Contacts of the helix formed by residues 171 - 182 (chain C) in PDB entry 2X1L
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 TYR 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ALA* 5.5 0.2 - - - +
116C ASP* 2.6 37.1 + - - -
166C PHE* 4.0 16.8 - + - -
167C ARG 3.2 25.8 - - - -
168C LEU 3.1 8.4 + - - +
170C ALA* 1.3 79.6 - - - +
172C THR* 1.3 63.8 + - - +
173C ASP 3.5 2.2 - - - -
174C ARG* 3.3 26.9 + - - +
175C LEU* 2.9 29.4 + - + +
276C ALA* 4.3 11.9 - - + -
279C MET* 3.7 40.1 - - + -
280C SER* 3.3 17.2 - - - -
602C CXS 3.5 31.6 - - + +
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Residues in contact with THR 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 LEU 3.7 1.7 + - - -
169C SER* 3.6 15.6 + - - -
170C ALA 3.6 1.6 - - - -
171C TYR* 1.3 78.5 - - - +
173C ASP* 1.3 67.3 + - - +
175C LEU* 3.3 4.2 + - - +
176C LEU* 3.1 30.3 + - + +
199C VAL* 3.4 30.7 - - + +
200C SER 5.8 0.2 - - - -
202C GLY* 4.5 4.9 - - - -
203C LEU* 3.4 40.9 + - - +
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Residues in contact with ASP 173 (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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170C ALA 5.5 0.4 + - - -
171C TYR 3.5 0.2 - - - -
172C THR* 1.3 84.2 - - - +
174C ARG* 1.3 61.3 + - - +
176C LEU* 3.6 23.8 - - - +
177C ALA* 2.9 27.5 + - - +
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Residues in contact with ARG 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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170C ALA 5.6 0.2 + - - -
171C TYR* 3.3 26.0 + - - +
173C ASP* 1.3 76.2 - - - +
175C LEU* 1.3 61.6 + - - +
177C ALA* 3.5 7.4 + - + +
178C LEU* 3.1 24.1 + - - +
279C MET* 3.4 50.5 + - - +
602C CXS 2.8 43.3 + - - +
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Residues in contact with LEU 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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168C LEU* 4.6 1.1 - - + -
171C TYR* 2.9 27.8 + - + +
172C THR 3.5 3.8 - - - +
174C ARG* 1.3 75.8 - - - +
176C LEU* 1.3 62.8 + - - +
178C LEU* 3.1 11.8 + - + +
179C TYR* 3.1 48.9 + - + +
199C VAL* 4.4 2.5 - - + -
203C LEU* 3.8 27.6 - - + -
271C THR 4.2 0.2 - - - +
272C VAL* 3.7 22.0 - - + +
275C PRO* 3.6 33.4 - - + -
276C ALA* 4.5 3.1 - - + -
279C MET* 3.7 20.0 - - + -
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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 THR* 3.1 20.1 + - + +
173C ASP* 3.6 29.8 - - - +
174C ARG 3.4 0.2 - - - -
175C LEU* 1.3 76.5 - - - +
177C ALA* 1.3 60.5 + - - +
179C TYR* 3.5 13.8 + - + +
180C GLU* 3.2 23.2 + - - +
196C VAL* 3.9 12.8 - - + +
199C VAL* 3.8 22.9 - - + -
200C SER* 3.6 34.3 - - - +
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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 ASP 2.9 18.3 + - - +
174C ARG* 3.7 10.3 - - + +
175C LEU 3.2 0.2 - - - -
176C LEU* 1.3 72.8 - - - +
178C LEU* 1.3 60.7 + - - +
180C GLU* 4.0 5.3 - - - +
181C GLU* 3.1 31.9 + - - +
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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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174C ARG 3.1 13.5 + - - +
175C LEU* 3.1 13.6 + - + +
177C ALA* 1.3 76.3 - - - +
179C TYR* 1.3 62.7 + - + +
181C GLU* 5.0 1.3 - - - -
182C HIS* 2.8 60.0 + - + +
185C PHE* 3.8 43.3 - - + -
275C PRO* 4.1 10.1 - - + -
279C MET* 5.7 2.9 - - - -
285C LEU* 3.8 33.4 - - + -
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Residues in contact with TYR 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 LEU* 3.1 33.8 + - + +
176C LEU* 3.7 15.3 - - + +
177C ALA 3.4 0.2 - - - -
178C LEU* 1.3 82.2 - - + +
180C GLU* 1.3 61.5 + - - +
182C HIS 4.3 4.7 - - - -
183C PRO* 3.5 24.9 - - - +
185C PHE* 4.2 14.1 - + + -
186C ILE* 3.7 24.7 - - + -
192C ARG* 4.3 10.2 + - + +
195C ILE* 3.6 16.1 - - + +
196C VAL* 3.8 33.0 - - + -
199C VAL* 3.7 29.9 - - + +
271C THR 2.7 28.8 + - - -
272C VAL* 3.7 2.8 - - - +
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Residues in contact with GLU 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 3.2 14.9 + - - +
177C ALA* 4.0 6.1 - - - +
179C TYR* 1.3 82.4 - - - +
181C GLU* 1.3 61.9 + - - +
183C PRO* 3.8 11.8 - - - +
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Residues in contact with GLU 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 3.1 18.6 + - - +
180C GLU* 1.3 76.6 - - - +
182C HIS* 1.3 87.1 + - + +
183C PRO* 3.4 8.1 - - - +
184C GLU* 4.7 0.5 - - - +
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Residues in contact with HIS 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 46.0 + - + +
179C TYR* 3.6 4.5 - - - +
181C GLU* 1.3 101.0 + - + +
183C PRO* 1.4 63.8 - - - +
184C GLU* 3.0 27.4 + - - +
185C PHE* 3.1 22.8 + - + +
192C ARG* 5.2 0.5 - - - -
287C LYS 6.0 0.2 - - - +
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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