Contacts of the helix formed by residues 166 - 181 (chain A) in PDB entry 3LRA
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 LYS 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LYS 3.5 12.3 + - - +
163A LEU* 2.9 25.7 + - + +
165A SER* 1.3 78.1 - - - +
167A PRO* 1.3 71.4 - - + +
168A ASN* 3.1 24.6 - - - +
169A VAL* 3.9 2.2 - - + +
170A LYS* 2.9 30.4 + - - +
200A ARG* 3.9 22.8 - - - +
204A ASP* 2.4 37.0 + - - +
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Residues in contact with PRO 167 (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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165A SER 3.7 3.5 - - - +
166A LYS* 1.3 92.7 - - + +
168A ASN* 1.3 58.9 + - + +
170A LYS* 3.7 11.5 - - + +
171A ALA* 2.9 30.0 + - - +
194A ALA* 3.8 19.8 - - + +
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Residues in contact with ASN 168 (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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166A LYS* 3.1 31.6 - - - +
167A PRO* 1.3 74.5 - - + +
169A VAL* 1.3 74.8 + - - +
171A ALA* 3.3 3.3 + - - +
172A LEU* 3.1 21.1 + - - +
194A ALA 3.2 13.0 + - - +
195A LEU* 3.3 26.8 + - - +
200A ARG* 4.7 2.8 - - - +
201A LEU* 3.4 40.1 - - + +
204A ASP* 3.3 22.4 + - - +
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Residues in contact with VAL 169 (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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163A LEU* 3.3 34.5 - - + +
164A LEU* 4.4 17.0 - - + +
166A LYS* 3.3 4.7 + - + +
168A ASN* 1.3 96.6 + - - +
170A LYS* 1.3 68.5 + - - +
172A LEU* 2.9 17.3 + - + +
173A LEU* 3.0 26.1 + - + +
201A LEU* 4.5 2.5 - - - -
204A ASP* 4.6 9.2 - - + -
205A ILE* 4.1 25.1 - - + -
208A ALA* 6.0 3.8 - - + -
233A LEU* 5.9 4.5 - - + -
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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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138A ALA* 5.5 1.0 - - - +
164A LEU 3.2 25.4 - - - +
165A SER* 3.2 29.2 + - - +
166A LYS 2.9 16.9 + - - +
167A PRO* 3.7 10.1 - - + +
169A VAL* 1.3 76.9 - - - +
171A ALA* 1.3 56.8 + - - +
173A LEU* 3.7 9.2 + - + +
174A SER* 3.0 27.9 + - - -
191A GLN* 5.2 1.6 - - - -
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Residues in contact with ALA 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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167A PRO 2.9 18.6 + - - +
168A ASN 3.5 5.8 - - - +
169A VAL 3.0 0.2 - - - -
170A LYS* 1.3 75.9 - - - +
172A LEU* 1.3 55.3 + - - +
174A SER* 3.1 5.8 + - - -
175A VAL* 2.6 40.6 + - - +
191A GLN* 3.8 26.5 - - + +
194A ALA* 4.2 7.4 - - + -
195A LEU* 3.6 19.5 - - + -
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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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168A ASN 3.1 12.2 + - - +
169A VAL* 2.9 11.9 + - + +
171A ALA* 1.3 74.5 - - - +
173A LEU* 1.3 55.8 + - + +
175A VAL* 3.7 1.8 - - - +
176A HIS* 2.7 35.7 + - + +
195A LEU* 3.9 21.0 - - + +
201A LEU* 4.3 4.3 - - + -
205A ILE* 3.6 34.5 - - + -
233A LEU* 4.6 4.9 - - + -
238A CYS* 4.3 19.5 - - - -
241A VAL* 4.2 17.5 - - + -
242A ARG* 3.6 37.5 - - + -
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Residues in contact with LEU 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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137A ALA* 3.7 22.9 - - + +
138A ALA* 3.9 13.9 - - + +
141A ALA* 3.2 35.7 - - + -
164A LEU* 5.5 6.7 - - + +
169A VAL* 3.0 28.6 + - + +
170A LYS* 3.8 8.1 - - - +
172A LEU* 1.3 77.7 - - + +
174A SER* 1.3 65.4 + - - +
176A HIS* 3.1 8.1 - - + +
177A ASP* 3.0 29.6 + - - -
229A LEU* 4.4 14.8 - - + -
232A VAL* 5.2 1.6 - - + -
233A LEU* 4.4 17.9 - - + -
238A CYS* 6.2 1.3 - - - -
