Contacts of the helix formed by residues 167 - 182 (chain J) 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 ASN 167 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165J PHE* 3.6 18.5 - - + -
166J ILE* 1.3 78.7 - - - +
168J ASP* 1.3 68.7 + - - +
169J GLU* 3.4 22.8 + - - +
170J ILE* 3.3 12.9 + - + +
171J PHE* 2.7 37.5 + - - +
303K ASP* 4.4 7.3 - - - +
348K SER 4.4 1.9 - - - +
349K ASN* 4.1 4.7 - - - +
350K VAL* 2.8 56.7 + - + +
351K THR* 4.9 0.8 - - - +
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Residues in contact with ASP 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167J ASN* 1.3 78.1 + - - +
169J GLU* 1.3 56.2 + - - +
171J PHE* 3.3 8.5 + - - +
172J VAL* 3.0 34.6 + - - +
243J LYS* 5.4 7.8 + - - -
247J LEU* 3.5 28.5 - - + +
303K ASP* 4.5 6.9 - - - +
348K SER* 2.9 39.2 - - - +
349K ASN* 3.1 21.0 + - - +
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Residues in contact with GLU 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J LYS* 3.9 14.3 + - - +
34J ARG* 3.8 26.5 + - - -
167J ASN* 3.7 17.4 + - - +
168J ASP* 1.3 78.2 - - - +
170J ILE* 1.3 73.6 + - + +
172J VAL* 4.0 5.3 + - - +
173J GLU* 3.5 29.4 + - - +
335K LYS* 4.3 19.9 - - + +
336K MET 4.9 0.4 + - - -
349K ASN* 4.2 7.7 - - - +
350K VAL 3.6 14.6 - - - +
351K THR* 4.0 13.4 + - - +
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Residues in contact with ILE 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J TYR* 4.4 19.5 - - + -
26J LEU* 5.6 9.0 - - + -
27J ARG* 4.5 17.9 - - + +
30J LYS* 5.7 9.0 - - + +
165J PHE* 3.7 28.3 - - + -
166J ILE* 3.8 17.7 - - + -
167J ASN* 3.3 16.5 + - + +
169J GLU* 1.3 95.9 - - + +
171J PHE* 1.3 58.7 + - - +
172J VAL 3.5 0.2 - - - -
173J GLU* 4.0 11.9 - - + +
174J LEU* 2.9 28.9 + - + +
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Residues in contact with PHE 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166J ILE* 4.0 17.0 - - + +
167J ASN 2.7 21.5 + - - +
168J ASP* 3.3 7.8 + - - +
170J ILE* 1.3 72.5 - - - +
172J VAL* 1.3 61.1 + - + +
174J LEU* 4.0 6.6 - - + +
175J VAL* 3.1 58.4 + - + +
224J PHE* 4.4 2.5 - + - -
227J ILE* 3.6 20.9 - - + -
240J LEU* 3.7 34.8 - - + -
243J LYS* 4.3 13.7 - - + -
244J TYR* 3.9 29.2 - + + -
247J LEU* 4.2 16.6 - - + -
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Residues in contact with VAL 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J ASP 3.0 18.5 + - - +
169J GLU* 4.4 5.8 - - - +
171J PHE* 1.3 77.4 - - + +
173J GLU* 1.3 54.3 + - + +
175J VAL* 3.5 5.9 + - - +
176J ASN* 2.7 38.4 + - + +
244J TYR* 5.0 10.0 - - + -
247J LEU* 3.3 31.2 - - + -
248J THR* 4.3 22.4 - - + -
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Residues in contact with GLU 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J LEU* 3.8 21.5 - - + +
30J LYS* 3.8 40.9 + - - +
169J GLU 3.5 19.4 + - - +
170J ILE* 4.0 10.2 - - + +
171J PHE 3.3 0.4 - - - -
172J VAL* 1.3 78.1 - - + +
174J LEU* 1.3 54.4 - - - +
176J ASN* 3.4 12.9 + - - +
177J ALA* 2.6 37.1 + - - +
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Residues in contact with LEU 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J VAL* 3.9 38.6 - - + +
22J GLU* 4.0 16.8 - - + -
23J TYR* 4.0 26.9 - - + +
26J LEU* 3.6 11.8 - - + +
166J ILE* 4.8 10.5 - - + -
