Contacts of the helix formed by residues 222 - 231 (chain D) in PDB entry 5LS6
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 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D LYS* 3.5 32.5 - - + +
12D PRO* 5.1 11.1 + - - +
15D TRP* 3.5 52.3 - - + +
220D SER* 3.4 6.6 - - - -
221D ASP* 1.3 79.5 - - - +
223D ILE* 1.3 60.0 + - - +
224D PHE 3.5 0.2 - - - -
225D GLU* 3.5 32.6 + - - +
226D ALA* 4.1 16.2 - - - +
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Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D TRP* 3.4 38.8 - - + -
175D VAL* 5.1 12.6 - - + +
178D LEU* 3.6 37.6 - - + +
179D GLY* 6.4 1.1 - - - -
220D SER* 3.4 36.3 - - - +
222D LYS* 1.3 73.9 - - - +
224D PHE* 1.3 88.7 + - + +
225D GLU 3.1 2.9 - - - -
226D ALA* 3.0 24.1 + - + +
227D ILE* 3.3 19.3 + - + +
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Residues in contact with PHE 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D PHE* 4.6 0.9 - + - -
175D VAL* 4.5 17.7 - - + -
216D ARG 4.1 11.9 - - - -
220D SER 3.4 26.5 - - - -
221D ASP* 4.3 6.7 + - - +
222D LYS 3.5 0.8 - - - -
223D ILE* 1.3 88.7 - - + +
225D GLU* 1.3 59.5 + - - +
227D ILE* 3.7 13.9 - - + +
228D SER* 3.4 17.3 + - - -
237D ALA* 3.1 29.8 - - + +
240D LEU* 3.4 30.1 - - + +
241D LYS* 3.5 37.9 - - + -
244D TYR* 3.8 31.9 - + + -
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Residues in contact with GLU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ASP 2.9 22.3 - - - +
222D LYS* 3.6 35.7 - - - +
223D ILE 3.1 0.4 - - - -
224D PHE* 1.3 77.0 - - - +
226D ALA* 1.3 64.6 + - - +
228D SER* 3.1 14.3 + - - -
229D SER* 3.2 13.0 + - - -
237D ALA* 3.8 16.6 - - + -
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Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO 5.3 0.9 - - - +
15D TRP* 3.7 37.2 - - + +
16D ARG* 4.2 11.4 - - + +
19D VAL* 4.9 7.0 - - + -
222D LYS* 3.9 10.5 + - - +
223D ILE* 3.0 13.6 + - + +
225D GLU* 1.3 78.5 - - - +
227D ILE* 1.3 62.2 + - - +
229D SER* 2.6 24.4 + - - -
230D MET* 3.4 11.7 + - - +
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Residues in contact with ILE 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 3.6 34.3 - - + -
171D PHE* 3.5 33.4 - - + -
174D LEU* 4.3 17.3 - - + -
175D VAL* 5.1 3.1 - - + -
178D LEU* 4.0 12.3 - - + -
223D ILE* 3.3 9.2 + - + +
224D PHE* 3.7 25.4 - - + +
226D ALA* 1.3 79.0 - - - +
228D SER* 1.3 59.1 + - - +
230D MET* 3.3 8.5 + - - +
231D PHE* 3.1 35.7 + - + +
240D LEU* 3.7 20.0 - - + -
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LYS* 5.5 0.9 + - - -
224D PHE 3.4 13.3 + - - -
225D GLU* 3.1 18.5 + - - -
226D ALA 3.3 0.2 - - - -
227D ILE* 1.3 80.8 - - - +
229D SER* 1.3 57.5 + - - +
231D PHE 3.1 26.1 - - - +
232D PRO* 3.2 8.3 - - - +
235D GLY* 3.9 9.5 + - - -
236D THR* 4.0 1.1 - - - -
237D ALA* 3.8 18.7 + - - +
240D LEU* 3.5 22.7 - - - -
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 3.4 38.3 + - - -
162D GLU* 4.8 4.5 - - - +
225D GLU 3.2 8.9 + - - -
226D ALA* 2.6 22.9 + - - -
228D SER* 1.3 79.5 + - - +
230D MET* 1.3 62.2 + - - +
232D PRO* 3.5 16.5 - - - +
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Residues in contact with MET 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 4.1 30.5 - - + +
19D VAL* 4.5 17.9 - - + -
20D LYS* 3.9 18.2 - - + -
161D ARG* 3.5 16.5 - - - +
162D GLU* 3.8 36.3 + - + +
163D CYS* 3.5 32.6 + - + -
226D ALA 3.4 11.2 + - - +
227D ILE* 3.3 4.8 + - - +
229D SER* 1.3 78.8 + - - +
231D PHE* 1.3 75.4 + - + +
232D PRO* 3.4 7.5 - - - +
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Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 5.5 4.3 - - + -
23D TYR* 4.1 17.9 - + - -
161D ARG* 3.3 23.8 - - - +
163D CYS* 3.6 32.8 - - + -
165D PHE 3.8 6.3 - - - -
166D ILE* 3.5 41.5 - - + -
174D LEU* 4.9 12.8 - - + -
227D ILE* 3.1 20.7 + - + +
228D SER* 3.1 6.5 - - - +
230D MET* 1.3 91.9 - - + +
232D PRO* 1.4 59.3 - - - +
233D ASP* 3.2 3.8 - - - -
234D LYS* 2.8 36.2 + - + +
235D GLY 3.2 8.3 + - - -
240D LEU* 5.9 0.7 - - + -
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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