 - - - +
164D ILE* 3.6 23.7 - - + +
170D VAL* 4.4 16.4 - - + -
172D VAL* 5.3 0.2 - - + -
182D GLY 2.9 18.8 + - - +
183D ILE* 3.6 7.0 - - - +
185D GLY* 1.3 74.8 - - - +
187D LYS* 1.3 59.1 + - - +
189D ARG* 2.9 18.0 + - - +
190D GLY 3.1 0.5 + - - -
191D ALA* 3.0 25.6 + - + +
194D ILE* 4.0 12.3 - - + -
240D ILE* 4.6 2.2 - - + -
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Residues in contact with LYS 187 (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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188C LEU* 4.1 15.5 - - + +
312C LYS 5.6 2.3 + - - -
313C ARG* 3.6 41.8 - - - +
183D ILE 3.1 11.0 + - - +
184D ALA* 3.4 8.7 - - - +
186D ALA* 1.3 78.3 - - - +
188D LEU* 1.3 64.7 + - + +
190D GLY* 2.9 20.3 + - - -
191D ALA 3.9 5.5 + - - +
194D ILE* 3.7 13.4 - - + +
209D PHE 5.3 4.0 + - - -
210D TYR 3.7 17.9 + - - +
211D GLY* 4.1 6.6 - - - -
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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
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166C MET* 3.7 13.5 - - + -
187C LYS* 4.5 28.0 - - + +
188C LEU* 2.9 4.5 - - + +
189C ARG 2.9 2.8 - - - +
190C GLY* 2.8 37.4 + - - +
156D PHE* 3.9 33.9 - - + -
184D ALA* 2.8 19.7 + - + +
185D GLY 3.1 5.4 + - - +
187D LYS* 1.3 82.4 - - + +
189D ARG* 1.3 58.8 + - - +
190D GLY 3.3 0.2 - - - -
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Residues in contact with ARG 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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163C ASP* 5.3 5.1 + - - -
164C ILE 2.8 25.3 + - - +
165C GLU* 4.7 0.2 - - - +
166C MET* 3.9 28.2 - - - +
188C LEU 2.8 8.6 - - - +
189C ARG* 2.8 93.3 + - - +
159D ALA* 4.1 22.7 + - + +
160D GLU* 5.0 11.4 + - - +
163D ASP* 5.4 5.3 + - - +
164D ILE* 3.9 26.2 + - + +
166D MET* 4.5 1.2 - - - +
185D GLY 2.8 18.1 + - - +
186D ALA 2.9 6.4 + - - +
188D LEU* 1.3 75.8 - - - +
190D GLY* 1.3 59.5 + - - +
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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
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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