Contacts of the helix formed by residues 173 - 181 (chain J) 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 GLN 173 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169J GLU* 2.7 37.2 + - + +
170J LYS* 4.6 4.5 - - - -
172J LEU* 1.3 92.3 - - - +
174J LEU* 1.3 57.0 + - + +
175J GLU 2.6 15.1 + - - -
176J LYS* 2.9 28.8 + - - +
177J ALA* 2.9 12.4 + - - +
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Residues in contact with LEU 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170J LYS* 3.2 31.1 + - + +
171J ASN* 4.0 3.3 + - - +
173J GLN* 1.3 77.6 - - + +
175J GLU* 1.3 58.4 + - - +
177J ALA* 3.9 16.5 - - + +
178J ALA* 3.6 13.5 + - - +
188K SER* 4.3 7.2 - - - -
191K SER* 4.1 20.6 - - - +
192K VAL* 3.5 29.4 - - + +
195K HIS* 4.6 16.2 - - + -
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Residues in contact with GLU 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J ILE* 6.5 0.9 - - - -
134J LYS* 5.7 4.7 + - - +
137J VAL* 4.6 25.6 - - + +
141J LEU* 5.9 2.9 - - - +
171J ASN 3.2 11.3 + - - +
172J LEU* 2.8 47.3 - - - +
173J GLN 2.6 5.9 + - - -
174J LEU* 1.3 73.2 - - - +
176J LYS* 1.3 94.1 + - + +
177J ALA 3.1 1.1 - - - -
178J ALA* 3.4 4.3 + - - +
179J SER* 2.9 29.3 + - - -
192K VAL* 5.6 0.9 - - - -
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Residues in contact with LYS 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J LEU* 3.0 33.2 - - - +
173J GLN* 2.9 14.7 + - - +
175J GLU* 1.3 104.3 - - + +
177J ALA* 1.3 60.3 + - - +
179J SER* 3.6 9.2 - - - -
180J TYR* 3.0 58.7 + - + +
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Residues in contact with ALA 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J GLN 2.9 15.5 + - - +
174J LEU* 3.9 20.9 - - + +
176J LYS* 1.3 77.2 - - - +
178J ALA* 1.3 62.8 + - - +
179J SER 3.0 1.5 + - - -
180J TYR* 3.2 5.1 + - - +
181J ILE* 3.1 30.5 + - + +
188K SER* 4.6 5.4 - - - -
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Residues in contact with ALA 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J GLN* 3.0 30.5 + - + +
133J ILE* 5.2 10.3 - - + -
174J LEU 3.6 10.9 + - - +
175J GLU* 3.4 4.1 + - - +
177J ALA* 1.3 79.6 - - - +
179J SER* 1.3 56.8 + - - +
181J ILE* 3.1 16.5 - - + +
188K SER* 2.7 31.8 + - - +
189K MET* 4.7 10.0 - - - +
192K VAL* 4.7 3.8 - - + -
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Residues in contact with SER 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J GLN* 2.7 31.2 + - - +
134J LYS* 4.6 25.4 + - - +
175J GLU 2.9 18.7 + - - -
176J LYS* 3.7 11.0 - - - -
177J ALA 3.0 0.4 - - - -
178J ALA* 1.3 75.9 - - - +
180J TYR* 1.3 69.1 + - - +
182J ALA* 4.1 4.7 - - - +
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Residues in contact with TYR 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J LYS* 3.0 41.1 + - + +
177J ALA* 3.2 3.5 + - - +
179J SER* 1.3 87.8 - - - +
181J ILE* 1.3 53.0 + - - +
182J ALA* 2.5 23.3 + - - +
183J ASN* 3.9 9.9 + - - -
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Residues in contact with ILE 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J GLN* 3.4 2.5 - - - +
177J ALA* 3.1 14.3 + - + +
178J ALA* 3.1 33.0 - - + +
179J SER 3.4 0.2 - - - -
180J TYR* 1.3 74.0 - - + +
182J ALA* 1.3 54.0 + - - +
183J ASN* 2.9 18.7 + - + +
184J LEU* 3.0 26.3 - - + +
181K THR 5.7 1.6 - - - +
184K GLY 4.8 6.5 - - - +
185K SER* 3.3 47.3 - - - +
188K SER* 3.8 4.5 - - - +
189K MET* 4.2 9.2 - - + -
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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