Contacts of the helix formed by residues 182 - 195 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176C SER* 3.8 0.7 - - - -
181C LEU* 1.3 76.2 - - - +
183C SER* 1.3 64.8 + - - +
184C GLY* 3.6 3.6 + - - -
185C TYR* 3.1 24.2 + - - +
186C LEU* 3.0 21.7 + - - +
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 4.0 14.7 - - - +
173C SER* 3.4 18.4 - - - -
176C SER* 3.0 26.6 + - - -
182C SER* 1.3 73.2 - - - +
184C GLY* 1.3 53.8 + - - +
186C LEU* 3.8 2.2 - - - +
187C SER* 2.8 36.1 + - - -
231D GLU* 3.6 21.8 - - - -
232D ASP* 4.6 1.3 - - - -
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Residues in contact with GLY 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C SER* 3.1 5.8 + - - -
183C SER* 1.3 79.6 - - - +
185C TYR* 1.3 59.8 + - - +
187C SER* 3.3 11.2 - - - -
188C ILE* 3.2 23.9 - - - +
231D GLU 4.7 1.0 + - - -
232D ASP* 4.4 11.1 - - - +
233D VAL* 5.7 2.7 - - - -
234D ASN* 4.3 1.4 - - - +
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Residues in contact with TYR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C LEU* 3.8 37.7 - - + -
182C SER* 3.1 22.1 + - - +
184C GLY* 1.3 73.0 - - - +
186C LEU* 1.3 68.9 + - - +
187C SER 3.0 1.7 + - - -
188C ILE* 3.2 25.3 + - + +
189C MSE 2.9 42.7 + - + +
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 4.9 5.2 - - + -
172C LEU* 3.7 21.3 - - + -
175C LEU* 3.8 22.4 - - + -
176C SER* 3.4 37.0 - - - +
179C LEU* 4.3 11.0 - - + -
181C LEU* 4.4 5.6 - - + -
182C SER 3.0 15.8 + - - +
183C SER 3.8 3.4 - - - +
185C TYR* 1.3 80.1 - - - +
187C SER* 1.3 53.6 + - - +
189C MSE 3.6 33.0 - - + -
190C PHE* 2.7 47.1 + - + +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 4.2 10.7 - - - +
183C SER 2.8 19.8 + - - -
184C GLY 3.3 8.7 - - - -
185C TYR 3.0 0.4 - - - -
186C LEU* 1.3 78.7 - - - +
188C ILE* 1.3 58.5 + - - +
190C PHE* 3.7 4.0 - - - +
191C LYS* 3.1 26.7 + - - +
197C PRO* 5.8 0.7 - - - +
198C PHE* 5.5 3.3 + - - +
199C GLN* 5.6 0.3 + - - -
232D ASP* 2.5 37.8 + - - -
234D ASN* 3.2 13.2 + - - +
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C GLY 3.2 15.7 - - - +
185C TYR* 3.2 35.5 + - + +
187C SER* 1.3 72.0 - - - +
189C MSE 1.3 70.1 + - - +
191C LYS* 3.9 5.2 - - - +
192C LYS* 2.7 37.9 + - + +
234D ASN* 3.4 22.9 - - - +
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Residues in contact with MSE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ALA* 5.0 8.5 - - + -
157C ILE* 3.6 30.5 - - + -
179C LEU* 5.0 5.6 - - + -
181C LEU* 4.1 17.5 - - + -
185C TYR* 2.9 38.9 + - + +
186C LEU* 3.6 27.8 - - + +
188C ILE* 1.3 81.2 - - - +
190C PHE* 1.3 64.2 + - - +
192C LYS* 3.2 9.2 - - + +
193C ASN* 3.0 38.6 + - - +
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 4.0 11.2 - - + -
161C ILE* 3.8 22.9 - - + -
175C LEU* 5.7 0.4 - - + -
186C LEU* 2.7 30.3 + - + +
187C SER 3.7 4.3 - - - +
189C MSE 1.3 78.2 - - - +
191C LYS* 1.3 52.4 + - - +
193C ASN* 3.1 1.8 + - - -
194C PHE* 2.7 78.5 + + + -
196C ILE 3.3 21.8 - - - -
197C PRO 3.7 1.6 - - - -
198C PHE* 3.3 41.5 - + + -
201C TYR* 3.5 29.4 - + + -
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Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C SER 3.1 16.9 + - - +
188C ILE* 3.9 6.1 - - - +
190C PHE* 1.3 74.1 - - - +
192C LYS* 1.3 62.7 + - - +
195C GLY* 2.7 48.6 + - - -
196C ILE 3.5 20.6 - - - +
197C PRO* 4.5 20.4 - - + -
234D ASN* 5.4 14.4 - - + +
238D THR* 5.8 5.8 - - - -
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Residues in contact with LYS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ILE* 2.7 25.3 + - + +
189C MSE 3.2 9.6 - - + +
191C LYS* 1.3 76.4 - - - +
193C ASN* 1.3 72.3 + - - +
195C GLY* 4.3 2.1 + - - -
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Residues in contact with ASN 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ASN 5.7 1.8 - - - +
153C ALA* 4.7 9.0 - - - +
154C LYS* 3.3 48.8 + - + +
157C ILE* 6.0 0.2 - - + -
189C MSE 3.0 40.7 + - - +
190C PHE* 4.9 0.4 - - - -
192C LYS* 1.3 89.7 - - - +
194C PHE* 1.3 76.1 + - + +
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Residues in contact with PHE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LYS* 3.6 53.0 + - + +
157C ILE* 3.9 21.1 - - + -
158C GLN* 3.7 22.7 - - + -
190C PHE* 2.7 69.0 + + + +
193C ASN* 1.3 83.3 - - + +
195C GLY* 1.3 56.1 + - - +
196C ILE* 3.2 16.3 + - + +
201C TYR* 3.7 26.9 - + - -
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Residues in contact with GLY 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 2.7 43.4 + - - -
192C LYS 4.3 1.3 + - - -
193C ASN 3.7 0.8 - - - -
194C PHE* 1.3 70.5 - - - +
196C ILE* 1.3 66.6 + - - +
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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