Contacts of the helix formed by residues 131 - 151 (chain A) in PDB entry 2PO5
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 PRO 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 5.0 1.3 - - + -
129A GLY 3.9 5.6 - - - +
130A SER* 1.3 90.7 - - - +
132A ILE* 1.3 64.7 + - - +
133A LYS 3.3 2.9 - - - -
134A ILE* 3.0 30.6 + - + +
135A TRP* 3.0 32.3 + - + +
340A ASP* 3.7 21.3 - - + +
341A HIS* 4.7 1.8 - - - -
345A LEU* 4.0 26.7 - - + -
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASN* 4.1 20.0 - - - +
77A GLY* 3.7 19.1 - - - -
78A GLY 3.7 4.0 - - - +
130A SER* 2.8 25.4 + - - +
131A PRO* 1.3 77.5 - - - +
133A LYS* 1.3 58.4 + - - +
135A TRP* 3.4 1.4 + - - +
136A THR* 2.7 44.8 + - - +
163A PHE* 3.8 20.4 - - + -
339A SER* 4.4 12.3 + - - +
340A ASP 3.6 17.9 - - - +
341A HIS* 3.2 35.4 - - + +
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 3.3 40.6 + - + +
130A SER 4.9 1.6 + - - +
131A PRO 3.3 1.2 - - - -
132A ILE* 1.3 77.6 - - - +
134A ILE* 1.3 61.0 + - + +
136A THR* 3.8 1.4 - - - -
137A SER* 2.8 46.4 + - - +
161A ILE* 4.3 8.7 - - + -
163A PHE* 3.8 24.1 - - + -
167A HIS 5.0 0.6 + - - -
168A PRO* 4.1 26.9 - - + +
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A SER 5.4 1.8 - - - +
131A PRO* 3.0 22.6 + - + +
133A LYS* 1.3 80.9 - - + +
135A TRP* 1.3 73.3 + - + +
137A SER* 3.4 5.7 + - - -
138A LYS* 3.1 23.5 + - + +
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Residues in contact with TRP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A PRO* 3.0 46.3 + - + +
132A ILE 4.0 1.8 - - - +
134A ILE* 1.3 83.3 - - + +
136A THR* 1.3 67.0 + - - +
138A LYS* 3.4 26.1 + - + +
139A GLN* 3.0 31.7 + - - +
339A SER* 3.9 19.3 - - - -
340A ASP* 4.3 9.3 + - - +
372A ASN* 3.5 49.5 + - + +
373A GLY* 3.4 26.0 - - - -
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 4.0 28.4 - - + +
75A ASN* 5.3 4.7 + - + +
132A ILE* 2.7 41.4 + - - +
133A LYS* 3.8 4.7 - - - -
135A TRP* 1.3 71.6 - - - +
137A SER* 1.3 59.5 + - - +
139A GLN* 3.3 12.0 + - - +
140A GLY* 2.8 28.6 + - - -
161A ILE* 3.8 28.9 - - + -
163A PHE* 4.0 7.0 - - + -
190A GLN* 5.3 5.3 - - + +
339A SER* 5.4 1.4 + - - -
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LYS* 2.8 31.5 + - - +
134A ILE* 3.6 7.0 - - - -
136A THR* 1.3 77.0 - - - +
138A LYS* 1.3 56.3 + - - +
140A GLY 3.4 0.2 + - - -
141A GLU* 2.9 42.6 + - - +
159A TYR* 3.5 22.7 + - - -
161A ILE* 3.4 14.6 - - - +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE* 3.1 18.4 + - + +
135A TRP* 3.8 30.1 - - + +
137A SER* 1.3 74.0 - - - +
139A GLN* 1.3 65.3 + - + +
141A GLU* 3.6 9.8 + - - +
142A GLY* 3.1 19.1 + - - -
373A GLY* 3.9 30.1 + - - -
378A SER* 4.3 1.9 + - - -
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 4.5 2.0 - - + +
135A TRP* 3.0 28.3 + - - +
136A THR* 3.7 13.5 + - - +
138A LYS* 1.3 75.8 - - + +
140A GLY* 1.3 60.9 + - - +
142A GLY 3.3 0.7 + - - -
143A MET* 2.9 29.1 + - - +
190A GLN* 4.5 8.1 - - - +
338A THR* 3.4 22.4 + - - -
339A SER* 4.2 6.9 - - - -
372A ASN* 2.9 31.9 + - - +
373A GLY* 5.3 0.9 - - - -
377A PHE* 3.1 33.1 - - + -
378A SER* 3.6 14.3 + - - +
381A LEU* 3.8 19.8 - - + +
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 3.6 27.3 - - - +
136A THR 2.8 14.0 + - - -
137A SER 3.8 0.9 - - - -
139A GLN* 1.3 77.3 - - - +
141A GLU* 1.3 55.9 + - - +
143A MET* 3.1 7.4 + - - +
144A VAL* 2.9 33.4 + - - +
