Contacts of the helix formed by residues 132 - 146 (chain A) in PDB entry 2FE2
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 LYS 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LYS* 4.5 5.6 - - - +
130A ALA 3.5 6.8 + - - +
131A LYS* 1.3 81.4 - - - +
133A PRO* 1.3 88.0 - - + +
134A ALA* 3.0 23.2 - - - +
135A GLY* 3.0 12.7 + - - +
136A ALA 3.2 8.0 + - - -
218A LYS* 4.4 17.9 - - + +
221A ALA* 3.8 8.1 - - + -
225A LYS* 3.9 5.8 - - - +
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Residues in contact with PRO 133 (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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132A LYS* 1.3 100.5 - - + +
134A ALA* 1.3 61.1 + - - +
136A ALA* 3.3 2.8 + - - +
137A THR* 3.1 27.2 + - + +
221A ALA* 3.1 16.8 - - + +
224A LYS* 3.0 51.6 - - + +
225A LYS* 3.5 21.5 - - + +
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Residues in contact with ALA 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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117A GLU* 5.5 6.3 - - + -
132A LYS* 3.0 24.9 - - + +
133A PRO* 1.3 77.7 - - - +
135A GLY* 1.3 59.0 + - - +
137A THR* 2.6 24.0 + - - -
138A PRO* 2.8 16.8 - - + +
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Residues in contact with GLY 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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117A GLU* 3.8 21.1 - - - -
118A ALA* 3.7 9.7 - - - -
120A PRO* 5.7 0.9 - - - -
131A LYS* 2.9 23.1 - - - -
132A LYS* 3.0 8.1 + - - +
134A ALA* 1.3 79.5 - - - +
136A ALA* 1.3 62.4 + - - +
138A PRO* 3.5 5.7 - - - +
139A LYS* 3.2 15.6 + - - +
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Residues in contact with ALA 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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131A LYS* 3.0 17.6 - - - +
132A LYS 3.2 2.0 + - - +
133A PRO* 3.5 9.2 - - + +
134A ALA 3.1 0.4 - - - -
135A GLY* 1.3 77.3 - - - +
137A THR* 1.3 64.6 + - + +
139A LYS* 2.9 18.0 + - + +
140A LYS* 3.0 13.0 + - - +
225A LYS* 3.7 38.6 - - + +
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Residues in contact with THR 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 PRO* 3.1 13.3 + - + +
134A ALA* 2.6 24.7 + - - -
136A ALA* 1.3 77.1 - - + +
138A PRO* 1.3 72.5 - - - +
140A LYS* 3.1 12.7 + - + +
141A ALA* 2.9 20.5 + - - +
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Residues in contact with PRO 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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114A ALA 5.8 0.4 - - - +
115A SER* 3.4 33.9 + - - +
117A GLU* 3.8 20.6 - - + -
118A ALA* 4.2 4.0 - - - +
134A ALA 2.8 24.0 - - - +
135A GLY 4.0 3.6 - - - +
136A ALA 3.4 0.4 - - - -
137A THR* 1.3 87.0 - - - +
139A LYS* 1.3 63.2 + - - +
141A ALA* 3.9 8.1 - - + -
142A LYS* 2.9 27.5 + - - +
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Residues in contact with LYS 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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67A ALA* 5.3 12.5 - - - +
118A ALA* 3.8 16.7 - - + +
121A LYS* 3.9 23.0 - - + +
131A LYS* 4.5 14.3 - - - +
135A GLY 3.2 11.7 + - - +
136A ALA* 2.9 15.3 + - + +
138A PRO* 1.3 77.6 - - - +
140A LYS* 1.3 64.6 + - - +
142A LYS* 3.3 11.3 + - - +
143A LYS* 3.4 13.0 + - - +
201A LYS* 6.1 0.3 - - - -
203A LYS* 6.0 1.3 - - - +
204A ALA* 4.0 30.1 - - + -
208A LYS* 6.1 4.8 - - - +
215A ALA* 4.1 17.2 - - - +
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Residues in contact with LYS 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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136A ALA 3.0 6.3 + - - +
137A THR* 3.5 13.0 - - + +
139A LYS* 1.3 79.0 - - - +
141A ALA* 1.3 75.3 + - - +
143A LYS* 3.4 7.4 + - + +
144A ALA* 3.1 39.0 + - + +
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Residues in contact with ALA 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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115A SER* 3.5 12.6 - - - +
137A THR 2.9 14.0 + - - +
138A PRO* 3.0 11.2 + - + +
140A LYS* 1.3 92.0 - - - +
142A LYS* 1.3 62.6 + - - +
144A ALA* 3.2 3.1 + - - +
145A ALA* 3.1 22.9 + - - +
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Residues in contact with LYS 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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115A SER* 2.9 55.0 - - - +
116A GLY* 4.3 1.0 - - - -
118A ALA* 4.6 2.5 - - + -
138A PRO 2.9 12.0 + - - +
139A LYS* 3.5 9.4 - - - +
141A ALA* 1.3 75.0 - - - +
143A LYS* 1.3 64.5 + - - +
145A ALA* 3.2 17.4 + - - +
146A GLY* 3.5 4.2 + - - -
189A PRO* 5.3 2.0 - - - +
195A VAL* 2.8 28.6 + - - +
196A LYS 2.8 22.4 + - - -
197A PRO* 3.2 44.3 - - + +
200A ALA* 2.9 24.3 - - + +
201A LYS* 4.6 4.1 - - + +
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Residues in contact with LYS 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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139A LYS 3.4 7.4 + - - +
140A LYS* 3.7 10.5 - - + +
141A ALA 3.3 0.4 - - - -
142A LYS* 1.3 80.3 - - - +
144A ALA* 1.3 65.9 + - - +
146A GLY 3.2 19.6 + - - +
201A LYS* 3.0 57.4 + - + +
204A ALA* 6.0 4.3 - - - -
205A ALA* 6.5 0.4 - - - -
208A LYS* 4.2 21.2 - - - +
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Residues in contact with ALA 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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140A LYS* 3.1 37.0 + - + +
141A ALA 3.7 4.7 - - - +
143A LYS* 1.3 81.0 - - - +
145A ALA* 1.3 61.1 + - - +
146A GLY 3.4 4.9 + - - +
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Residues in contact with ALA 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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110A ASN* 3.6 22.2 + - - +
141A ALA 3.1 9.7 + - - +
142A LYS 3.3 11.2 - - - +
143A LYS 3.1 0.4 - - - -
144A ALA* 1.3 79.3 - - - +
146A GLY* 1.3 58.4 + - - +
197A PRO* 4.1 8.3 - - + -
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Residues in contact with GLY 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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110A ASN* 4.2 10.5 - - - -
142A LYS 3.5 4.9 + - - -
143A LYS 3.2 17.2 + - - +
144A ALA 3.9 4.1 - - - +
145A ALA* 1.3 81.5 - - - +
147A ALA* 1.4 64.4 + - - +
150A ALA* 5.1 6.5 - - - -
151A VAL* 5.2 2.7 - - - -
197A PRO* 5.8 0.4 - - - -
198A LYS* 6.0 3.8 - - - -
201A LYS* 4.0 10.0 + - - -
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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