Contacts of the helix formed by residues 171 - 180 (chain D) 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 THR 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C GLN* 4.9 5.5 + - - +
171C THR* 6.2 4.0 - - + -
231C GLU* 4.0 13.0 - - - +
168D SER 4.6 5.2 - - - +
169D GLN* 3.2 16.0 + - - +
170D PHE* 1.3 81.7 - - - +
172D LEU* 1.3 66.6 + - - +
173D SER* 3.4 16.3 + - - -
174D VAL* 2.9 19.3 + - - +
175D LEU* 3.0 13.5 + - - +
198D PHE* 3.7 12.4 - - - -
202D LEU* 4.9 0.9 - - - -
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C GLU* 4.0 24.2 + - + +
232C ASP* 3.3 39.0 - - + +
171D THR* 1.3 73.3 - - - +
173D SER* 1.3 58.2 + - - +
175D LEU* 3.2 4.2 + - + +
176D SER* 2.8 28.6 + - - -
183D SER* 3.9 22.4 - - - +
186D LEU* 3.7 32.3 - - + -
187D SER* 4.9 5.6 - - - +
190D PHE* 5.8 0.2 - - + -
198D PHE* 3.2 43.9 - - + -
199D GLN* 4.3 2.5 - - - +
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Residues in contact with SER 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 4.1 0.7 + - - -
168C SER* 4.8 0.9 + - - -
169C GLN* 2.9 34.8 + - - -
231C GLU* 5.0 6.5 + - - +
171D THR* 3.2 10.4 + - - -
172D LEU* 1.3 78.4 - - - +
174D VAL* 1.3 60.6 - - - +
176D SER* 3.3 5.6 - - - -
177D GLU* 3.1 32.6 + - - +
183D SER* 4.1 15.8 + - - -
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Residues in contact with VAL 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D GLN* 3.4 24.9 - - + +
170D PHE* 3.7 20.2 - - + -
171D THR* 2.9 17.5 + - - +
173D SER* 1.3 77.4 - - - +
175D LEU* 1.3 65.9 + - - +
177D GLU* 3.0 24.1 + - - +
178D LYS* 3.0 36.4 + - + +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ILE* 4.3 22.9 - - + -
160D ILE* 3.8 29.8 - - + -
161D ILE* 4.4 3.6 - - + -
170D PHE* 4.1 14.3 - - + -
171D THR 3.0 11.2 + - - +
172D LEU 3.5 7.6 - - - +
174D VAL* 1.3 75.5 - - - +
176D SER* 1.3 64.6 + - - +
178D LYS* 3.1 3.4 + - - -
179D LEU* 2.9 40.3 + - + +
186D LEU* 3.6 22.4 - - + -
190D PHE* 4.6 2.9 - - + -
198D PHE* 3.7 30.5 - - + -
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Residues in contact with SER 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 3.3 11.2 + - - -
172D LEU 2.8 11.3 + - - -
173D SER* 3.3 14.1 - - - -
175D LEU* 1.3 76.7 - - - +
177D GLU* 1.3 56.5 + - - +
179D LEU* 3.3 1.6 + - - -
180D ASP* 2.9 25.1 + - - -
181D LEU 2.7 30.9 + - - -
182D SER 3.3 1.4 - - - -
183D SER* 3.2 26.9 + - - -
186D LEU* 3.4 16.0 - - - +
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Residues in contact with GLU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LYS* 3.4 38.5 + - + +
222A TYR* 3.2 13.7 + - - +
223A GLU* 4.4 16.5 - - - +
173D SER* 3.1 20.4 + - - +
174D VAL* 3.0 29.6 + - - +
176D SER* 1.3 75.6 - - - +
178D LYS* 1.3 64.3 + - + +
180D ASP* 3.2 9.5 + - - +
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Residues in contact with LYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ILE* 4.3 29.7 - - + +
164D SER* 4.4 18.0 + - - -
170D PHE* 5.1 1.1 - - + -
174D VAL* 3.0 36.5 + - + +
175D LEU* 3.1 6.9 + - - +
177D GLU* 1.3 77.7 - - + +
179D LEU* 1.3 62.1 + - - +
180D ASP* 3.4 0.6 - - - +
211E LYS* 3.0 22.9 + - - -
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 4.9 3.6 - - + -
157D ILE* 4.0 23.6 - - + -
160D ILE* 3.4 31.2 - - + -
175D LEU* 2.9 31.4 + - + +
176D SER* 4.1 2.7 - - - +
178D LYS* 1.3 76.9 - - - +
180D ASP* 1.3 70.0 + - - +
181D LEU* 3.7 14.6 - - + +
186D LEU* 3.8 31.2 - - + -
189D MSE 4.5 6.1 - - + -
211E LYS* 4.0 13.0 - - - +
215E LEU* 3.8 29.9 - - + +
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Residues in contact with ASP 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LYS* 3.8 29.0 - - + +
221A ASN* 4.4 15.9 + - - +
222A TYR* 3.9 12.1 + - - -
176D SER 2.9 7.1 + - - -
177D GLU 3.2 11.0 + - - +
178D LYS 3.4 0.8 - - - +
179D LEU* 1.3 80.8 - - - +
181D LEU* 1.3 67.3 + - - +
211E LYS* 5.8 1.6 - - - +
212E LEU* 5.9 0.5 - - - +
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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