Contacts of the helix formed by residues 220 - 228 (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 LYS 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B GLU* 3.4 31.7 + - - +
180B ASP* 3.4 24.5 - - - +
218C GLU 4.2 12.6 + - - +
219C LEU* 1.3 76.5 - - - +
221C ASN* 1.3 67.3 + - - +
222C TYR* 3.5 28.0 - - + +
223C GLU* 2.8 32.1 + - + +
224C ILE* 3.0 12.6 + - - +
252C ARG* 4.6 2.2 - - - +
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Residues in contact with ASN 221 (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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180B ASP* 4.4 12.1 + - - +
214C LEU* 4.0 10.6 - - - +
219C LEU 3.9 0.4 + - - -
220C LYS* 1.3 72.3 - - - +
222C TYR* 1.3 57.5 + - - +
224C ILE* 3.1 5.4 + - - +
225C ALA* 2.9 31.0 + - - +
233C VAL* 3.5 16.9 - - + +
236C PHE* 3.9 8.5 - - + -
237C ILE* 3.4 26.8 - - + +
248C PRO* 3.3 31.7 - - - +
249C LYS* 4.9 7.4 + - - +
252C ARG* 4.4 6.1 + - - +
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Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B SER 4.2 0.3 + - - -
176B SER* 3.3 10.7 - - - -
177B GLU* 3.2 35.9 + - - +
180B ASP* 3.7 10.7 + - - -
181B LEU* 3.5 30.7 - - - -
182B SER* 3.5 35.4 - - - +
183B SER 4.8 1.8 - - - -
220C LYS* 3.5 23.1 - - + -
221C ASN* 1.3 78.4 - - - +
223C GLU* 1.3 74.7 + - + +
225C ALA* 3.8 2.1 + - - +
226C GLU* 3.2 30.1 + - - +
233C VAL* 3.3 28.1 - - + +
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Residues in contact with GLU 223 (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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177B GLU* 4.0 18.6 - - - +
218C GLU 4.8 0.2 - - - +
219C LEU* 3.5 29.9 - - + +
220C LYS* 2.8 39.4 + - - +
222C TYR* 1.3 106.0 + - + +
224C ILE* 1.3 62.6 + - - +
226C GLU* 3.5 5.8 + - - +
227C GLN* 3.0 40.5 + - - +
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Residues in contact with ILE 224 (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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210C ALA* 3.8 37.0 - - + +
213C LEU* 4.1 15.5 - - + -
214C LEU* 3.6 38.4 - - + +
219C LEU* 3.6 34.8 - - + +
220C LYS 3.0 9.7 + - - +
221C ASN* 3.1 8.0 + - - +
223C GLU* 1.3 76.5 - - - +
225C ALA* 1.3 64.6 + - - +
227C GLN* 3.1 5.8 + - - +
228C VAL* 3.0 24.7 + - + +
236C PHE* 4.0 9.4 - - + -
252C ARG* 4.1 5.8 - - - +
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Residues in contact with ALA 225 (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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221C ASN 2.9 16.4 + - - +
222C TYR 3.9 4.3 - - - +
224C ILE* 1.3 79.2 - - - +
226C GLU* 1.3 61.4 + - - +
228C VAL* 3.5 2.6 + - - +
229C GLY 3.4 2.4 + - - -
230C PHE* 2.9 39.4 + - + +
232C ASP* 4.2 1.8 - - - -
233C VAL* 3.8 20.0 - - - +
236C PHE* 3.7 30.9 - - + -
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Residues in contact with GLU 226 (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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226A GLU* 4.5 11.3 - - - +
182B SER* 5.8 3.3 - - - -
166C THR 3.9 8.7 - - - +
222C TYR* 3.2 22.0 + - - +
223C GLU* 3.8 6.5 - - - +
224C ILE 3.2 0.2 - - - -
225C ALA* 1.3 80.8 - - - +
227C GLN* 1.3 64.6 + - + +
229C GLY* 3.4 8.3 + - - -
230C PHE 4.4 6.5 - - - +
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Residues in contact with GLN 227 (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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165C TYR* 4.6 1.6 + - - -
166C THR* 3.5 25.7 - - - +
209C LYS* 5.3 2.9 - - - +
213C LEU* 3.7 19.8 - - + +
219C LEU* 3.6 37.6 - - - +
223C GLU* 3.0 21.8 + - - +
224C ILE 3.1 3.8 + - - +
226C GLU* 1.3 80.6 - - + +
228C VAL* 1.3 57.7 + - - +
229C GLY 3.3 0.9 - - - -
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Residues in contact with VAL 228 (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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165C TYR* 3.2 13.5 - - - +
166C THR* 4.0 1.1 - - - -
206C ARG* 3.0 45.3 - - - +
207C MSE 5.1 0.7 - - + -
209C LYS* 3.4 30.5 - - + -
210C ALA* 3.7 24.9 - - + +
213C LEU* 4.1 8.3 - - + -
224C ILE 3.0 21.1 + - - +
225C ALA* 3.9 6.3 - - - +
226C GLU 3.4 0.2 - - - -
227C GLN* 1.3 79.6 - - - +
229C GLY* 1.3 57.5 + - - +
230C PHE* 3.8 21.3 - - + -
236C PHE* 5.1 1.1 - - + -
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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