Contacts of the helix formed by residues 182 - 195 (chain A) in PDB entry 3LSG
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 SER 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A SER* 3.8 1.1 - - - -
181A LEU* 1.3 76.8 - - - +
183A SER* 1.3 57.9 + - - +
184A GLY* 3.8 4.5 + - - -
185A TYR* 3.0 25.8 + - - +
186A LEU* 2.9 28.1 + - - +
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Residues in contact with SER 183 (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* 3.8 13.5 - - - +
173A SER* 3.2 28.5 + - - -
176A SER* 3.2 22.3 + - - -
182A SER* 1.3 72.4 - - - +
184A GLY* 1.3 57.6 + - - +
186A LEU* 4.4 1.6 - - - -
187A SER* 2.8 33.3 + - - -
231B GLU* 3.4 21.8 - - - -
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Residues in contact with GLY 184 (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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182A SER* 3.2 5.0 + - - -
183A SER* 1.3 80.1 - - - +
185A TYR* 1.3 61.1 + - - +
187A SER* 3.6 2.6 + - - -
188A ILE* 3.6 25.0 + - - +
231B GLU 4.3 2.7 + - - -
232B ASP* 4.7 11.6 - - - +
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Residues in contact with TYR 185 (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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181A LEU* 4.1 31.9 - - + -
182A SER* 3.0 22.4 + - - +
184A GLY* 1.3 72.7 - - - +
186A LEU* 1.3 68.4 + - - +
188A ILE* 3.2 16.9 + - + +
189A MSE 2.9 52.4 + - + +
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Residues in contact with LEU 186 (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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157A ILE* 4.5 4.7 - - + -
172A LEU* 3.5 24.5 - - + -
175A LEU* 3.6 30.3 - - + -
176A SER* 3.7 21.8 - - - +
179A LEU* 3.9 19.7 - - + -
181A LEU* 4.2 6.5 - - + -
182A SER 2.9 17.8 + - - +
183A SER 3.9 2.9 - - - +
185A TYR* 1.3 82.3 - - - +
187A SER* 1.3 56.3 + - - +
189A MSE 4.1 23.6 - - + +
190A PHE* 2.7 46.7 + - + +
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Residues in contact with SER 187 (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* 4.1 9.8 - - - +
183A SER 2.8 18.2 + - - -
184A GLY 3.8 4.9 - - - -
185A TYR 3.2 0.4 - - - -
186A LEU* 1.3 78.0 - - - +
188A ILE* 1.3 62.8 + - - +
190A PHE* 3.9 4.0 - - - +
191A LYS* 3.2 23.4 + - - +
197A PRO* 5.6 0.7 - - - +
198A PHE* 5.4 4.8 + - - +
199A GLN* 5.6 0.7 + - - -
232B ASP* 2.7 39.6 + - - -
234B ASN* 4.3 10.9 + - - +
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Residues in contact with ILE 188 (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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184A GLY 3.6 15.7 + - - +
185A TYR* 3.2 18.7 + - + +
187A SER* 1.3 75.8 - - - +
189A MSE 1.3 63.4 + - + +
191A LYS* 3.5 5.1 + - - +
192A LYS* 3.0 29.0 + - + +
233B VAL* 6.3 4.5 - - + -
234B ASN* 6.5 1.3 - - + -
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Residues in contact with MSE 189 (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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153A ALA* 5.6 8.1 - - + -
157A ILE* 3.9 31.0 - - + -
179A LEU* 5.1 0.9 - - + -
181A LEU* 3.7 30.3 - - + -
185A TYR* 2.9 44.3 + - + +
186A LEU* 4.0 5.4 - - + +
188A ILE* 1.3 76.2 - - - +
190A PHE* 1.3 71.1 + - - +
192A LYS* 3.2 5.8 + - - +
193A ASN* 2.9 50.1 + - - +
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Residues in contact with PHE 190 (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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157A ILE* 3.7 28.3 - - + -
161A ILE* 3.8 10.3 - - + -
175A LEU* 4.8 4.7 - - + -
186A LEU* 2.7 31.1 + - + +
187A SER 3.9 3.6 - - - +
189A MSE 1.3 79.6 - - - +
191A LYS* 1.3 56.9 + - - +
193A ASN 3.1 1.6 + - - -
194A PHE* 2.8 59.9 + + + -
196A ILE 3.3 22.0 - - - -
198A PHE* 3.3 39.5 - + + -
201A TYR* 3.5 35.2 - + + -
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Residues in contact with LYS 191 (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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187A SER* 3.2 15.4 + - - +
188A ILE* 3.9 5.8 - - - +
190A PHE* 1.3 78.9 - - - +
192A LYS* 1.3 64.3 + - - +
195A GLY* 3.0 36.4 + - - -
196A ILE 3.6 18.6 - - - +
197A PRO* 4.2 23.5 - - + +
234B ASN* 4.1 31.2 - - + +
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Residues in contact with LYS 192 (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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188A ILE* 3.0 18.4 + - + +
189A MSE 3.5 11.2 - - - +
190A PHE 3.2 0.2 - - - -
191A LYS* 1.3 80.4 - - - +
193A ASN* 1.3 69.4 + - - +
195A GLY* 4.1 3.1 + - - -
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Residues in contact with ASN 193 (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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151A SER* 4.4 16.4 + - - -
153A ALA* 5.6 3.4 - - - +
154A LYS* 3.1 34.6 + - + +
157A ILE* 5.8 0.6 - - - +
189A MSE 2.9 40.2 + - - +
192A LYS* 1.3 88.0 - - - +
194A PHE* 1.3 77.0 + - + +
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Residues in contact with PHE 194 (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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154A LYS* 3.4 46.6 + - + +
157A ILE* 3.6 26.9 - - + -
158A GLN* 3.6 27.4 - - + -
190A PHE* 2.8 56.9 + + + +
193A ASN* 1.3 83.9 - - + +
195A GLY* 1.3 58.3 + - - +
196A ILE* 3.2 13.0 + - + +
201A TYR* 3.6 32.5 - + + -
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Residues in contact with GLY 195 (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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191A LYS* 3.0 32.4 + - - -
192A LYS 4.1 2.4 + - - -
193A ASN 3.6 1.2 - - - -
194A PHE* 1.3 77.0 - - - +
196A ILE* 1.3 67.2 + - - +
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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