159A TYR* 3.6 13.0 - - - -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A SER* 2.9 27.8 + - - +
138A LYS* 3.9 7.5 - - - +
140A GLY* 1.3 75.8 - - - +
142A GLY* 1.3 62.4 + - - +
144A VAL* 3.4 4.5 + - - +
145A LYS* 3.1 23.4 + - - +
159A TYR* 3.1 33.8 + - + -
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 3.1 15.8 + - - -
139A GLN 3.8 2.2 - - - -
141A GLU* 1.3 76.0 - - - +
143A MET* 1.3 63.2 + - - +
145A LYS* 3.4 13.4 + - - +
146A LEU* 3.3 26.0 + - - +
378A SER* 4.0 16.2 - - - -
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Residues in contact with MET 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 3.6 34.1 - - + -
73A MET* 4.2 12.1 - - - +
139A GLN 2.9 14.6 + - - +
140A GLY 3.1 10.3 + - - +
142A GLY* 1.3 75.4 - - - +
144A VAL* 1.3 61.7 + - + +
146A LEU* 3.1 5.4 + - - +
147A LEU* 2.9 37.9 + - + +
159A TYR* 4.0 21.8 - - + -
188A PHE* 4.2 5.6 - - - -
378A SER* 4.1 11.8 - - - -
381A LEU* 3.9 26.2 - - + -
382A ALA* 4.0 15.3 - - - +
385A VAL* 3.9 19.7 - - - -
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 5.2 0.4 - - + -
140A GLY 2.9 19.2 + - - +
141A GLU* 3.8 6.5 - - - +
143A MET* 1.3 80.6 - - + +
145A LYS* 1.3 67.6 + - - +
147A LEU* 3.8 6.8 - - + +
148A ASP* 3.0 35.7 + - - +
157A HIS* 3.2 30.3 - - + +
158A LYS* 4.1 2.7 - - - -
159A TYR* 3.7 35.7 - - + +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU 3.1 14.6 + - - +
142A GLY* 3.6 12.8 + - - +
143A MET 3.3 0.2 - - - -
144A VAL* 1.3 78.5 - - - +
146A LEU* 1.3 90.1 + - - +
148A ASP* 3.7 9.6 + - - +
149A GLU* 3.6 19.7 + - + +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 3.3 10.7 + - - +
143A MET 3.1 6.3 + - - +
145A LYS* 1.3 97.2 - - - +
147A LEU* 1.3 61.8 + - - +
149A GLU* 3.0 9.7 + - + +
150A LEU* 2.8 35.6 + - + +
375A PRO 5.3 0.9 - - - +
378A SER* 3.8 10.5 - - - +
379A LYS* 3.5 43.3 - - + +
382A ALA* 3.7 11.0 - - + -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.1 20.0 - - + -
143A MET* 2.9 40.7 + - + +
144A VAL* 3.2 4.5 + - - +
146A LEU* 1.3 71.5 - - - +
148A ASP* 1.3 57.6 + - - +
150A LEU* 4.1 5.8 - - + -
151A SER* 2.8 31.4 + - - -
157A HIS* 3.4 29.6 - - + +
382A ALA* 3.5 30.1 - - + +
385A VAL* 3.6 31.4 - - + -
386A HIS* 4.0 12.6 - - + +
389A ILE* 5.3 0.7 - - + -
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.0 28.5 + - - +
145A LYS* 3.9 8.7 - - - +
146A LEU 3.2 0.2 - - - -
147A LEU* 1.3 76.4 - - - +
149A GLU* 1.3 68.0 + - - +
152A PRO* 3.9 20.1 - - - +
155A ALA* 4.3 9.0 - - + +
156A PRO* 3.7 9.9 - - - +
157A HIS* 2.9 41.9 + - - +
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Residues in contact with GLU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LYS* 3.6 16.8 - - + +
146A LEU* 3.0 8.4 + - + +
148A ASP* 1.3 85.2 - - - +
150A LEU* 1.3 64.2 + - + +
151A SER 3.5 0.2 - - - -
152A PRO* 3.8 12.6 - - - +
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 2.8 21.8 + - + +
147A LEU* 3.9 6.7 - - + +
149A GLU* 1.3 78.2 - - + +
151A SER* 1.3 57.6 + - - +
152A PRO* 3.4 6.9 - - - +
382A ALA* 3.9 40.6 - - + +
383A ASP* 4.5 4.3 - - - +
386A HIS* 3.5 44.3 + - + +
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 2.8 20.2 + - - -
150A LEU* 1.3 75.1 - - - +
152A PRO* 1.3 65.1 - - - +
153A ASN* 3.1 4.9 + - - +
154A THR* 2.6 43.9 + - - +
155A ALA 3.3 0.2 + - - -
157A HIS* 3.3 14.3 - - - -
386A HIS* 3.8 20.5 - - - -
389A ILE* 4.6 9.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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