Contacts of the helix formed by residues 176 - 190 (chain C) in PDB entry 1EZF
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 ALA 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172C CYS 2.9 8.7 + - - +
174C TYR 3.5 0.4 - - - -
175C VAL* 1.3 80.4 - - - +
177C GLY* 1.3 69.2 + - - +
178C LEU 3.1 1.8 - - - -
179C VAL* 2.9 19.1 + - - +
180C GLY 3.1 9.7 + - - -
208C GLY* 3.3 29.8 - - - +
212C GLN* 3.6 22.9 - - + +
995C IN0 3.9 13.6 - - + -
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Residues in contact with GLY 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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172C CYS 2.9 16.2 + - - -
173C HIS* 3.2 3.3 + - - -
176C ALA* 1.3 72.4 - - - +
178C LEU* 1.3 56.3 + - - +
180C GLY* 3.1 4.0 + - - -
181C ILE* 3.0 31.1 + - - +
205C ASN* 3.0 44.6 - - - -
208C GLY* 4.0 1.9 - - - -
209C LEU* 4.2 0.8 - - - +
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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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146C ILE* 3.4 36.8 - - + +
149C ARG* 3.7 41.5 - - + +
150C MET* 3.8 24.9 - - + +
173C HIS* 2.8 31.7 + - + +
174C TYR* 3.5 41.1 - - + +
176C ALA 3.1 0.4 - - - -
177C GLY* 1.3 70.3 - - - +
179C VAL* 1.3 59.4 + - - +
181C ILE* 3.4 8.4 + - + +
182C GLY 2.8 23.7 + - - -
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Residues in contact with VAL 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PHE* 3.9 7.0 - - + -
76C LEU* 3.8 41.7 - - + -
150C MET* 4.4 4.0 - - + -
175C VAL 3.5 25.6 - - - +
176C ALA 2.9 8.6 + - - +
178C LEU* 1.3 76.0 - - - +
180C GLY* 1.3 59.6 + - - +
182C GLY* 3.2 1.0 + - - -
183C LEU* 2.8 42.1 + - + +
995C IN0 3.7 43.7 - - + -
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Residues in contact with GLY 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 ALA 3.1 10.3 + - - -
177C GLY 3.1 0.4 + - - -
179C VAL* 1.3 76.8 - - - +
181C ILE* 1.3 53.6 + - - +
183C LEU* 3.8 2.5 - - - +
184C SER* 2.7 37.9 + - - -
204C ALA* 3.6 17.0 - - - -
276C TYR* 4.6 0.5 + - - -
995C IN0 3.3 31.3 - - - -
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Residues in contact with ILE 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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146C ILE* 4.3 8.3 - - + -
149C ARG* 5.0 9.0 - - - +
173C HIS* 5.0 5.8 - - + -
177C GLY 3.0 15.9 + - - +
178C LEU* 3.4 19.1 - - + +
180C GLY* 1.3 73.4 - - - +
182C GLY* 1.3 59.9 + - - +
184C SER* 3.2 3.9 + - - -
185C ARG* 2.9 53.2 + - + +
198C GLY 5.5 0.2 - - - +
201C THR* 2.9 61.9 - - + +
204C ALA* 3.7 8.5 - - + -
205C ASN* 3.8 7.9 - - + +
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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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72C PHE* 4.2 7.0 - - - -
142C VAL* 3.5 11.7 - - - +
146C ILE* 3.7 23.8 - - - +
178C LEU 2.8 11.5 + - - -
179C VAL 3.6 2.5 - - - -
181C ILE* 1.3 76.9 - - - +
183C LEU* 1.3 62.3 + - - +
185C ARG* 3.0 5.1 + - - +
186C LEU* 2.8 28.2 + - - +
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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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69C VAL* 4.4 14.1 - - + -
72C PHE* 3.8 16.6 - - + -
179C VAL* 2.8 24.4 + - + +
180C GLY* 3.8 4.0 - - - +
182C GLY* 1.3 68.7 - - - -
184C SER* 1.3 52.7 + - - +
186C LEU* 2.9 10.5 + - + +
187C PHE* 2.8 51.5 + - + -
276C TYR* 5.3 0.4 - - - +
288C PHE* 3.8 15.9 - - + -
995C IN0 3.3 79.9 - - + -
