Contacts of the strand formed by residues 147 - 163 (chain E) in PDB entry 1PPG
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 147 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145E GLY 2.6 7.4 + - - -
146E ARG* 1.3 84.7 - - + +
148E ARG* 1.3 89.5 + - - +
150E GLY 3.3 5.9 + - - -
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Residues in contact with ARG 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E VAL* 4.7 11.9 - - - +
18E GLY* 5.0 6.7 - - - +
144E LEU* 3.8 39.6 + - + +
145E GLY* 3.2 19.7 + - - +
146E ARG* 4.4 24.5 - - - +
147E ASN* 1.3 100.8 + - - +
150E GLY* 1.3 64.9 + - - +
151E ILE 4.2 4.2 - - - +
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Residues in contact with GLY 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LEU* 3.3 16.5 - - - +
144E LEU* 2.6 33.3 + - - +
145E GLY 4.3 2.6 + - - -
147E ASN 3.3 4.9 + - - -
148E ARG* 1.3 81.7 - - - +
151E ILE* 1.3 58.8 + - - +
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Residues in contact with ILE 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E HIS* 3.6 39.3 - - + +
73E LEU* 6.2 0.9 - - + -
141E TRP* 3.3 17.5 - - + +
142E GLY* 3.6 8.7 - - - -
143E LEU* 3.3 23.6 - - + +
144E LEU* 4.6 3.5 - - - +
148E ARG 4.2 3.8 - - - +
150E GLY* 1.3 79.9 - - - +
152E ALA* 1.4 70.0 + - - +
153E SER* 4.0 1.2 + - - -
192E PHE 4.6 3.8 - - - +
193E GLY* 5.0 2.9 - - - -
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E LEU* 4.6 5.7 - - - +
141E TRP* 3.2 41.9 + - + +
142E GLY 3.3 7.0 + - - +
144E LEU* 4.0 22.4 - - + +
151E ILE* 1.4 83.0 - - - +
153E SER* 1.3 63.7 + - - +
154E VAL 3.5 19.1 - - - +
156E GLN* 4.1 3.8 - - + -
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Residues in contact with SER 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E HIS 3.3 5.0 - - - +
72E ASN* 3.6 16.2 - - - -
73E LEU* 2.8 28.6 + - - +
74E SER* 3.7 22.1 + - - +
141E TRP* 3.3 8.6 + - - -
144E LEU* 5.8 0.2 - - - +
151E ILE 4.0 1.5 + - - -
152E ALA* 1.3 77.6 - - - +
154E VAL* 1.4 68.1 + - - +
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Residues in contact with VAL 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ARG* 3.8 46.7 - - + +
22E ALA 4.8 0.2 - - - +
71E HIS* 3.4 34.5 - - + +
72E ASN* 3.1 30.3 - - + +
141E TRP* 4.0 2.7 - - - -
152E ALA* 3.5 4.9 - - - +
153E SER* 1.4 79.4 - - - +
155E LEU* 1.4 60.8 + - - +
156E GLN* 2.8 31.5 + - - +
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Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ARG* 3.6 2.9 - - - -
22E ALA* 2.8 39.4 + - + +
27E TRP* 4.1 19.5 - - + +
30E MET* 3.9 25.8 - - + -
70E ALA 5.7 1.6 - - - +
71E HIS* 3.3 25.7 + - - +
139E MET* 4.8 3.8 - - + -
140E GLY* 3.5 35.2 - - - +
141E TRP* 3.3 39.0 - - + +
154E VAL* 1.4 73.5 - - - +
156E GLN* 1.3 65.5 + - - +
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Residues in contact with GLN 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.7 19.6 + - + +
19E GLY* 3.5 16.2 + - - +
20E ARG* 3.2 24.0 + - - +
21E ARG* 3.3 21.1 - - - +
22E ALA 4.7 0.2 - - - -
139E MET* 3.1 7.0 - - - +
140E GLY 3.0 39.0 + - - +
144E LEU* 3.6 33.8 - - + +
152E ALA* 4.1 2.2 - - + +
154E VAL* 2.8 20.7 - - - +
155E LEU* 1.3 77.7 - - - +
157E GLU* 1.3 58.6 + - - +
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Residues in contact with GLU 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 5.2 0.2 - - - -
