Contacts of the helix formed by residues 154 - 168 (chain O) 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 ASN 154 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150O VAL 3.9 7.1 + - - -
151O ALA 2.9 22.8 + - - +
152O LEU 3.0 1.5 - - - -
153O GLN* 1.3 82.7 - - - +
155O PRO* 1.3 70.4 - - - +
156O GLN* 3.0 12.3 - - + +
157O ALA* 2.9 23.2 + - + +
158O HIS* 3.6 6.6 + - - -
76V VAL* 3.4 23.0 - - + +
78V TYR 6.0 1.1 - - - +
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Residues in contact with PRO 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153O GLN 3.4 10.3 - - - +
154O ASN* 1.3 82.4 - - - +
156O GLN* 1.3 71.9 + - - +
158O HIS* 2.9 26.0 + - + +
159O VAL* 3.0 16.1 + - - +
250O ASP* 4.7 14.4 - - - +
254O HIS* 3.7 35.0 - - + +
325O TYR* 4.1 1.8 - - - -
427O SER* 4.5 7.9 - - - +
58V GLN* 5.8 0.9 - - - +
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Residues in contact with GLN 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154O ASN* 3.5 11.6 - - + +
155O PRO* 1.3 88.2 - - - +
157O ALA* 1.3 58.0 + - - +
159O VAL* 3.4 0.5 + - - +
160O ILE* 2.8 37.0 + - - +
254O HIS* 3.7 14.1 - - - -
325O TYR* 3.2 24.0 - - + +
58V GLN* 2.9 55.6 + - - +
60V ALA* 4.5 8.1 - - + -
78V TYR* 4.0 20.6 - - - +
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Residues in contact with ALA 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151O ALA* 3.5 21.3 - - + +
152O LEU* 4.0 13.7 - - + -
154O ASN* 2.9 16.4 + - + +
156O GLN* 1.3 78.3 - - - +
158O HIS* 1.3 63.3 + - - +
161O GLU* 3.1 30.4 + - - +
177O TYR* 5.1 1.3 - - + -
64V LEU* 4.1 24.0 - - + -
76V VAL* 4.6 9.0 - - + -
78V TYR 4.7 1.4 + - - +
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Residues in contact with HIS 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O LEU* 2.8 59.3 + - + +
154O ASN 3.6 8.9 + - - -
155O PRO* 2.9 16.3 + - + +
157O ALA* 1.3 79.1 - - - +
159O VAL* 1.3 60.3 + - + +
161O GLU* 3.4 3.6 + - - +
162O ASN* 3.0 36.7 + - - +
246O GLU* 2.9 36.7 + - - +
248O ASN* 5.9 2.4 + - - -
427O SER* 4.7 5.4 - - - +
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Residues in contact with VAL 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O PRO 3.0 9.0 + - - +
156O GLN 3.9 0.4 - - - +
158O HIS* 1.3 77.5 - - - +
160O ILE* 1.3 60.9 + - - +
162O ASN* 3.2 2.5 + - - +
163O LEU* 2.8 28.2 + - - +
254O HIS* 3.6 23.8 - - + +
255O ALA 4.4 0.2 - - - -
256O ALA* 3.9 16.2 - - + +
325O TYR* 3.7 27.4 - - + +
425O ALA* 3.6 26.0 - - + +
426O ALA 4.7 1.8 - - - +
427O SER* 3.5 29.6 - - - +
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Residues in contact with ILE 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156O GLN 2.8 24.9 + - - +
157O ALA 4.3 1.8 - - - +
159O VAL* 1.3 74.6 - - + +
161O GLU* 1.3 63.5 + - - +
163O LEU* 3.4 10.0 + - + +
164O HIS* 2.9 53.4 + - + +
312O PHE* 3.6 30.5 - - + -
325O TYR* 3.8 24.5 - - + -
60V ALA* 3.9 4.0 - - + -
64V LEU* 4.2 29.6 - - + +
78V TYR* 3.3 20.2 - - - +
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Residues in contact with GLU 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O ARG* 2.7 32.7 + - - +
152O LEU* 5.5 3.1 - - + -
157O ALA* 3.1 23.7 + - + +
158O HIS* 3.7 4.3 - - - +
160O ILE* 1.3 77.6 - - - +
162O ASN* 1.3 64.2 + - - +
164O HIS* 3.5 3.5 + - - +
165O ALA* 3.2 20.4 + - - +
173O ALA 4.8 1.2 - - - +
175O SER* 2.5 38.6 + - - +
