Contacts of the helix formed by residues 156 - 166 (chain P) in PDB entry 1PP9
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 ILE 156 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153P ILE* 4.2 9.6 - - + -
154P PRO 2.7 17.4 + - - +
155P TYR* 1.3 85.2 - - + +
157P GLY* 1.3 65.7 + - - +
158P THR 3.3 2.2 - - - -
159P ASN* 2.8 28.3 + - + +
160P LEU* 2.9 39.4 + - + +
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Residues in contact with GLY 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150P LEU 3.2 17.8 - - - +
151P SER* 3.7 9.2 - - - -
153P ILE* 2.9 28.2 + - - -
155P TYR 3.7 0.8 - - - -
156P ILE* 1.3 79.2 - - - +
158P THR* 1.3 61.8 + - - +
160P LEU* 3.2 7.3 + - - +
161P VAL* 3.1 24.4 + - - +
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Residues in contact with THR 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P SER* 4.1 14.8 + - - +
156P ILE 3.3 0.4 - - - -
157P GLY* 1.3 74.0 - - - +
159P ASN* 1.3 70.5 + - - +
161P VAL* 3.3 9.6 + - + +
162P GLU* 3.1 42.4 + - + +
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Residues in contact with ASN 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155P TYR 3.5 20.4 + - - -
156P ILE* 2.8 20.9 + - + +
158P THR* 1.3 82.1 - - - +
160P LEU* 1.3 58.1 + - - +
162P GLU* 3.4 12.8 + - - +
163P TRP* 2.9 30.6 + - - +
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150P LEU* 4.8 16.2 - - + -
153P ILE* 3.8 28.0 - - + -
156P ILE* 2.9 40.3 + - + +
157P GLY* 3.2 9.4 + - - +
159P ASN* 1.3 77.6 - - - +
161P VAL* 1.3 57.4 + - - +
163P TRP* 3.3 26.0 + - + +
164P ILE* 2.9 35.6 + - + +
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Residues in contact with VAL 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147P THR* 3.6 30.1 - - + +
148P ASN* 3.7 13.9 - - - +
150P LEU* 4.0 3.6 - - + -
151P SER* 3.7 19.3 - - - +
157P GLY 3.1 15.9 + - - +
158P THR* 3.5 7.9 - - + +
159P ASN 3.2 0.2 - - - -
160P LEU* 1.3 76.3 - - - +
162P GLU* 1.3 59.8 + - + +
164P ILE* 3.1 4.7 + - - +
165P TRP* 2.9 70.5 + - + -
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Residues in contact with GLU 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ALA 5.2 1.7 + - - -
94E LYS* 5.4 2.8 + - - -
158P THR* 3.1 33.9 + - + +
159P ASN* 3.9 11.5 - - - +
161P VAL* 1.3 77.7 - - + +
163P TRP* 1.3 57.8 + - - +
165P TRP* 4.3 8.3 - - + -
166P GLY* 2.8 24.8 + - - -
167P GLY 3.1 27.1 + - - +
168P PHE* 2.7 43.1 - - + +
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Residues in contact with TRP 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E VAL* 2.9 48.5 + - + +
62E MET* 3.4 38.6 - - + +
63E SER* 3.5 29.6 - - - +
159P ASN 2.9 18.7 + - - +
160P LEU* 3.5 24.0 - - + +
162P GLU* 1.3 78.4 - - - +
164P ILE* 1.3 87.3 + - + +
166P GLY 3.3 3.3 + - - -
177P ARG* 2.9 23.2 + - - -
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Residues in contact with ILE 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E MET* 5.2 7.0 - - + -
147P THR* 3.7 20.2 - - + -
150P LEU* 4.1 21.1 - - + -
160P LEU* 2.9 20.2 + - + +
161P VAL 3.1 6.9 + - - +
163P TRP* 1.3 99.7 - - + +
165P TRP* 1.3 58.3 + - + +
174P THR* 4.9 0.2 - - - +
177P ARG* 3.0 31.6 + - - +
178P PHE* 4.1 13.7 - - + -
181P PHE* 5.5 3.1 - - + -
3001P SMA 4.0 31.4 - - + -
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Residues in contact with TRP 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 5.8 0.7 - - - -
143P ALA 4.0 0.2 + - - -
144P THR* 3.9 15.3 - - + -
147P THR* 3.3 31.5 + - + -
148P ASN* 3.7 25.8 - - - -
161P VAL* 2.9 39.5 + - + +
162P GLU* 4.5 4.9 - - + -
164P ILE* 1.3 80.2 - - + +
166P GLY* 1.3 60.4 + - - +
167P GLY* 3.8 13.2 - - - +
168P PHE* 3.5 19.3 - - - -
169P SER* 3.4 31.9 - - - +
170P VAL* 3.4 27.4 - - + +
171P ASP* 5.2 0.5 + - - +
173P ALA* 3.6 3.1 - - - +
174P THR* 2.8 45.3 + - + +
177P ARG* 4.2 0.9 - - - -
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Residues in contact with GLY 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E MET 3.3 25.6 - - - -
63E SER 4.4 0.2 - - - -
64E ALA* 3.3 21.6 - - - +
65E SER 4.5 1.9 + - - -
68E VAL* 4.5 7.8 - - - +
162P GLU 2.8 11.2 + - - -
163P TRP 3.3 3.4 + - - -
165P TRP* 1.3 77.3 - - - +
167P GLY* 1.3 56.3 + - - +
173P ALA* 4.0 11.2 - - - +
177P ARG* 3.5 10.8 - - - -
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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