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Residues in contact with SER 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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138A ALA* 4.4 11.3 - - - +
170A LYS 3.0 16.5 + - - -
171A ALA 3.5 2.2 - - - -
173A LEU* 1.3 78.6 - - - +
175A VAL* 1.3 62.4 + - - +
177A ASP* 3.3 3.5 + - - +
178A THR* 3.1 22.6 + - - -
188A VAL* 4.7 3.3 - - - +
191A GLN* 2.8 41.8 + - - -
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Residues in contact with VAL 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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171A ALA 2.6 23.6 + - - +
172A LEU* 4.0 4.7 - - - +
174A SER* 1.3 72.1 - - - +
176A HIS* 1.3 63.0 + - - +
178A THR* 3.2 6.9 + - - -
179A VAL* 3.0 40.2 + - + +
188A VAL* 4.2 23.6 - - + +
191A GLN* 4.6 9.0 - - + -
192A GLY* 5.3 1.1 - - - +
195A LEU* 4.2 22.7 - - + -
241A VAL* 4.1 18.4 - - + -
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Residues in contact with HIS 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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132A PRO* 4.4 2.9 - - + -
133A ILE 5.0 2.2 - - - -
134A LEU 3.3 23.0 + - - -
137A ALA* 3.6 13.6 - - + +
172A LEU* 2.7 24.5 + - + +
173A LEU* 3.1 11.6 + - + +
175A VAL* 1.3 74.9 - - - +
177A ASP* 1.3 75.2 + - - +
179A VAL* 3.8 0.7 - - - -
180A ALA* 2.8 36.0 + - + +
232A VAL* 3.6 26.2 - - + +
235A SER* 5.0 0.7 - - - -
237A PHE* 3.5 41.0 - + - -
238A CYS* 4.2 19.1 - - + +
241A VAL* 4.8 9.1 - - + +
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Residues in contact with ASP 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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135A HIS 3.4 9.2 - - - +
136A GLY* 3.9 3.0 - - - -
137A ALA* 2.7 25.1 + - - +
138A ALA* 2.9 35.5 + - - +
139A ALA 4.4 0.2 + - - -
173A LEU 3.0 8.3 + - - +
174A SER* 3.8 4.0 - - - +
176A HIS* 1.3 85.5 - - - +
178A THR* 1.3 57.0 + - - +
180A ALA* 3.9 5.4 - - - -
181A GLN* 2.6 59.3 + - - +
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Residues in contact with THR 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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174A SER* 3.1 13.0 + - - -
175A VAL* 3.5 8.5 - - + +
177A ASP* 1.3 75.5 - - - +
179A VAL* 1.3 66.8 + - + +
181A GLN* 3.8 3.5 - - - +
182A LYS* 3.1 6.4 + - - -
183A ASN* 3.0 50.2 + - - +
184A TYR* 4.5 8.3 - - + -
188A VAL* 3.1 44.7 - - + +
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Residues in contact with VAL 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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126A GLU* 6.1 0.9 - - - +
175A VAL* 3.0 32.8 + - + +
176A HIS 4.0 2.0 - - - +
178A THR* 1.3 80.1 - - + +
180A ALA* 1.3 66.5 + - - +
182A LYS* 3.4 19.1 + - - +
237A PHE* 4.2 20.5 - - + -
241A VAL* 5.0 9.2 - - + -
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Residues in contact with ALA 180 (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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132A PRO* 4.1 19.9 - - + +
134A LEU 4.1 6.3 - - - +
135A HIS* 3.2 36.4 + - + +
176A HIS* 2.8 22.4 + - - +
177A ASP* 3.1 8.9 + - - +
179A VAL* 1.3 79.3 - - - +
181A GLN* 1.3 59.4 + - - +
182A LYS* 3.3 9.2 + - - +
237A PHE* 4.0 10.8 - - + -
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Residues in contact with GLN 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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135A HIS* 2.7 48.3 + - + +
136A GLY* 4.8 0.6 - - - -
177A ASP* 2.6 38.2 + - - +
178A THR* 4.1 3.1 - - - +
180A ALA* 1.3 71.7 - - - +
182A LYS* 1.3 70.9 + - - +
183A ASN* 3.3 18.9 + - + +
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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