Contacts of the helix formed by residues 169 - 181 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASP 4.1 1.0 + - - +
168A LYS* 1.3 71.3 - - - +
170A LYS* 1.3 60.9 + - - +
171A ASN* 2.8 8.6 + - - +
172A LEU* 2.5 57.8 + - + +
173A GLN* 3.4 21.3 + - - +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LYS* 3.1 38.0 - - + +
169A GLU* 1.3 89.1 + - - +
171A ASN* 1.3 58.8 + - - +
172A LEU 3.2 0.2 - - - -
173A GLN* 3.4 9.6 + - + +
174A LEU* 2.9 55.8 + - + +
195B HIS* 3.8 14.4 - - - -
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Residues in contact with ASN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.6 23.9 - - - +
168A LYS* 4.2 5.5 - - - +
169A GLU* 2.8 2.7 - - - -
170A LYS* 1.3 80.7 - - - +
172A LEU* 1.3 60.9 + - + +
174A LEU* 3.5 7.3 + - - +
175A GLU* 2.8 27.5 + - - +
192B VAL* 4.6 6.1 + - - +
195B HIS* 2.7 56.8 + - + +
196B LEU* 3.8 19.6 - - - +
199B LYS* 4.9 9.1 - - - +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 4.4 16.8 - - + -
141A LEU* 4.3 27.4 - - + -
169A GLU* 2.5 44.9 + - + +
171A ASN* 1.3 73.4 - - + +
173A GLN* 1.3 64.1 + - - +
175A GLU* 2.6 31.8 - - - +
176A LYS* 3.3 9.4 + - - +
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU* 3.6 26.5 + - - +
170A LYS* 3.5 13.9 - - + +
171A ASN 3.2 0.6 - - - -
172A LEU* 1.3 75.2 - - - +
174A LEU* 1.3 62.4 - - + +
176A LYS* 2.6 36.8 + - - +
177A ALA* 3.2 4.9 + - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS* 2.9 46.7 - - + +
171A ASN* 3.8 4.5 - - - +
173A GLN* 1.3 85.4 - - + +
175A GLU* 1.3 62.4 + - - +
176A LYS 3.0 1.0 + - - -
177A ALA* 3.1 8.5 + - - +
178A ALA* 3.1 23.4 + - - +
188B SER 5.0 1.2 - - - +
191B SER* 5.3 10.1 - - - +
192B VAL* 4.0 16.2 - - + +
195B HIS* 4.1 17.5 - - + -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ILE* 5.6 2.2 - - + +
134A LYS* 6.0 4.7 - - + +
137A VAL* 3.7 38.4 - - + -
171A ASN* 2.8 22.4 + - - +
172A LEU* 2.6 35.4 - - - +
174A LEU* 1.3 73.7 - - - +
176A LYS* 1.3 94.8 + - - +
178A ALA* 3.7 4.3 - - - +
179A SER* 3.3 26.2 + - - +
192B VAL* 4.0 12.7 - - + +
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Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU 3.4 7.9 - - - +
173A GLN* 2.6 25.4 + - - +
175A GLU* 1.3 89.9 + - - +
177A ALA* 1.3 55.1 + - - +
179A SER* 3.9 2.3 + - - +
180A TYR* 2.5 86.7 + - + +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN 3.2 4.6 + - - +
174A LEU* 3.1 10.3 + - - +
176A LYS* 1.3 76.1 - - - +
178A ALA* 1.3 54.6 + - - +
179A SER 2.5 15.2 + - - -
180A TYR* 4.5 1.8 - - - -
181A ILE* 2.5 49.6 + - + +
188B SER* 5.6 8.7 - - - -
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 3.7 17.3 + - - +
133A ILE* 4.9 11.2 - - + +
174A LEU 3.1 13.9 + - - +
175A GLU* 3.7 6.1 - - - +
177A ALA* 1.3 76.8 - - - +
179A SER* 1.3 57.3 + - - +
181A ILE* 3.9 14.0 - - - +
184A LEU* 5.0 0.2 - - - +
188B SER* 3.9 21.8 + - - +
189B MET* 4.0 23.4 - - + +
192B VAL* 4.2 12.3 - - + -
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 2.7 38.5 + - - +
134A LYS* 5.2 16.6 - - - -
175A GLU* 3.3 19.1 + - - -
176A LYS* 3.1 12.4 + - - +
177A ALA 2.5 4.8 + - - -
178A ALA* 1.3 75.4 - - - +
180A TYR* 1.3 83.7 + - - +
181A ILE 3.2 1.3 + - - -
182A ALA* 3.3 5.4 + - - +
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Residues in contact with TYR 180 (chain A).
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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176A LYS* 2.5 64.9 + - + +
177A ALA* 4.5 1.8 - - - -
179A SER* 1.3 80.5 + - - +
181A ILE* 1.3 51.8 + - + +
182A ALA* 2.4 21.8 + - - +
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Residues in contact with ILE 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLN* 3.8 5.4 + - - -
177A ALA* 2.5 59.1 + - + +
178A ALA* 3.9 11.2 - - - +
179A SER 3.6 1.8 - - - -
180A TYR* 1.3 68.5 - - + +
182A ALA* 1.3 53.8 + - - +
183A ASN* 3.2 29.2 + - - +
184A LEU* 4.0 5.4 - - + +
184B GLY 5.1 2.0 - - - +
185B SER* 3.5 38.1 - - - +
188B SER* 6.0 4.0 - - - -
189B MET* 6.2 0.9 - - + -
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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