176O LEU* 2.7 21.8 + - - +
177O TYR* 4.0 9.4 + - + -
64V LEU* 3.6 23.3 - - + +
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Residues in contact with ASN 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158O HIS* 3.0 21.8 + - - +
159O VAL* 3.8 4.6 - - - +
161O GLU* 1.3 76.5 - - - +
163O LEU* 1.3 61.2 + - - +
165O ALA* 3.1 6.1 + - - +
166O ALA* 2.8 27.5 + - - +
244O ILE* 3.3 41.5 + - + +
246O GLU* 3.4 32.7 + - - +
425O ALA* 3.9 11.2 - - + +
426O ALA 5.5 2.0 + - - +
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Residues in contact with LEU 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159O VAL 2.8 17.9 + - - +
160O ILE* 3.6 8.3 - - + +
161O GLU 3.3 0.2 - - - -
162O ASN* 1.3 77.0 - - - +
164O HIS* 1.3 58.7 + - - +
166O ALA* 3.2 4.0 + - - +
167O ALA* 2.8 30.8 + - - +
256O ALA* 3.5 38.4 - - + +
258O VAL* 3.8 32.8 - - + -
312O PHE* 4.1 21.8 - - + -
321O LEU* 4.4 7.9 - - + -
423O SER 3.7 19.7 - - - +
424O MET* 3.8 8.5 - - - -
425O ALA* 3.6 9.3 - - + +
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Residues in contact with HIS 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O ARG* 3.3 43.5 - - - +
160O ILE* 2.9 42.2 + - + +
162O ASN 3.2 0.2 - - - -
163O LEU* 1.3 78.3 - - + +
165O ALA* 1.3 65.8 + - - +
167O ALA* 4.4 4.9 - - - +
168O TYR* 3.2 26.2 + + - -
172O LEU* 3.5 15.9 - - + +
173O ALA* 3.4 11.5 - - - +
312O PHE* 4.5 11.7 - + - -
314O ALA* 4.7 0.4 - - - +
316O TYR* 2.6 35.6 + + - -
321O LEU* 3.9 20.9 - - + +
63V PRO* 5.1 1.8 - - + -
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Residues in contact with ALA 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B PHE* 5.9 1.9 - - - -
161O GLU 3.2 12.5 + - - +
162O ASN* 3.1 12.0 + - - +
164O HIS* 1.3 77.3 - - - +
166O ALA* 1.3 61.0 + - - +
168O TYR 3.3 14.6 - - - +
173O ALA* 3.7 20.3 + - - +
244O ILE* 3.7 14.9 - - + +
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Residues in contact with ALA 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162O ASN 2.8 15.8 + - - +
163O LEU* 3.7 4.5 - - - +
165O ALA* 1.3 77.7 - - - +
167O ALA* 1.3 62.1 + - - +
168O TYR 4.7 0.3 - - - +
240O HIS* 4.3 5.2 + - - -
241O GLY 3.3 22.9 + - - +
242O GLY* 3.5 23.7 + - - +
243O GLU 4.1 0.2 - - - +
244O ILE* 3.7 20.8 - - + +
423O SER* 4.1 1.6 - - - -
424O MET 4.0 11.7 - - - +
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Residues in contact with ALA 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O LEU 2.8 16.2 + - - +
164O HIS 3.4 0.4 + - - +
166O ALA* 1.3 78.5 - - - +
168O TYR* 1.3 69.7 + - + +
239O TYR* 3.5 4.4 - - + -
240O HIS* 2.5 34.0 + - - -
241O GLY 2.9 5.4 + - - -
321O LEU* 3.9 22.7 - - + -
423O SER* 3.0 26.2 + - - +
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Residues in contact with TYR 168 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B PHE* 4.7 4.9 - - - -
164O HIS* 3.2 18.6 + + - -
165O ALA 3.3 17.0 - - - +
166O ALA 4.7 0.9 - - - +
167O ALA* 1.3 81.5 - - + +
169O ARG* 1.3 64.0 + - - +
170O ASN 3.4 17.9 - - - +
172O LEU* 3.6 34.8 - - + +
173O ALA* 3.4 12.0 - - + +
237O ALA* 3.9 11.4 - - + -
238O LYS 3.5 4.7 - - - +
239O TYR* 3.7 28.9 - - + -
240O HIS* 4.3 3.6 + - - +
316O TYR* 4.4 2.2 - + - -
319O SER* 2.7 37.0 + - - -
320O GLY* 3.6 5.9 + - - -
321O LEU* 3.4 44.3 - - + +
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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