Contacts of the helix formed by residues 171 - 183 (chain C) in PDB entry 4X4R
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 SER 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C TYR 4.4 1.6 - - - -
163C ALA* 3.5 28.8 - - - +
169C GLY 3.8 1.0 + - - -
170C PHE* 1.3 76.0 - - - +
172C GLY* 1.3 61.0 + - - +
173C TYR 4.0 3.4 + - - -
174C LEU* 2.9 39.5 + - - +
175C CYS* 3.1 11.1 + - - -
226C VAL* 3.7 16.8 + - - +
501C APC 3.8 25.5 + - - -
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Residues in contact with GLY 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LYS* 3.1 24.7 - - - -
161C TYR* 3.1 34.9 + - - -
170C PHE 3.7 0.8 + - - -
171C SER* 1.3 72.8 - - - +
173C TYR* 1.3 57.7 + - - +
175C CYS* 3.7 0.6 + - - -
176C GLU* 3.3 16.3 + - - +
501C APC 4.4 17.1 + - - +
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Residues in contact with TYR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C HIS* 3.2 38.6 - + + -
136C TRP* 5.0 1.9 - - - -
137C LEU* 3.4 33.9 - - + -
171C SER* 3.1 2.1 - - - +
172C GLY* 1.3 76.3 - - - +
174C LEU* 1.3 63.5 + - - +
175C CYS 3.2 0.4 - - - -
176C GLU* 3.2 9.9 + - - +
177C LEU* 3.0 53.4 + - + +
218C ASP* 2.7 29.1 + - - -
219C PRO* 3.7 3.3 - - - +
220C VAL* 4.2 4.2 - - - +
226C VAL* 3.6 21.3 - - + -
501C APC 3.6 48.9 + + + +
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Residues in contact with LEU 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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169C GLY 5.2 1.1 - - - +
170C PHE* 3.5 40.8 - - + -
171C SER* 2.9 23.2 + - - +
173C TYR* 1.3 79.1 - - - +
175C CYS* 1.3 62.2 + - - +
177C LEU* 3.4 3.0 + - + +
178C LEU* 3.2 31.2 + - + +
214C PHE* 5.6 0.2 - - + -
216C VAL* 3.6 39.9 - - + -
226C VAL* 3.7 17.9 - - + +
227C ALA* 3.5 29.2 - - + -
230C LEU* 5.2 0.7 - - + -
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Residues in contact with CYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C VAL* 4.6 2.0 - - + -
151C LEU* 3.6 21.4 - - + +
152C LYS* 3.9 18.8 - - + -
155C LEU* 3.3 35.0 - - - -
161C TYR* 4.1 13.7 - - - -
170C PHE* 4.1 7.4 - - - -
171C SER 3.1 15.7 + - - -
172C GLY 3.8 8.7 - - - +
174C LEU* 1.3 78.5 - - - +
176C GLU* 1.3 60.7 + - - +
178C LEU* 3.2 13.0 + - - +
179C ILE* 3.3 19.6 + - - +
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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
----------------------------------------------------------
50C ARG* 3.1 38.5 + - - -
52C THR* 3.1 26.6 + - - +
137C LEU* 3.9 18.6 - - + +
141C ILE* 3.7 11.9 - - + +
148C VAL* 3.7 28.3 - - + -
152C LYS* 4.2 3.3 + - - +
172C GLY 3.3 17.7 + - - +
173C TYR* 3.2 15.4 + - - +
175C CYS* 1.3 77.6 - - - +
177C LEU* 1.3 62.2 + - - +
179C ILE 3.3 9.4 + - - -
180C VAL* 3.3 19.2 + - - +
501C APC 4.1 3.7 + - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C TRP* 3.7 19.5 - - + -
137C LEU* 4.1 2.5 - - + -
173C TYR* 3.0 43.2 + - + +
174C LEU* 3.7 11.0 - - + +
175C CYS 3.3 0.4 - - - -
176C GLU* 1.3 76.5 - - - +