19E GLY* 3.3 2.7 - - - -
20E ARG* 2.9 77.3 + - + +
21E ARG 4.8 0.5 - - - +
22E ALA* 3.6 20.1 - - + +
23E ARG 4.7 1.3 + - - -
26E ALA* 5.3 0.5 - - - +
27E TRP* 2.7 37.6 + - - +
137E LEU* 3.8 19.8 - - + +
138E ALA 3.2 7.4 - - - +
139E MET* 4.1 5.4 - - + -
155E LEU 4.4 0.2 + - - -
156E GLN* 1.3 73.9 - - - +
158E LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.9 17.3 - - + -
17E VAL 4.1 0.2 - - - +
18E GLY 3.7 11.7 - - - +
19E GLY* 3.5 21.1 - - - +
20E ARG* 5.3 1.1 - - - +
137E LEU* 3.5 7.4 - - - +
138E ALA* 2.7 39.8 + - + +
157E GLU* 1.3 77.7 - - - +
159E ASN* 1.3 66.7 + - - +
160E VAL* 3.5 19.0 + - + +
185E VAL* 4.2 1.8 - - + -
186E ARG* 3.7 17.3 - - - +
188E ALA* 4.1 5.4 - - + -
189E GLY* 3.4 44.4 - - - +
190E VAL* 4.6 0.7 - - + +
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Residues in contact with ASN 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A NAG 1.5 68.5 + - + +
20E ARG* 2.6 43.6 + - - +
135E GLN* 5.0 4.4 - - - +
136E CYS 3.6 7.3 + - - -
137E LEU* 3.9 2.4 - - - +
158E LEU* 1.3 77.8 - - - +
160E VAL* 1.3 61.7 + - - +
185E VAL* 3.5 15.1 - - - +
186E ARG* 5.1 3.3 - - - +
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Residues in contact with VAL 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLN* 3.5 7.2 + - - +
136E CYS* 2.7 48.2 + - + +
137E LEU 4.4 0.4 - - - +
138E ALA* 4.0 9.9 - - + -
158E LEU* 3.7 22.0 - - + +
159E ASN* 1.3 79.4 - - - +
161E THR* 1.3 63.1 + - - +
183E THR* 3.6 30.1 - - + +
184E LEU 4.0 7.9 - - - +
185E VAL* 3.8 16.4 - - + +
189E GLY* 5.7 1.6 - - - -
190E VAL* 6.3 0.4 - - + -
199E LEU* 3.7 23.3 - - + -
226E ASP* 5.9 0.9 - - - +
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Residues in contact with THR 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLY* 3.4 36.6 - - - +
134E VAL 3.4 2.7 - - - +
135E GLN* 3.3 17.6 + - - +
136E CYS* 5.9 0.2 - - - -
160E VAL* 1.3 76.2 - - - +
162E VAL* 1.4 63.9 + - - +
163E VAL* 3.8 2.8 - - - +
183E THR* 2.9 12.4 - - - -
184E LEU 2.7 36.2 + - - -
185E VAL* 5.6 0.2 - - - -
186E ARG* 4.8 22.6 + - - +
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Residues in contact with VAL 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E LEU* 3.7 55.0 - - + +
131E GLY 3.8 12.6 - - - +
132E ASN* 3.7 5.3 - - - +
133E GLY 3.1 22.7 + - - -
134E VAL* 3.0 26.3 + - + +
136E CYS* 4.0 10.1 - - - -
161E THR* 1.4 70.9 - - - +
163E VAL* 1.3 73.6 - - - +
164E THR* 4.9 3.8 - - + -
181E VAL* 4.5 12.1 - - + -
182E CYS 3.1 14.4 - - - +
183E THR* 4.8 2.9 - - + -
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Residues in contact with VAL 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E ASN* 3.5 6.1 - - - +
161E THR* 3.8 6.1 - - - +
162E VAL* 1.3 83.7 - - - +
164E THR* 1.3 65.3 + - - +
165E SER* 4.0 8.3 - - - +
168E CYS* 4.1 2.4 - - - +
182E CYS* 3.1 26.7 + - + +
184E LEU* 3.7 29.6 - - + -
186E ARG* 3.5 28.5 - - - +
225E PRO* 3.3 37.9 - - + -
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Residues in contact with THR 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E LEU 4.8 7.9 - - - +
132E ASN* 2.9 35.5 + - + +
162E VAL* 4.9 3.4 - - + -
163E VAL* 1.3 75.2 - - - +
165E SER* 1.3 67.1 + - - +
168E CYS* 3.3 21.9 + - - +
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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