Contacts of the helix formed by residues 169 - 181 (chain D) in PDB entry 1LWU
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 GLU 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D ASP 4.1 1.0 + - - +
168D LYS* 1.3 71.3 - - - +
170D LYS* 1.3 61.7 + - - +
171D ASN* 2.8 8.6 + - - +
172D LEU* 2.5 57.3 + - + +
173D GLN* 3.4 21.0 + - - +
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Residues in contact with LYS 170 (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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168D LYS* 3.1 37.5 - - + +
169D GLU* 1.3 89.2 + - - +
171D ASN* 1.3 58.6 + - - +
172D LEU 3.2 0.2 - - - -
173D GLN* 3.4 10.7 + - + +
174D LEU* 2.9 55.9 + - + +
195E HIS* 3.8 14.4 - - - -
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Residues in contact with ASN 171 (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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137D VAL* 3.6 24.3 - - - +
168D LYS* 4.2 5.3 - - - +
169D GLU* 2.8 2.4 - - - +
170D LYS* 1.3 81.4 - - - +
172D LEU* 1.3 61.5 + - + +
174D LEU* 3.5 6.9 + - - +
175D GLU* 2.8 27.0 + - - +
192E VAL* 4.6 6.3 + - - +
195E HIS* 2.7 56.3 + - + +
196E LEU* 3.8 19.1 - - - +
199E LYS* 4.8 10.8 - - - +
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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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137D VAL* 4.4 17.5 - - + -
141D LEU* 4.3 27.6 - - + -
169D GLU* 2.5 45.0 + - + +
171D ASN* 1.3 74.1 - - + +
173D GLN* 1.3 63.6 + - - +
175D GLU* 2.6 33.0 - - - +
176D LYS* 3.3 6.9 + - - +
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Residues in contact with GLN 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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169D GLU* 3.7 26.7 + - - +
170D LYS* 3.5 13.7 - - + +
171D ASN 3.2 0.4 - - - -
172D LEU* 1.3 76.0 - - - +
174D LEU* 1.3 62.3 - - + +
176D LYS* 2.7 36.4 + - - +
177D ALA* 3.2 4.9 + - - +
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Residues in contact with LEU 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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170D LYS* 2.9 46.0 - - + +
171D ASN* 3.8 5.2 - - - +
173D GLN* 1.3 80.9 - - + +
175D GLU* 1.3 62.0 + - - +
176D LYS 3.1 0.9 + - - -
177D ALA* 3.2 8.5 + - - +
178D ALA* 3.1 23.0 + - - +
188E SER 5.0 1.2 - - - +
191E SER* 5.3 10.1 - - - +
192E VAL* 4.0 17.3 - - + +
195E HIS* 4.1 17.7 - - + -
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Residues in contact with GLU 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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133D ILE* 5.6 2.5 - - + +
134D LYS* 6.0 4.9 - - + +
137D VAL* 3.7 38.4 - - + -
171D ASN* 2.8 22.6 + - - +
172D LEU* 2.6 35.7 - - - +
173D GLN 3.2 0.2 - - - -
174D LEU* 1.3 72.7 - - - +
176D LYS* 1.3 95.9 + - - +
178D ALA* 3.8 4.0 - - - +
179D SER* 3.2 25.3 + - - +
192E VAL* 4.0 12.7 - - + +
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Residues in contact with LYS 176 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D LEU 3.4 7.6 - - - +
173D GLN* 2.7 25.9 + - - +
175D GLU* 1.3 90.8 + - - +
177D ALA* 1.3 53.3 + - - +
179D SER* 3.8 2.3 + - - +
180D TYR* 2.5 87.4 + - + +
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Residues in contact with ALA 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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173D GLN 3.2 4.8 + - - +
174D LEU* 3.2 10.6 + - - +
176D LYS* 1.3 75.6 - - - +
178D ALA* 1.3 55.2 + - - +
179D SER 2.4 15.6 + - - -
180D TYR* 4.5 1.6 - - - -
181D ILE* 2.5 50.9 + - + +
188E SER* 5.6 8.3 - - - -
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Residues in contact with ALA 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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130D GLN* 3.7 17.4 + - - +
133D ILE* 4.9 11.4 - - + +
174D LEU 3.1 13.7 + - - +
175D GLU* 3.8 6.1 - - - +
177D ALA* 1.3 77.1 - - - +
179D SER* 1.3 57.0 + - - +
181D ILE* 3.9 13.6 - - - +
188E SER* 3.9 21.6 + - - +
189E MET* 4.1 23.6 - - + +
192E VAL* 4.2 12.3 - - + -
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Residues in contact with SER 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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130D GLN* 2.8 37.8 + - - +
134D LYS* 5.2 17.0 - - - -
175D GLU* 3.2 20.5 + - - -
176D LYS* 3.1 12.4 + - - +
177D ALA 2.4 6.0 + - - -
178D ALA* 1.3 74.2 - - - +
180D TYR* 1.3 82.8 + - - +
181D ILE 3.2 0.4 - - - -
182D ALA* 3.0 7.6 + - - +
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Residues in contact with TYR 180 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176D LYS* 2.5 65.5 + - + +
177D ALA* 4.5 1.6 - - - -
179D SER* 1.3 76.2 + - - +
181D ILE* 1.3 52.0 + - + +
182D ALA* 2.3 26.8 + - - +
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Residues in contact with ILE 181 (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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130D GLN* 3.9 4.9 + - - -
177D ALA* 2.5 57.4 + - + +
178D ALA* 3.9 11.7 - - - +
179D SER 3.5 2.0 - - - -
180D TYR* 1.3 68.7 - - + +
182D ALA* 1.3 53.8 + - - +
183D ASN* 3.0 32.4 + - - +
184D LEU* 4.8 2.8 - - + +
184E GLY 5.1 1.8 - - - +
185E SER* 3.5 39.0 + - - +
188E SER* 6.0 3.8 - - - -
189E MET* 6.2 0.4 - - + -
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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