Contacts of the helix formed by residues 133 - 152 (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 ARG 133 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96F GLU* 2.5 43.1 + - - +
99F ARG* 4.0 7.3 - - - +
100F GLU* 2.9 19.2 + - - -
76O THR* 3.5 22.4 + - - +
81O SER* 6.3 0.2 - - - -
131O GLU* 2.8 39.6 + - + +
132O PHE* 1.3 73.0 - - - +
134O ARG* 1.3 56.8 - - - +
135O TRP* 3.6 36.2 - - + -
136O GLU* 2.9 31.5 + - + +
137O VAL* 2.7 33.5 + - - +
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Residues in contact with ARG 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ARG 5.4 0.4 + - - -
49F ARG* 2.9 31.7 + - - +
50F LEU 3.8 10.1 + - - -
51F PRO* 3.5 24.1 - - - +
93F TYR* 3.9 1.2 - - - -
132O PHE 3.3 3.6 + - - -
133O ARG* 1.3 70.1 - - - +
135O TRP* 1.3 77.5 + - + +
137O VAL* 3.4 2.3 + - - +
138O ALA* 2.9 29.0 + - + +
188O PRO* 4.0 22.7 - - + +
2010O PO4 2.5 46.5 + - - +
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Residues in contact with TRP 135 (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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48F ARG* 4.4 23.4 + - - +
49F ARG* 3.3 80.4 - - + +
93F TYR* 4.1 19.7 - + - -
96F GLU* 5.2 4.0 - - + -
100F GLU* 4.9 0.4 + - - -
3011F JZR 4.5 4.5 - - - -
133O ARG* 3.6 36.2 - - + +
134O ARG* 1.3 104.9 - - + +
136O GLU* 1.3 88.4 + - + +
138O ALA* 3.8 6.1 - - - +
139O ALA* 3.0 28.2 + - - +
2010O PO4 4.8 5.2 - - - -
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Residues in contact with GLU 136 (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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3011F JZR 2.8 31.7 + - - +
75O LEU* 3.3 28.5 - - + +
76O THR* 2.6 49.8 + - - +
82O SER* 4.6 1.3 - - - -
132O PHE 5.9 0.2 + - - -
133O ARG* 2.9 26.0 + - + +
135O TRP* 1.3 93.6 + - + +
137O VAL* 1.3 64.1 + - - +
139O ALA* 3.5 6.4 + - - +
140O LEU* 3.2 22.9 + - - +
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Residues in contact with VAL 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O LEU* 4.3 3.3 - - + +
75O LEU* 4.1 12.6 - - + -
132O PHE* 3.7 28.0 - - + +
133O ARG 2.7 18.6 + - - +
134O ARG 3.8 4.5 - - - +
136O GLU* 1.3 77.9 - - - +
138O ALA* 1.3 61.8 + - - +
140O LEU* 3.2 13.4 + - + +
141O GLN* 3.3 32.4 + - - +
186O VAL 4.0 6.5 - - - +
188O PRO* 4.1 16.2 - - + -
191O LEU* 3.9 28.7 - - + -
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Residues in contact with ALA 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134O ARG* 2.9 18.8 + - + +
135O TRP* 3.8 8.3 - - - +
136O GLU 3.3 0.2 - - - -
137O VAL* 1.3 77.2 - - - +
139O ALA* 1.3 62.2 + - - +
140O LEU 3.2 0.9 + - - -
141O GLN* 3.4 22.6 + - - +
142O PRO* 3.8 6.4 - - - +
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Residues in contact with ALA 139 (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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48F ARG* 6.2 3.1 - - - +
135O TRP 3.0 19.1 + - - +
136O GLU* 3.9 7.0 - - - +
137O VAL 3.3 0.2 - - - -
138O ALA* 1.3 75.9 - - - +
140O LEU* 1.3 57.2 + - - +
142O PRO* 3.1 18.0 - - - +
143O GLN 5.2 0.3 + - - -
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Residues in contact with LEU 140 (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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68O LEU* 3.7 23.5 - - + +
71O LEU* 3.8 20.6 - - + +
72O ALA* 3.6 31.6 - - + -
75O LEU* 4.2 17.9 - - + -
136O GLU 3.2 15.0 + - - +
137O VAL* 3.6 7.0 - - - +
138O ALA 3.1 0.8 - - - -
139O ALA* 1.3 75.5 - - - +
141O GLN* 1.3 65.6 + - - +
142O PRO* 3.1 4.0 - - - -
143O GLN* 2.9 37.5 + - + +
144O LEU 3.9 1.4 + - - -
191O LEU* 6.4 0.2 - - + -
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Residues in contact with GLN 141 (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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68O LEU* 3.5 18.1 - - - +
137O VAL* 3.3 20.7 + - - +
138O ALA* 3.4 13.4 + - - +
140O LEU* 1.3 74.2 - - - +
142O PRO* 1.3 64.4 - - + +
144O LEU* 2.9 44.1 + - - +
183O ILE* 3.8 7.8 - - + +
184O GLY* 2.8 50.5 + - - +
185O LYS 3.5 1.9 + - - -
186O VAL* 2.7 32.5 + - - +
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Residues in contact with PRO 142 (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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138O ALA 3.8 4.3 - - - +
139O ALA* 3.1 22.2 - - - +
140O LEU 3.1 1.3 - - - -
141O GLN* 1.3 95.2 - - + +
143O GLN* 1.3 60.9 + - - +
145O ARG* 3.1 22.5 + - + +
146O ILE* 3.3 18.8 + - + +
183O ILE* 5.3 2.0 - - + -
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Residues in contact with GLN 143 (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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282N CYS 3.0 28.0 + - - +
