Contacts of the helix formed by residues 173 - 181 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169G GLU* 2.7 36.3 + - + +
170G LYS* 4.6 5.2 - - - +
172G LEU* 1.3 92.9 - - - +
174G LEU* 1.3 56.2 + - + +
175G GLU 2.6 15.7 + - - -
176G LYS* 2.9 27.1 + - - +
177G ALA* 2.9 12.4 + - - +
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Residues in contact with LEU 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G LYS* 3.2 29.2 + - + +
171G ASN* 4.0 3.5 + - - +
173G GLN* 1.3 78.4 - - + +
175G GLU* 1.3 58.2 + - - +
177G ALA* 3.9 16.1 - - + +
178G ALA* 3.6 13.5 + - - +
188H SER* 4.3 7.6 - - - -
191H SER* 4.1 19.5 - - - +
192H VAL* 3.5 28.6 - - + +
195H HIS* 4.7 15.7 - - + -
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Residues in contact with GLU 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G ILE* 6.5 0.9 - - - -
134G LYS* 5.7 4.7 + - - +
137G VAL* 4.6 26.4 - - + +
141G LEU* 5.9 3.1 - - - +
171G ASN 3.2 11.6 + - - +
172G LEU* 2.8 48.0 - - - +
173G GLN 2.6 5.3 + - - -
174G LEU* 1.3 73.0 - - - +
176G LYS* 1.3 95.6 + - + +
177G ALA 3.1 1.3 - - - -
178G ALA* 3.4 4.0 + - - +
179G SER* 2.9 30.1 + - - -
192H VAL* 5.6 1.1 - - - -
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Residues in contact with LYS 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172G LEU* 3.0 33.3 - - - +
173G GLN* 2.9 14.2 + - - +
175G GLU* 1.3 105.0 - - + +
177G ALA* 1.3 60.0 + - - +
179G SER* 3.6 8.3 - - - -
180G TYR* 3.0 57.3 + - + +
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Residues in contact with ALA 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173G GLN 2.9 15.1 + - - +
174G LEU* 3.9 20.2 - - + -
175G GLU 3.1 0.2 - - - -
176G LYS* 1.3 77.3 - - - +
178G ALA* 1.3 62.1 + - - +
179G SER 3.0 1.7 + - - -
180G TYR* 3.2 5.7 + - - +
181G ILE* 3.1 30.0 + - + +
188H SER* 4.6 5.2 - - - -
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Residues in contact with ALA 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G GLN* 3.0 31.1 + - + +
133G ILE* 5.2 10.3 - - + -
174G LEU 3.6 10.2 + - - +
175G GLU* 3.4 4.5 + - - +
177G ALA* 1.3 79.0 - - - +
179G SER* 1.3 57.3 - - - +
181G ILE* 3.1 17.2 - - + +
188H SER* 2.7 31.4 + - - +
189H MET* 4.7 9.4 - - - +
192H VAL* 4.8 4.3 - - + -
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Residues in contact with SER 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G GLN* 2.8 32.4 + - - +
134G LYS* 4.6 24.2 + - - +
175G GLU 2.9 18.9 + - - -
176G LYS* 3.7 11.0 - - - -
177G ALA 3.0 0.4 - - - -
178G ALA* 1.3 75.5 - - - +
180G TYR* 1.3 69.1 + - - +
182G ALA* 4.0 4.9 - - - +
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Residues in contact with TYR 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G LYS* 3.0 39.8 + - + +
177G ALA* 4.0 3.1 - - - +
179G SER* 1.3 89.9 - - - +
181G ILE* 1.3 51.9 + - + +
182G ALA* 2.5 23.8 + - - +
183G ASN* 4.0 10.2 + - - +
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Residues in contact with ILE 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G GLN* 3.4 2.9 - - + +
177G ALA* 3.1 14.6 + - + +
178G ALA* 3.1 32.5 - - + +
180G TYR* 1.3 72.1 - - + +
182G ALA* 1.3 48.3 + - - +
183G ASN* 2.9 22.9 - - - +
184G LEU* 2.8 35.0 - - + +
181H THR 5.8 0.9 - - - +
184H GLY 4.8 6.3 - - - +
185H SER* 3.3 47.8 - - - +
188H SER* 3.7 5.4 - - - +
189H MET* 4.2 8.5 - - + -
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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