Contacts of the helix formed by residues 176 - 188 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLY 3.6 3.0 + - - -
175C ILE* 1.3 78.4 - - - +
177C ALA* 1.3 66.6 + - - -
178C VAL 3.3 2.7 - - - -
179C GLY 3.0 3.0 + - - +
180C LEU* 2.9 23.4 + - - +
203C CYS* 4.5 9.9 - - - -
340C LYS* 5.7 6.5 - - - -
345C ILE* 5.1 2.2 - - - -
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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
----------------------------------------------------------
151C MET* 3.4 30.3 - - + -
176C GLY* 1.3 69.8 - - - +
178C VAL* 1.3 63.6 + - + +
180C LEU* 3.3 2.6 + - - +
181C MET* 3.1 27.1 + - - +
319C LEU* 4.0 11.5 - - + +
340C LYS* 6.1 0.6 - - - +
345C ILE* 3.9 29.2 + - + +
346C LYS* 4.2 13.5 - - + -
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C CYS* 6.3 0.7 - - - -
38C THR* 5.9 2.2 - - - +
150C ASP* 5.4 0.2 - - - +
151C MET* 4.1 31.6 - - + -
154C THR* 3.6 26.7 - - + -
155C GLY* 3.6 6.6 - - - +
176C GLY 3.3 1.0 - - - -
177C ALA* 1.3 76.1 - - - +
179C GLY* 1.3 51.4 + - - +
181C MET 3.1 3.3 + - - -
182C GLY* 2.8 30.1 + - - -
242C ALA* 4.5 12.6 - - + +
265C ILE* 3.4 34.5 - - + +
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Residues in contact with GLY 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C VAL* 3.6 5.3 - - - +
174C GLY 3.2 26.7 - - - -
175C ILE* 4.5 1.8 - - - -
176C GLY 3.0 7.2 + - - +
178C VAL* 1.3 75.7 - - - +
180C LEU* 1.3 60.4 + - - +
182C GLY* 3.1 2.5 + - - -
183C ILE* 2.9 33.2 + - - +
242C ALA* 3.5 16.8 + - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE* 3.3 21.1 - - + +
176C GLY 2.9 20.4 + - - +
177C ALA 3.7 4.3 - - - +
179C GLY* 1.3 76.0 - - - +
181C MET* 1.3 60.0 + - - +
183C ILE* 3.4 6.9 + - + +
184C ALA* 3.0 26.3 + - - +
203C CYS* 3.6 7.2 - - - +
206C ALA* 3.6 21.5 - - + +
207C ALA* 3.3 43.7 - - + +
210C TYR* 3.8 11.6 - - + +
319C LEU* 3.8 24.0 - - + -
345C ILE* 4.0 14.1 - - + -
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Residues in contact with MET 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C MET 3.4 28.5 - - - +
152C MET* 4.2 20.4 - - - -
155C GLY* 3.7 6.7 - - - -
156C PHE* 3.2 26.6 - - + -
177C ALA 3.1 8.2 + - - +
178C VAL 3.1 6.5 + - - +
180C LEU* 1.3 76.1 - - - +
182C GLY* 1.3 56.8 + - - +
184C ALA* 4.0 4.9 - - + -
185C GLY 2.7 28.1 + - - -
210C TYR* 3.5 50.3 - - + +
314C VAL* 4.1 9.6 - - + -
316C PRO* 4.6 1.8 - - + -
319C LEU* 3.6 28.0 - - + -
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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
----------------------------------------------------------
155C GLY* 3.5 17.9 - - - -
159C ALA* 4.2 0.7 - - - +
172C VAL* 4.4 8.3 - - - -
178C VAL 2.8 14.1 + - - -
179C GLY* 3.1 6.4 + - - -
181C MET* 1.3 74.9 - - - +
183C ILE* 1.3 53.9 + - - +
185C GLY* 3.3 0.9 + - - -
186C ALA* 2.7 37.1 + - - +
240C ILE* 4.2 12.3 - - - +
265C ILE* 5.0 4.5 - - - -
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Residues in contact with ILE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C VAL* 3.7 23.0 - - + +
175C ILE* 4.1 16.6 - - + -
179C GLY 2.9 18.1 + - - +
180C LEU* 3.6 10.3 - - + +
182C GLY* 1.3 73.1 - - - +
184C ALA* 1.3 58.7 + - - +
186C ALA* 3.2 5.6 + - - +
187C LYS* 2.9 27.5 + - - +
194C ILE* 3.8 12.3 - - + +
196C GLY* 4.6 4.7 - - - -
207C ALA* 3.8 30.7 - - + +
210C TYR* 3.6 21.8 - - + +
211C GLY 3.9 2.7 - - - -
212C ALA* 3.6 27.1 - - + +
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Residues in contact with ALA 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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156C PHE* 4.0 9.0 - - + -
180C LEU 3.0 17.9 + - - +
181C MET* 3.7 14.1 - - + +
182C GLY 3.3 0.2 - - - -
183C ILE* 1.3 78.4 - - - +
185C GLY* 1.3 57.9 + - - +
187C LYS* 3.1 4.3 + - - +
188C LEU* 2.9 33.1 + - + +
210C TYR* 3.7 33.4 - - + +
314C VAL* 4.5 7.4 - - + -
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Residues in contact with GLY 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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156C PHE* 3.4 21.2 - - - -
159C ALA* 3.4 13.9 - - - -
181C MET 2.7 21.4 + - - -
182C GLY 3.7 1.1 - - - -
184C ALA* 1.3 72.9 - - - +
186C ALA* 1.3 62.5 + - - +
188C LEU* 3.1 7.2 + - - +
189C ARG* 2.9 27.4 + - - +
166D MET* 4.2 2.4 - - - +
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Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ALA* 3.4 1.6 - - - +
164C ILE* 3.8 24.2 - - + +
170C VAL* 4.4 17.7 - - + -
182C GLY 2.7 21.3 + - - +
183C ILE* 3.4 9.0 - - - +
185C GLY* 1.3 71.8 - - - +
187C LYS* 1.3 61.0 + - - +
189C ARG* 3.1 11.4 + - - +
190C GLY 3.3 0.3 + - - -
191C ALA* 3.2 23.5 + - + +
194C ILE* 4.1 12.8 - - + -
240C ILE* 4.5 3.8 - - + -
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Residues in contact with LYS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ILE 2.9 13.8 + - - +
184C ALA* 3.1 8.5 + - - +
186C ALA* 1.3 76.4 - - - +
188C LEU* 1.3 68.1 + - + +
189C ARG 3.1 0.2 - - - -
190C GLY* 3.1 19.5 + - - +
191C ALA 4.5 8.3 - - - +
194C ILE* 3.9 16.4 - - + -
210C TYR 4.0 13.7 + - - +
211C GLY* 4.9 13.0 - - - +
188D LEU* 4.0 22.5 - - + +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C PHE* 3.8 33.0 - - + -
184C ALA* 2.9 17.1 + - + +
185C GLY 3.1 5.8 + - - +
187C LYS* 1.3 84.4 - - + +
189C ARG* 1.3 56.9 + - - +
308C LEU* 4.7 6.3 - - + -
313C ARG* 3.8 42.0 - - + +
314C VAL* 4.4 5.4 - - + -
166D MET* 3.7 11.9 - - + -
187D LYS* 4.3 20.0 - - + +
188D LEU* 2.9 7.3 - - + +
189D ARG 2.8 2.8 - - - +
190D GLY* 2.7 34.9 + - - +
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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