283N THR* 3.7 18.0 + - - +
284N TYR 5.1 5.2 - - - -
285N GLY* 6.5 1.1 - - - -
302N LYS* 6.0 0.3 + - - -
71O LEU* 3.9 20.6 - - + +
139O ALA 5.2 0.2 + - - -
140O LEU* 2.9 32.7 + - + +
142O PRO* 1.3 78.8 - - - +
144O LEU* 1.3 53.6 + - - +
146O ILE* 3.7 22.0 - - - +
147O ASP* 2.8 42.6 + - - +
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Residues in contact with LEU 144 (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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67O HIS* 3.6 28.8 - - + +
68O LEU* 3.7 40.2 - - + +
71O LEU* 3.6 20.2 - - + -
141O GLN* 2.9 36.5 + - - +
143O GLN* 1.3 78.3 - - - +
145O ARG* 1.3 54.2 + - - +
148O LYS* 3.0 32.2 + - - +
178O CYS* 4.1 21.9 - - + +
183O ILE* 4.0 21.7 - - + +
186O VAL* 4.5 3.4 - - + -
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Residues in contact with ARG 145 (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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141O GLN 4.0 0.4 + - - -
142O PRO* 3.1 13.4 + - + +
144O LEU* 1.3 77.6 - - - +
146O ILE* 1.3 61.2 + - + +
148O LYS* 3.5 3.0 + - - +
149O ALA* 2.9 33.4 + - + +
180O ASP* 4.8 14.5 + - - +
183O ILE* 3.4 54.3 + - + +
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Residues in contact with ILE 146 (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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282N CYS* 4.0 43.3 - - + +
283N THR* 4.9 1.1 - - + -
302N LYS* 6.1 5.2 - - + +
142O PRO* 3.7 15.9 - - + +
143O GLN* 3.2 27.0 + - - +
145O ARG* 1.3 74.8 - - + +
147O ASP* 1.3 66.2 + - - +
149O ALA* 3.3 4.9 + - - +
150O VAL* 3.0 28.4 + - + +
42V VAL* 4.7 10.3 - - + +
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Residues in contact with ASP 147 (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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283N THR* 4.7 7.4 - - - +
67O HIS* 2.8 30.0 + - - +
70O ARG* 4.2 2.8 + - - -
71O LEU* 3.7 20.1 - - + +
143O GLN* 2.8 27.4 + - - +
144O LEU 4.0 0.4 - - - +
146O ILE* 1.3 75.3 - - - +
148O LYS* 1.3 62.0 + - - +
150O VAL* 3.4 6.5 + - - +
151O ALA* 3.1 22.0 + - - +
177O TYR* 4.0 10.3 - - - -
68V VAL* 4.0 8.4 - - - +
74V ALA* 3.8 24.6 - - - +
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Residues in contact with LYS 148 (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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67O HIS* 4.4 5.8 - - + -
144O LEU 3.0 19.1 + - - +
145O ARG* 3.9 3.4 - - - +
147O ASP* 1.3 75.5 - - - +
149O ALA* 1.3 59.3 + - - +
151O ALA* 3.2 1.7 + - - +
152O LEU* 2.8 57.7 + - + +
177O TYR* 4.0 30.3 + - + -
178O CYS 2.9 26.9 + - - +
179O PRO* 3.9 3.2 - - - +
180O ASP* 2.7 38.1 + - - +
183O ILE* 4.7 5.4 - - + -
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Residues in contact with ALA 149 (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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145O ARG* 2.9 20.9 + - + +
146O ILE* 3.8 5.2 - - - +
148O LYS* 1.3 76.0 - - - +
150O VAL* 1.3 64.5 + - - +
152O LEU* 3.4 6.6 + - - +
153O GLN* 3.3 23.7 + - - +
42V VAL* 4.3 18.5 - - + +
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Residues in contact with VAL 150 (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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282N CYS* 4.5 2.2 - - - -
283N THR* 3.9 18.6 - - + -
146O ILE* 3.0 24.2 + - + +
147O ASP 3.7 4.9 - - - +
148O LYS 3.2 0.2 - - - -
149O ALA* 1.3 78.3 - - - +
151O ALA* 1.3 64.5 + - - +
153O GLN* 3.3 25.8 + - - +
154O ASN* 3.9 5.7 + - - -
40V SER* 3.4 37.0 - - - +
41V PRO 4.8 0.7 - - - -
42V VAL* 4.3 20.4 - - + -
74V ALA* 5.5 9.2 - - + +
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Residues in contact with ALA 151 (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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147O ASP 3.1 9.9 + - - +
148O LYS 3.7 5.4 - - - +
150O VAL* 1.3 77.4 - - - +
152O LEU* 1.3 61.9 + - + +
153O GLN 3.1 1.8 + - - -
154O ASN* 2.9 27.8 + - - +
157O ALA* 3.5 10.8 - - + +
177O TYR* 3.2 48.5 - - + +
76V VAL* 4.3 10.5 - - + -
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Residues in contact with LEU 152 (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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148O LYS* 2.8 49.5 + - + +
149O ALA* 3.4 7.4 + - - +
150O VAL 3.3 0.4 - - - -
151O ALA* 1.3 77.7 - - + +
153O GLN* 1.3 58.9 + - - +
154O ASN 3.0 5.8 - - - -
157O ALA* 4.0 18.6 - - + +
158O HIS* 2.8 59.2 + - + +
161O GLU* 5.5 3.6 - - + -
177O TYR* 4.7 12.3 - - + -
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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