Contacts of the helix formed by residues 161 - 172 (chain C) in PDB entry 6UZA
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 VAL 161 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C LEU* 4.2 9.0 - - + -
153C LEU* 4.2 17.9 - - + -
158C LEU* 4.2 31.4 - - + +
159C SER 4.3 3.4 - - - +
160C ARG* 1.3 76.6 - - - +
162C GLY* 1.3 62.2 + - - +
163C ASP 3.3 1.6 - - - -
164C ALA* 3.3 2.4 + - - +
165C LEU* 2.9 27.0 + - - +
180C ILE* 4.1 14.1 - - + +
183C HIS* 4.2 31.9 - - + +
186C PHE* 4.3 7.6 - - + -
206C PHE* 4.9 10.4 + - + -
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Residues in contact with GLY 162 (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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161C VAL* 1.3 78.3 - - - +
163C ASP* 1.3 56.6 + - - +
165C LEU* 3.3 7.0 + - - +
166C LEU* 3.0 23.2 + - - +
186C PHE* 4.4 1.6 - - - -
206C PHE* 4.0 25.7 + - - -
207C TYR* 3.4 36.0 - - - -
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Residues in contact with ASP 163 (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 GLN* 2.4 34.7 + - - +
160C ARG* 4.2 3.6 - - + -
161C VAL 3.3 2.0 - - - +
162C GLY* 1.3 72.8 - - - +
164C ALA* 1.3 60.3 + - - +
166C LEU* 3.7 7.9 - - - +
167C LEU* 2.9 28.1 + - - +
206C PHE 4.4 0.8 + - - -
207C TYR* 4.2 13.9 - - - +
208C ALA 3.8 17.9 - - - +
209C TYR* 3.4 10.3 - - + +
215C ARG* 3.0 47.2 + - - +
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Residues in contact with ALA 164 (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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137C LEU* 3.8 24.9 - - + +
138C GLN* 5.0 6.5 - - + -
141C VAL* 3.5 20.3 - - + +
160C ARG 3.6 18.8 + - - +
161C VAL* 3.3 6.2 + - - +
162C GLY 3.3 0.4 - - - -
163C ASP* 1.3 78.9 + - - +
165C LEU* 1.3 58.9 + - - +
167C LEU* 3.4 5.6 + - - -
168C ALA* 3.0 30.5 + - - +
180C ILE* 3.9 7.8 - - + +
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Residues in contact with LEU 165 (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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161C VAL 2.9 14.2 + - - +
162C GLY* 3.5 7.4 - - - +
164C ALA* 1.3 77.0 - - - +
166C LEU* 1.3 57.1 + - - +
168C ALA* 3.4 2.8 + - - +
169C ILE* 2.9 47.0 + - + +
177C VAL* 4.4 11.2 - - + +
180C ILE* 3.8 29.1 - - + +
181C LEU* 3.8 30.3 - - + -
186C PHE* 3.7 26.9 - - + -
192C LEU* 4.4 0.9 - - + -
207C TYR* 4.7 4.5 - - + -
222C PRO* 3.8 29.6 - - + -
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Residues in contact with LEU 166 (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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162C GLY 3.0 17.6 + - - +
163C ASP* 3.3 10.3 + - - +
165C LEU* 1.3 76.7 - - - +
167C LEU* 1.3 57.8 + - - +
169C ILE* 3.4 2.8 + - + -
170C SER* 2.9 28.8 + - - -
207C TYR* 3.7 30.7 - - + +
214C THR* 6.4 1.1 - - - -
215C ARG* 6.0 1.1 - - + +
216C PHE* 4.1 29.4 - - + +
220C VAL* 4.4 12.6 - - + +
221C THR 4.3 3.6 - - - +
222C PRO* 4.0 39.5 - - + -
225C LEU* 3.3 22.4 - - + +
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Residues in contact with LEU 167 (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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872B ILE* 6.5 0.7 - - + -
134C GLN* 5.2 1.1 - - - +
138C GLN* 4.0 14.8 - - + +
141C VAL* 4.2 10.1 - - + -
142C ALA* 3.9 27.1 - - + +
163C ASP* 2.9 17.5 + - - +
164C ALA* 3.8 5.2 - - - +
165C LEU 3.3 0.2 - - - -
166C LEU* 1.3 78.3 - - - +
168C ALA* 1.3 55.9 + - - +
170C SER* 3.3 7.6 + - - -
171C LYS* 3.0 51.8 + - + +
215C ARG* 4.1 38.4 - - - +
216C PHE* 4.7 4.2 - - + -
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Residues in contact with ALA 168 (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 VAL* 3.8 6.9 - - + +
164C ALA 3.0 18.5 + - - +
165C LEU 3.9 2.0 - - - +
167C LEU* 1.3 75.1 - - - +
169C ILE* 1.3 59.5 + - - +
172C GLY* 3.0 22.3 + - - -
173C TYR* 3.1 21.0 + - + +
176C ILE* 3.8 28.5 - - + -
177C VAL* 3.7 20.8 - - + +
180C ILE* 4.6 2.5 - - + -
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Residues in contact with ILE 169 (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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165C LEU* 2.9 33.6 + - + +
166C LEU* 3.8 5.2 - - - +
168C ALA* 1.3 74.7 - - - +
170C SER* 1.3 65.1 + - - +
172C GLY* 3.5 10.4 + - - -
177C VAL* 3.7 19.3 - - + -
222C PRO* 3.7 34.1 - - + +
225C LEU* 3.9 12.3 - - + -
226C ALA* 3.7 34.3 - - + +
229C CYS* 4.5 2.8 - - - -
231C GLU* 4.0 13.0 - - - +
234C ILE* 3.9 13.4 - - + +
238C LEU* 4.0 12.8 - - + -
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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
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166C LEU 2.9 18.8 + - - -
167C LEU* 3.6 10.3 - - - +
168C ALA 3.3 0.2 - - - -
169C ILE* 1.3 78.2 - - - +
171C LYS* 1.3 62.2 + - - +
172C GLY 3.7 0.2 + - - -
216C PHE* 3.7 27.7 - - - -
225C LEU* 4.3 5.3 - - - +
229C CYS* 4.2 22.7 - - - +
231C GLU* 4.4 3.6 - - - +
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Residues in contact with LYS 171 (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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872B ILE* 6.4 1.3 - - - +
875B GLU* 4.3 12.7 + - - -
141C VAL 4.6 0.2 - - - +
142C ALA* 3.7 28.7 + - - +
167C LEU* 3.0 41.0 + - + +
168C ALA 4.4 0.2 - - - +
170C SER* 1.3 79.3 - - - +
172C GLY* 1.3 60.0 + - - +
173C TYR* 3.6 46.0 + - + +
231C GLU* 4.5 1.9 - - - +
882C GLY 5.6 3.6 + - - -
885C LYS* 4.3 9.5 - - - +
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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
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168C ALA 3.0 6.8 + - - -
169C ILE 3.5 2.4 + - - -
170C SER 3.4 2.8 - - - -
171C LYS* 1.3 79.6 - - - +
173C TYR* 1.3 65.2 + - - +
174C VAL* 3.4 13.7 + - - +
231C GLU* 3.6 29.7 - - - +
234C ILE* 4.4 6.1 - - - -
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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