178C LEU* 1.3 57.7 + - - +
180C VAL* 3.5 5.8 + - - +
181C PHE* 3.1 28.4 + - - +
203C VAL* 4.2 16.7 - - + +
216C VAL* 4.4 5.4 - - + -
217C VAL 4.4 4.3 - - - +
219C PRO* 3.6 37.0 - - + -
226C VAL* 3.6 30.3 - - + -
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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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151C LEU* 4.1 14.8 - - + -
170C PHE* 5.0 9.9 - - + -
174C LEU* 3.2 32.5 + - + +
175C CYS* 3.5 9.4 - - - +
176C GLU 3.2 1.0 - - - -
177C LEU* 1.3 75.8 - - - +
179C ILE* 1.3 60.0 + - - +
181C PHE* 4.3 2.0 - - + -
182C TYR* 2.9 55.9 + - + +
188C THR* 3.6 25.5 + - + -
195C TRP* 4.0 24.7 - - + -
201C ILE* 4.6 14.4 - - + -
203C VAL* 6.3 0.4 - - + -
216C VAL* 5.0 6.5 - - + -
238C PHE* 5.6 2.5 - - + -
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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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141C ILE* 4.2 2.9 - - + -
144C LYS* 3.7 21.3 - - + +
147C GLU* 3.2 41.3 - - + +
148C VAL* 3.6 24.0 - - + -
151C LEU* 4.1 13.9 - - + -
175C CYS 3.4 13.2 - - - +
176C GLU 3.3 7.0 + - - +
178C LEU* 1.3 75.0 - - - +
180C VAL* 1.3 58.2 + - - +
183C GLY* 2.6 42.9 + - - +
185C PHE* 4.0 13.9 - - - +
188C THR* 4.0 15.9 - - - +
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Residues in contact with VAL 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C TRP* 4.5 15.3 - - + -
137C LEU* 4.1 17.9 - - + -
140C ARG* 3.9 34.8 - - + +
141C ILE* 3.5 28.5 - - + -
144C LYS* 4.8 12.1 + - - +
176C GLU 3.3 7.4 + - - +
177C LEU* 3.8 8.7 - - - +
178C LEU 3.4 0.2 - - - -
179C ILE* 1.3 77.9 - - - +
181C PHE* 1.3 59.6 + - - +
182C TYR 3.8 0.2 + - - -
183C GLY* 4.4 1.7 + - - -
203C VAL* 4.8 6.3 - - + -
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Residues in contact with PHE 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 LEU 3.1 17.5 + - - +
178C LEU* 3.8 7.2 - - + +
179C ILE 3.2 0.2 - - - -
180C VAL* 1.3 79.7 - - - +
182C TYR* 1.3 93.3 + + - +
201C ILE* 3.7 17.5 - - + -
202C ASP 3.6 8.7 - - - -
203C VAL* 3.6 27.8 - - + -
206C GLY* 3.6 30.7 - - - -
207C GLU 3.6 22.0 - - - -
208C VAL* 3.6 20.2 - - + -
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Residues in contact with TYR 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* 2.9 39.3 + - + +
181C PHE* 1.3 107.7 - + - +
183C GLY* 1.3 58.3 + - - +
184C SER 3.3 6.6 + - - -
187C GLU* 3.4 27.9 - - + +
188C THR* 3.3 44.9 - - + +
191C ASN* 3.6 30.9 - - + +
195C TRP* 3.5 26.7 + + - -
201C ILE* 3.6 11.2 - - + +
208C VAL* 4.6 6.3 - - + +
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Residues in contact with GLY 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LYS* 3.8 30.8 - - - +
147C GLU* 3.7 13.3 - - - +
179C ILE* 2.6 27.1 + - - +
180C VAL 4.4 1.3 + - - -
181C PHE 3.8 0.6 - - - -
182C TYR* 1.3 71.3 - - - +
184C SER* 1.3 60.6 + - - +
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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