Contacts of the helix formed by residues 155 - 170 (chain C) in PDB entry 4PKO
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 ASP 155 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C THR* 3.2 17.6 + - - +
152C ALA* 3.8 15.2 + - + +
153C ASN 3.4 0.8 - - - +
154C SER* 1.3 75.7 - - - +
156C GLU* 1.3 64.0 + - - +
157C THR* 3.3 24.6 + - - -
158C VAL* 3.4 31.4 + - + +
159C GLY 3.4 6.1 + - - -
185C ASP* 5.3 2.1 - - - +
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Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C THR* 3.7 18.2 + - + -
154C SER 3.8 5.5 + - - +
155C ASP* 1.3 71.9 + - - +
157C THR* 1.3 56.8 + - - +
159C GLY* 3.2 0.9 + - - -
160C LYS* 2.7 43.7 + - + +
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Residues in contact with THR 157 (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 ASP* 3.3 11.0 + - - -
156C GLU* 1.3 77.8 - - - +
158C VAL* 1.3 54.4 + - - +
160C LYS* 4.0 7.3 - - + +
161C LEU* 2.7 46.2 + - + +
185C ASP* 3.3 33.4 - - + +
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Residues in contact with VAL 158 (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 GLY 4.2 3.4 - - - +
152C ALA* 3.5 28.3 - - + -
155C ASP* 3.4 28.9 + - + +
156C GLU 3.2 0.4 - - - -
157C THR* 1.3 77.2 - - - +
159C GLY* 1.3 56.2 + - - +
161C LEU* 3.9 5.3 - - - +
162C ILE* 3.0 49.9 + - + +
185C ASP* 5.0 8.3 - - - +
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Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE 4.7 0.3 - - - +
145C ALA* 3.2 16.3 - - - -
148C GLY* 4.0 4.3 - - - -
149C THR* 3.0 29.6 - - - +
155C ASP 3.4 4.9 + - - -
156C GLU 3.2 3.2 + - - -
158C VAL* 1.3 81.2 - - - +
160C LYS* 1.3 56.3 + - - +
162C ILE* 4.0 1.3 - - - +
163C ALA* 3.0 32.4 + - - +
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Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ALA* 4.2 11.5 - - + +
149C THR* 4.3 0.2 + - - -
156C GLU* 2.7 25.6 + - - +
157C THR* 4.0 6.3 - - + +
159C GLY* 1.3 72.8 - - - +
161C LEU* 1.3 61.3 + - - +
163C ALA* 4.0 1.4 - - - +
164C GLU* 3.2 47.9 + - + +
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C THR* 2.7 28.3 + - + +
158C VAL* 3.9 5.8 - - - +
160C LYS* 1.3 73.3 - - - +
162C ILE* 1.3 65.1 + - + +
164C GLU* 3.4 14.4 + - - +
165C ALA* 3.2 21.3 + - - +
185C ASP* 3.4 43.1 - - + +
186C GLU* 4.3 7.4 - - - +
187C LEU* 4.0 30.5 - - + +
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 4.8 5.2 - - + +
148C GLY* 4.9 14.8 - - - +
158C VAL* 3.0 38.7 + - + +
159C GLY* 4.1 3.1 - - - +
161C LEU* 1.3 74.3 - - + +
163C ALA* 1.3 61.2 + - - +
165C ALA* 3.1 8.0 + - + +
166C MET* 2.9 46.9 + - + +
175C ILE* 6.3 7.2 - - + -
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Residues in contact with ALA 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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141C SER* 3.5 33.0 + - - +
144C ILE* 3.6 16.2 - - + +
145C ALA* 3.6 13.9 - - + +
159C GLY 3.0 19.5 + - - +
160C LYS* 4.0 4.3 - - - +
162C ILE* 1.3 76.5 - - - +
164C GLU* 1.3 58.2 + - + +
166C MET* 3.6 2.3 + - - +
167C ASP* 2.8 30.8 + - - +
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Residues in contact with GLU 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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160C LYS* 3.2 40.7 + - + +
161C LEU* 3.6 13.8 - - - +
162C ILE 3.2 0.4 - - - -
163C ALA* 1.3 77.8 - - + +
165C ALA* 1.3 56.7 + - - +
167C ASP* 3.1 7.0 + - + +
168C LYS* 2.7 61.6 + - - +
187C LEU* 4.4 9.5 - - + +
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Residues in contact with ALA 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 LEU 3.2 10.6 + - - +
162C ILE* 3.1 12.2 + - + +
164C GLU* 1.3 77.8 - - - +
166C MET* 1.3 62.6 + - - +
168C LYS* 3.3 3.6 + - - +
169C VAL* 3.0 34.3 + - + +
175C ILE* 4.5 22.9 - - + -
187C LEU* 3.8 28.9 - - + +
189C VAL* 6.0 1.3 - - - -
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Residues in contact with MET 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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144C ILE* 4.0 31.2 - - + -
162C ILE* 2.9 31.1 + - + +
163C ALA 3.9 3.4 - - - +
165C ALA* 1.3 76.8 - - + +
167C ASP* 1.3 57.1 + - - +
169C VAL* 4.6 1.3 - - - -
170C GLY* 2.8 38.5 + - - +
171C LYS* 3.6 46.4 + - + +
175C ILE* 4.7 16.6 - - + -
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C SER* 2.8 24.0 + - - +
144C ILE* 5.6 0.9 - - - +
163C ALA 2.8 20.9 + - - +
164C GLU* 3.1 10.3 + - - +
166C MET* 1.3 79.8 - - - +
168C LYS* 1.3 65.3 + - + +
170C GLY* 4.1 2.9 + - - -
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C GLU* 2.7 44.5 + - - +
165C ALA* 3.9 3.4 - - - +
167C ASP* 1.3 82.5 - - - +
169C VAL* 1.3 68.2 + - + +
170C GLY 3.7 0.2 + - - -
187C LEU* 4.7 12.6 + - + +
189C VAL* 4.5 23.6 - - + +
191C GLU* 5.3 5.0 - - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ALA* 3.0 20.8 + - + +
166C MET* 4.6 0.4 - - - -
168C LYS* 1.3 79.0 - - + +
170C GLY* 1.3 62.1 + - - +
172C GLU* 4.4 2.3 + - - +
173C GLY* 3.4 41.6 + - - +
174C VAL 4.6 4.7 - - - +
175C ILE* 4.8 8.1 - - + -
189C VAL* 4.1 27.4 - - + -
191C GLU* 5.0 4.9 - - - +
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Residues in contact with GLY 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C MET* 2.8 32.2 + - - +
167C ASP 4.1 3.2 + - - -
168C LYS 3.4 3.0 + - - -
169C VAL* 1.3 86.5 - - - +
171C LYS* 1.3 68.1 + - - +
172C GLU 3.4 0.9 - - - -
173C GLY* 3.4 5.9 + - - +
175C ILE* 5.4 0.7 - - - +
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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