Contacts of the helix formed by residues 171 - 182 (chain C) in PDB entry 6O81
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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170C PHE* 1.3 85.6 - - - +
172C ARG* 1.3 67.5 + - - +
173C THR* 4.2 8.8 - - - -
174C VAL* 3.3 27.9 + - - +
175C GLU* 3.3 22.2 + - - +
203C MET* 4.8 0.4 - - - +
235C GLY* 4.4 12.9 + - - -
236C THR 5.9 0.9 - - - -
273C LYS* 5.0 12.8 - - - -
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Residues in contact with ARG 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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29C ARG* 4.2 21.6 + - - +
30C SER* 3.5 38.6 + - - +
33C GLU* 5.4 0.8 + - - -
148C MET* 4.0 10.6 - - - +
170C PHE* 4.2 32.2 - - + -
171C SER* 1.3 72.7 - - - +
173C THR* 1.3 59.5 + - - +
174C VAL 3.5 0.2 - - - -
175C GLU* 3.9 11.1 - - - +
176C ALA* 2.9 32.2 + - - +
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Residues in contact with THR 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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148C MET* 4.5 17.9 - - + +
151C ILE* 3.9 30.5 - - + +
171C SER* 3.2 8.3 - - - -
172C ARG* 1.3 79.8 - - - +
174C VAL* 1.3 58.5 + - - +
176C ALA* 3.9 1.6 - - - +
177C PHE* 2.9 27.5 + - - +
268C CYS* 3.7 30.7 - - + +
270C PRO* 4.7 13.1 - - + +
273C LYS* 5.1 5.6 + - - -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C THR* 4.0 15.5 - - + -
168C ILE 5.8 0.9 - - - +
170C PHE* 5.8 0.2 - - - -
171C SER* 3.3 25.5 + - - +
173C THR* 1.3 74.6 - - - +
175C GLU* 1.3 62.1 + - - +
177C PHE* 3.3 6.9 - - - +
178C LEU* 3.0 34.7 + - + +
203C MET* 3.8 17.7 - - + -
233C ILE* 4.3 8.5 - - + -
234C ILE* 3.6 33.4 - - - +
235C GLY* 3.7 6.5 - - - +
268C CYS* 3.9 22.2 - - + +
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Residues in contact with GLU 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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170C PHE* 3.2 27.9 - - - -
171C SER 3.3 17.3 + - - +
172C ARG* 4.0 9.5 - - - +
173C THR 3.3 0.6 - - - -
174C VAL* 1.3 79.8 - - - +
176C ALA* 1.3 55.4 + - - +
178C LEU 3.5 0.2 + - - -
179C LYS* 2.8 60.4 + - - +
203C MET* 4.1 17.9 - - + +
206C ASN* 3.4 29.1 + - + +
207C LEU* 3.5 21.6 - - + +
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Residues in contact with ALA 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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148C MET* 3.7 30.3 - - + +
152C ALA* 5.5 0.9 - - - -
172C ARG 2.9 19.4 + - - +
173C THR 3.9 2.2 - - - +
175C GLU* 1.3 74.4 - - - +
177C PHE* 1.3 65.4 + - - +
179C LYS* 3.5 15.7 - - + +
180C GLU* 3.0 31.2 + - + +
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Residues in contact with PHE 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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151C ILE* 3.6 28.5 - - + -
152C ALA* 5.3 3.3 - - - +
155C ALA* 3.6 35.4 - - + -
158C HIS* 4.5 15.0 - + + -
159C ILE* 4.1 24.0 - - + -
173C THR 2.9 18.8 + - - +
174C VAL* 3.3 9.9 - - - +
176C ALA* 1.3 74.8 - - - +
178C LEU* 1.3 66.9 + - + +
180C GLU* 3.5 10.6 - - - +
181C ALA* 2.9 30.0 + - - +
233C ILE* 4.3 22.2 - - + -
266C ILE* 5.2 2.7 - - + -
268C CYS* 3.6 26.5 - - + -
325C ILE* 4.7 7.6 - - + -
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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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159C ILE* 4.7 6.5 - - + -
165C ILE* 3.9 17.5 - - + -
167C THR* 4.0 14.6 - - - +
174C VAL* 3.0 23.0 + - + +
175C GLU 4.1 2.2 - - - +
177C PHE* 1.3 90.2 - - + +
179C LYS* 1.3 57.6 + - - +
181C ALA* 3.7 3.1 - - - -
182C ALA* 2.9 32.4 + - - +
187C PHE* 3.7 27.8 - - + -
189C VAL* 3.8 16.2 - - + -
203C MET* 4.1 4.7 - - + -
207C LEU* 3.8 28.7 - - + -
212C ILE* 3.7 8.1 - - + +
233C ILE* 4.8 6.5 - - + -
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Residues in contact with LYS 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 GLU* 2.8 51.8 + - - +
176C ALA* 3.3 17.9 + - + +
178C LEU* 1.3 75.8 - - - +
180C GLU* 1.3 63.0 + - + +
182C ALA* 4.3 4.7 + - - +
183C ARG* 3.8 25.7 + - - +
206C ASN* 4.5 13.9 + - - +
207C LEU* 4.2 7.0 - - + -
210C ALA* 4.4 19.7 - - + +
212C ILE* 3.9 9.6 - - - +
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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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152C ALA* 2.8 46.8 - - + +
155C ALA* 3.3 20.3 - - - +
156C LEU* 3.9 14.5 - - - +
176C ALA 3.0 20.9 + - - +
177C PHE 3.5 6.0 - - - +
179C LYS* 1.3 77.5 - - + +
181C ALA* 1.3 66.8 + - - +
182C ALA 3.2 1.8 - - - -
183C ARG* 3.2 39.8 + - - +
184C LYS 4.6 0.7 + - - -
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Residues in contact with ALA 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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155C ALA* 4.9 7.4 - - + +
156C LEU* 5.3 10.5 - - + +
159C ILE* 4.2 27.6 - - + -
177C PHE* 2.9 24.1 + - + +
178C LEU* 3.9 3.4 - - - +
180C GLU* 1.3 84.9 - - - +
182C ALA* 1.3 59.3 + - - +
183C ARG 3.2 1.2 + - - -
184C LYS* 3.9 1.6 + - - +
185C ARG* 3.4 29.4 + - + +
187C PHE* 3.7 8.9 - - + -
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Residues in contact with ALA 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 16.2 + - - +
179C LYS 4.7 4.5 - - - +
180C GLU 3.2 0.6 - - - -
181C ALA* 1.3 75.3 - - - +
183C ARG* 1.3 62.6 + - - +
184C LYS 3.3 1.5 - - - -
185C ARG 3.3 18.7 - - - +
186C LYS* 4.9 9.9 + - + +
187C PHE* 3.7 5.1 - - + -
210C ALA* 5.4 4.4 - - + +
211C GLY 5.0 3.9 - - - +
212C ILE* 3.7 36.1 - - + -
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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