Contacts of the helix formed by residues 151 - 165 (chain E) in PDB entry 3LSG
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 SER 151 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152E ASN* 1.3 63.3 + - - +
153E ALA* 3.4 7.3 - - - +
154E LYS* 3.2 36.4 - - - +
155E GLU* 3.1 32.7 + - - +
193E ASN* 4.3 9.5 + - - -
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Residues in contact with ASN 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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151E SER* 1.3 77.1 - - - +
153E ALA* 1.3 59.4 + - - +
155E GLU* 3.4 9.1 + - - +
156E LEU* 3.0 28.1 + - - +
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Residues in contact with ALA 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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151E SER 3.4 6.1 - - - +
152E ASN* 1.3 82.2 - - - +
154E LYS* 1.3 61.5 + - - +
156E LEU* 3.3 9.4 + - - +
157E ILE* 3.0 31.0 + - + +
179E LEU* 5.8 0.2 - - - +
189E MSE 4.4 22.4 - - + -
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Residues in contact with LYS 154 (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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253A GLU* 2.7 43.7 + - - -
151E SER* 3.2 27.8 - - - +
153E ALA* 1.3 79.1 - - - +
155E GLU* 1.3 56.8 + - + +
157E ILE* 3.3 8.8 + - - +
158E GLN* 2.9 42.0 + - - +
189E MSE 5.9 0.2 - - - -
193E ASN* 3.0 39.3 + - - +
194E PHE* 3.7 29.6 - - + -
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Residues in contact with GLU 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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244A TYR 4.2 12.8 - - - +
245A GLN* 4.5 11.5 - - + +
246A ILE* 4.0 28.4 - - + +
251A TYR* 5.6 3.3 - - - -
151E SER 3.1 20.7 + - - +
152E ASN* 3.8 8.1 - - - +
154E LYS* 1.3 74.3 - - + +
156E LEU* 1.3 62.2 + - - +
158E GLN* 3.1 18.1 + - - +
159E ASN* 2.8 39.2 + - - +
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Residues in contact with LEU 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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152E ASN 3.0 17.6 + - - +
153E ALA* 3.7 9.2 - - - +
154E LYS 3.3 0.2 - - - -
155E GLU* 1.3 76.3 - - - +
157E ILE* 1.3 63.8 + - - +
159E ASN* 3.3 14.6 + - + +
160E ILE* 2.9 47.2 + - + +
178E LYS 5.8 1.3 - - - +
179E LEU* 3.7 20.9 - - + -
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Residues in contact with ILE 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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153E ALA* 3.0 22.3 + - + +
154E LYS* 3.5 6.5 - - - +
156E LEU* 1.3 74.3 - - - +
158E GLN* 1.3 64.5 + - - +
160E ILE* 3.3 7.4 + - - +
161E ILE* 2.9 46.6 + - + +
175E LEU* 4.1 7.6 - - + -
179E LEU* 3.8 26.0 - - + -
186E LEU* 4.3 5.6 - - + -
189E MSE 3.7 37.2 - - + -
190E PHE* 3.8 19.7 - - + -
194E PHE* 4.1 14.8 - - + -
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Residues in contact with GLN 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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246A ILE* 3.7 17.2 - - + +
250A GLN* 3.0 53.9 + - + +
253A GLU* 3.0 31.3 + - - +
154E LYS* 2.9 24.7 + - - +
155E GLU* 3.1 25.9 + - - +
157E ILE* 1.3 77.2 - - - +
159E ASN* 1.3 57.4 + - - +
161E ILE* 3.6 3.8 + - - +
162E GLU 3.0 22.5 + - - -
194E PHE* 3.7 20.0 - - + -
201E TYR* 4.0 6.2 + - - +
205E LYS* 5.0 0.2 + - - -
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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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241A LYS* 4.9 7.9 - - - +
245A GLN* 3.0 30.5 + - - +
246A ILE* 4.0 5.0 - - - +
250A GLN* 5.0 1.4 - - - +
155E GLU* 2.8 29.3 + - - +
156E LEU* 3.5 16.8 - - + +
158E GLN* 1.3 70.3 - - - +
160E ILE* 1.3 68.3 + - + +
162E GLU* 3.2 5.5 + - - +
163E GLU* 3.0 34.6 + - + +
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Residues in contact with ILE 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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156E LEU* 2.9 38.8 + - + +
157E ILE 3.8 2.7 - - - +
159E ASN* 1.3 74.8 - - + +
161E ILE* 1.3 63.5 + - - +
163E GLU* 3.1 5.7 + - - -
164E SER* 2.7 38.2 + - - +
170E PHE* 4.1 7.2 - - + -
175E LEU* 3.7 23.6 - - + -
178E LYS* 4.0 32.8 - - + +
179E LEU* 3.7 29.8 - - + -
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Residues in contact with ILE 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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157E ILE* 2.9 41.2 + - + +
158E GLN 4.1 2.9 - - - +
160E ILE* 1.3 76.3 - - - +
162E GLU* 1.3 63.4 + - - +
165E TYR* 3.0 26.2 + - + +
170E PHE* 3.8 23.8 - - + -
175E LEU* 4.7 2.7 - - + -
190E PHE* 3.8 17.5 - - + -
198E PHE* 3.8 15.3 - - + -
201E TYR* 3.7 33.0 - - + -
202E LEU* 4.3 20.4 - - + -
205E LYS* 4.0 11.7 - - + -
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Residues in contact with GLU 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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241A LYS* 3.6 18.0 + - - +
247A THR* 3.7 17.2 + - - +
250A GLN* 3.3 25.0 + - - +
158E GLN 3.0 10.9 + - - +
159E ASN* 3.2 5.1 + - - +
161E ILE* 1.3 77.3 - - - +
163E GLU* 1.3 75.8 + - - +
165E TYR* 3.2 26.5 - - - -
166E THR* 5.8 0.2 - - - +
205E LYS* 2.8 26.6 + - - +
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Residues in contact with GLU 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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241A LYS* 2.8 31.2 + - - -
159E ASN* 3.0 23.2 + - + +
160E ILE* 3.9 4.3 - - - +
162E GLU* 1.3 86.7 - - - +
164E SER* 1.3 59.4 + - - +
165E TYR* 3.8 0.4 - - - -
166E THR* 5.0 6.3 + - - -
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Residues in contact with SER 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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160E ILE* 2.7 28.6 + - - +
163E GLU* 1.3 82.3 - - - +
165E TYR* 1.3 58.6 + - - +
166E THR* 3.2 3.1 - - - -
167E ASP* 2.9 33.7 + - - +
170E PHE* 3.3 40.2 - - - +
178E LYS* 4.3 9.4 + - - -
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Residues in contact with TYR 165 (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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161E ILE* 3.0 17.1 + - + +
162E GLU* 3.2 38.6 - - - -
164E SER* 1.3 78.9 - - - +
166E THR* 1.3 78.4 + - + +
167E ASP 3.0 4.2 + - - -
170E PHE* 4.5 0.7 - - - -
202E LEU* 3.6 28.5 - - + -
205E LYS* 4.0 21.8 - - + -
206E ARG* 2.8 49.5 + - + +
209E LYS* 3.4 50.7 + - + +
228E VAL* 3.7 5.2 - - - +
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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