Contacts of the helix formed by residues 169 - 179 (chain C) in PDB entry 5PRC
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 ARG 169 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C VAL 5.6 1.3 - - - +
167C GLU 3.2 18.4 + - - +
168C THR* 1.3 69.9 - - - +
170C SER* 1.3 57.6 + - - +
171C GLY 2.9 11.0 + - - -
172C TYR* 3.0 22.7 + - - +
175C ARG* 3.9 6.3 - - - +
296C ARG* 6.2 3.6 - - - +
76M GLU 4.3 5.9 - - - +
78M HIS* 4.2 42.7 + - + +
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Residues in contact with SER 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C VAL* 4.5 0.5 - - - +
168C THR* 3.4 19.2 - - - +
169C ARG* 1.3 77.0 - - - +
171C GLY* 1.3 57.1 + - - +
172C TYR 3.4 0.6 + - - -
173C VAL 5.0 0.2 + - - -
76M GLU 5.1 0.6 - - - +
77M VAL* 3.2 36.3 - - - +
78M HIS* 4.1 5.3 - - - +
80M ASP* 3.7 25.9 + - - -
83M GLN* 3.8 11.4 - - - +
87M GLN* 3.0 27.4 + - - +
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C VAL* 3.5 31.7 - - - +
168C THR 3.0 5.0 + - - -
169C ARG 2.9 2.0 - - - -
170C SER* 1.3 81.0 + - - +
172C TYR* 1.3 63.5 + - - +
173C VAL 3.5 2.0 - - - -
174C VAL* 3.3 6.9 + - - +
175C ARG* 3.1 31.0 + - - +
87M GLN* 4.2 3.6 - - - -
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Residues in contact with TYR 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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149C GLU* 5.8 2.0 - - + -
150C PRO* 4.2 27.8 - - + +
169C ARG* 3.0 16.9 + - - +
170C SER 3.4 1.2 - - - -
171C GLY* 1.3 76.9 - - - +
173C VAL* 1.3 76.2 + - + +
175C ARG* 2.9 39.0 + - + +
176C LEU* 3.0 36.2 + - + +
186C ASN* 5.2 7.6 - - - -
188C ASP* 5.5 3.3 - - - +
76M GLU 5.0 5.2 - - - +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C SER 5.0 0.2 + - - -
171C GLY 3.5 0.4 - - - -
172C TYR* 1.3 88.8 - - + +
174C VAL* 1.3 58.3 + - + +
176C LEU* 3.3 7.0 + - - +
177C ALA* 2.8 26.7 + - + +
184C ALA* 6.0 2.0 - - - -
186C ASN* 5.0 5.8 - - - +
76M GLU* 3.6 37.0 + - + +
87M GLN* 3.4 21.2 + - + +
90M TRP* 3.7 37.7 - - + +
91M LEU* 4.1 13.9 - - + -
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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
----------------------------------------------------------
152C LEU* 4.0 6.1 - - + -
163C VAL* 5.9 0.7 - - + -
164C GLU* 6.4 1.3 - - + -
171C GLY* 3.3 7.6 + - - +
172C TYR 3.1 0.6 - - - -
173C VAL* 1.3 75.0 - - + +
175C ARG* 1.3 65.0 + - - +
176C LEU 3.0 1.8 - - - -
177C ALA* 4.1 5.6 - - - -
178C LYS* 2.9 43.6 + - + +
267L LEU* 4.2 17.9 - - + -
86M ARG* 3.7 30.3 - - - +
87M GLN* 3.4 40.6 - - + +
90M TRP* 6.5 0.2 - - + -
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Residues in contact with ARG 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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146C ARG* 4.5 0.9 + - - -
150C PRO* 3.2 44.3 + - + +
151C THR* 4.0 5.6 - - - +
152C LEU* 3.4 27.9 - - + +
163C VAL 2.9 28.6 + - - +
164C GLU* 3.4 16.4 + - - +
165C ARG 2.9 17.0 + - - -
166C VAL* 3.6 23.6 + - - +
168C THR 2.8 23.2 + - - -
169C ARG* 3.9 4.8 - - - +
171C GLY 3.1 14.5 + - - +
172C TYR* 2.9 34.4 + - + +
174C VAL* 1.3 76.5 - - - +
176C LEU* 1.3 58.9 + - - +
178C LYS 3.9 0.2 + - - -
179C TYR* 3.6 15.1 + - - +
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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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150C PRO* 3.9 18.8 - - + -
172C TYR* 3.0 37.6 + - + +
173C VAL* 3.5 9.6 - - - +
174C VAL 3.0 0.4 - - - -
175C ARG* 1.3 76.7 - - - +
177C ALA* 1.3 66.7 + - - +
178C LYS 3.1 1.1 - - - -
179C TYR* 2.9 18.0 + - + +
180C THR* 3.2 15.4 + - + +
185C LEU 4.0 9.6 - - - +
186C ASN* 4.0 17.0 - - - +
187C TYR 3.1 44.0 - - - +
188C ASP* 3.9 12.6 - - + +
189C PRO* 5.1 0.4 - - + -
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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 VAL 2.8 21.2 + - - +
174C VAL* 3.2 8.5 + - - +
176C LEU* 1.3 71.0 - - - +
178C LYS* 1.3 55.1 + - + +
180C THR* 3.1 12.7 + - - -
182C TYR* 2.6 33.5 + - - -
183C SER 3.4 24.0 - - - +
184C ALA* 5.4 0.4 - - - -
267L LEU* 4.7 10.3 - - + -
90M TRP* 4.0 20.9 - - + +
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Residues in contact with LYS 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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152C LEU* 3.8 29.3 - - + +
154C LEU* 3.8 21.1 - - + +
164C GLU* 4.7 12.3 + - - -
174C VAL* 2.9 35.9 + - + +
175C ARG 4.2 0.4 - - - +
177C ALA* 1.3 77.4 - - + +
179C TYR* 1.3 58.1 + - - +
180C THR 3.5 0.4 - - - -
181C ALA* 4.3 4.7 + - - -
182C TYR* 3.5 37.3 + - + +
238C ASP* 4.7 5.7 - - - +
267L LEU* 5.0 0.9 - - + -
268L ASP* 2.9 34.0 + - - -
86M ARG* 5.4 1.1 - - - +
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Residues in contact with TYR 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ARG* 3.4 46.3 - - - +
150C PRO* 5.3 0.4 - - + -
154C LEU* 4.0 8.7 - - + -
175C ARG 3.6 7.4 + - - +
176C LEU* 2.9 15.2 + - + +
178C LYS* 1.3 77.6 - - - +
180C THR* 1.3 61.7 + - + +
181C ALA 3.5 1.6 + - - -
188C ASP* 3.9 12.1 - - - -
189C PRO* 3.8 23.3 - - + -
190C PHE* 3.7 22.9 - - + +
194C LEU* 4.6 3.3 - - + +
235C SER* 3.5 36.0 + - - -
304C ASP* 2.6 41.1 + - - +
306C ARG* 3.8 21.3 + - - +
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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