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Residues in contact with SER 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 GLY 2.7 23.8 + - - -
181C ILE* 3.4 5.2 - - - -
183C LEU* 1.3 75.8 - - - +
185C ARG* 1.3 63.2 + - - +
187C PHE* 3.1 16.5 + - - +
188C SER* 3.0 24.6 + - - -
197C VAL* 3.4 22.2 - - - +
198C GLY* 3.8 6.9 + - - -
204C ALA* 3.2 8.3 - - - +
276C TYR* 2.9 30.2 + - - -
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Residues in contact with ARG 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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141C THR* 5.1 4.2 + - - +
142C VAL* 3.5 46.7 + - + +
145C ASP* 2.7 42.8 + - - +
146C ILE* 3.6 13.3 - - - +
149C ARG* 4.4 3.1 - - - +
181C ILE* 2.9 33.0 + - + +
182C GLY* 3.5 6.0 - - - +
184C SER* 1.3 74.6 - - - +
186C LEU* 1.3 58.6 + - - +
188C SER* 3.3 3.7 + - - +
189C ALA* 2.8 31.1 + - - +
198C GLY* 4.2 22.7 - - - +
201C THR* 6.0 1.8 - - - -
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Residues in contact with LEU 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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65C MET* 4.6 4.2 - - + +
68C ALA* 4.4 17.9 - - + +
69C VAL* 4.8 5.4 - - + -
72C PHE* 3.9 36.8 - - + -
139C TYR* 3.7 39.1 - - + +
142C VAL* 3.7 24.9 - - + -
143C ILE* 4.3 5.8 - - + -
182C GLY 2.8 17.3 + - - +
183C LEU* 3.3 14.1 - - + +
185C ARG* 1.3 75.2 - - - +
187C PHE* 1.3 68.2 + - + +
189C ALA* 3.7 4.5 - - - +
190C SER* 3.1 25.5 + - - -
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Residues in contact with PHE 187 (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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61C LEU* 5.0 1.8 - - + -
65C MET* 3.3 24.0 - - + -
69C VAL* 4.7 14.1 - - + -
183C LEU* 2.8 31.7 + - + -
184C SER* 3.1 8.3 + - - +
186C LEU* 1.3 79.0 - - + +
188C SER* 1.3 59.7 + - - +
190C SER* 2.8 17.3 + - - -
191C GLU 3.5 4.7 + - - -
193C GLU* 3.5 30.6 + - + -
197C VAL* 4.3 6.7 - - + -
276C TYR* 3.4 26.2 - - - -
280C LEU* 5.0 0.4 - - + -
285C VAL* 3.7 23.3 - - + -
288C PHE* 3.6 36.8 - + - -
289C CYS* 3.7 14.8 - - - -
995C IN0 5.5 0.2 - + - -
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Residues in contact with SER 188 (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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184C SER 3.0 8.3 + - - -
185C ARG* 3.9 4.0 - - - -
187C PHE* 1.3 73.8 - - - +
189C ALA* 1.3 67.2 + - - +
191C GLU* 3.2 16.6 + - - +
193C GLU 3.8 9.6 - - - +
194C ASP 2.8 24.5 + - - -
195C PRO* 3.6 15.2 - - - +
197C VAL* 3.8 1.6 - - - +
198C GLY* 2.9 25.2 + - - -
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Residues in contact with ALA 189 (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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138C LYS* 3.0 42.0 + - + +
139C TYR* 3.7 23.6 - - + -
142C VAL* 5.2 2.9 - - + -
185C ARG 2.8 22.3 + - - +
186C LEU* 3.3 2.7 + - - +
188C SER* 1.3 73.2 - - - +
190C SER* 1.3 60.5 + - - +
191C GLU* 3.3 10.0 + - - +
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Residues in contact with SER 190 (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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64C GLU* 5.1 1.6 - - - -
65C MET* 3.1 28.3 - - - +
138C LYS* 4.3 2.8 + - - +
139C TYR* 3.1 23.8 + - - -
186C LEU 3.1 10.0 + - - -
187C PHE 2.8 20.8 + - - -
189C ALA* 1.3 75.0 - - - +
191C GLU* 1.3 72.3 + - - +
192C PHE* 3.4 26.2 + - - -
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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