170J ILE* 2.9 21.8 + - + +
171J PHE* 4.0 9.0 - - + +
173J GLU* 1.3 72.1 - - - +
175J VAL* 1.3 57.9 + - + +
177J ALA 3.6 0.2 - - - -
178J LEU* 2.7 42.6 + - + +
227J ILE* 4.4 17.0 - - + -
231J PHE* 5.0 9.2 - - + -
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Residues in contact with VAL 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J PHE* 3.1 52.2 + - + +
172J VAL 3.8 3.4 - - - +
174J LEU* 1.3 76.9 - - + +
176J ASN* 1.3 56.7 + - - +
178J LEU* 3.6 8.2 + - + +
179J GLY* 3.0 23.9 + - - -
223J ILE* 4.8 10.2 - - + +
224J PHE* 4.4 15.3 - - + -
227J ILE* 4.4 8.3 - - + -
244J TYR* 3.6 40.6 - - + +
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Residues in contact with ASN 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172J VAL* 2.7 26.4 + - + +
173J GLU* 3.4 14.3 + - - +
175J VAL* 1.3 74.1 - - - +
177J ALA* 1.3 58.3 + - - +
179J GLY* 3.2 3.5 + - - -
180J GLN* 3.1 25.5 + - - +
244J TYR* 5.8 0.2 - - - -
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Residues in contact with ALA 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J GLU* 3.8 17.9 - - + +
25J ARG* 4.5 6.9 + - - +
26J LEU* 3.8 29.4 - - + -
173J GLU 2.6 21.2 + - - +
174J LEU 4.0 1.6 - - - +
176J ASN* 1.3 70.0 - - - +
178J LEU* 1.3 59.4 + - - +
180J GLN* 4.0 8.2 - - - +
181J TYR* 3.4 24.6 + - - +
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Residues in contact with LEU 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J TRP* 3.8 27.0 - - + -
18J ARG* 5.7 1.1 - - + -
19J VAL* 3.6 35.0 - - + +
22J GLU* 4.5 11.9 - - + +
174J LEU* 2.7 26.3 + - + +
175J VAL* 3.9 7.2 - - - +
177J ALA* 1.3 73.5 - - - +
179J GLY* 1.3 60.9 + - - +
180J GLN 3.5 0.2 - - - -
181J TYR* 3.9 7.6 - - + +
182J ASN* 3.5 17.3 + - - -
223J ILE* 3.6 42.0 - - + +
227J ILE* 4.0 12.8 - - + -
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Residues in contact with GLY 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J VAL 3.0 15.6 + - - -
176J ASN* 3.2 5.5 + - - -
178J LEU* 1.3 75.5 - - - +
180J GLN* 1.3 63.9 + - - +
182J ASN* 4.1 15.6 + - - +
212J SER* 5.8 1.6 - - - -
214J PRO* 6.0 1.7 - - - +
220J SER 6.1 3.1 - - - -
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Residues in contact with GLN 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J ASN* 3.1 14.7 + - - +
177J ALA* 4.2 8.3 - - - +
179J GLY* 1.3 73.1 - - - +
181J TYR* 1.3 70.7 + - - +
182J ASN* 3.5 4.3 + - - +
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Residues in contact with TYR 181 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J TRP* 5.2 2.5 - + - -
18J ARG* 2.8 61.0 + - + +
22J GLU* 3.2 35.9 - - - +
25J ARG* 5.8 1.3 - - - -
177J ALA 3.4 10.6 + - - +
178J LEU* 3.9 13.2 - - + +
179J GLY 3.5 0.4 - - - -
180J GLN* 1.3 81.8 - - - +
182J ASN* 1.3 93.6 + - - +
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Residues in contact with ASN 182 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J TRP* 4.1 22.6 - - - -
18J ARG* 4.4 6.2 + - - -
178J LEU 3.5 10.6 + - - -
179J GLY 4.1 9.9 - - - +
180J GLN 3.5 7.8 - - - +
181J TYR* 1.3 109.0 - - - +
211J GLU* 2.8 50.4 + - - +
212J SER* 3.5 13.0 - - - -
214J PRO* 4.7 9.7 - - - +
220J SER* 5.9 2.2 - - - -
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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