Contacts of the helix formed by residues 167 - 182 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G PHE* 3.5 21.5 - - + -
166G ILE* 1.3 77.8 - - - +
168G ASP* 1.3 72.8 + - - +
169G GLU* 3.3 24.5 + - - +
170G ILE* 3.3 11.3 + - + +
171G PHE* 2.6 36.8 + - - +
303H ASP* 4.6 7.6 - - + +
348H SER 4.5 2.4 - - - +
349H ASN* 4.3 3.4 - - - +
350H VAL* 2.7 53.3 + - + +
351H THR* 4.7 1.4 - - - +
352H ILE 5.6 0.4 - - - +
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Residues in contact with ASP 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ASN* 1.3 81.6 + - - +
169G GLU* 1.3 59.2 + - - +
171G PHE* 3.6 7.9 - - - +
172G VAL* 3.1 30.8 + - - +
243G LYS* 4.4 21.5 + - - -
247G LEU* 3.5 25.8 - - + +
303H ASP* 4.5 8.2 - - - +
348H SER* 3.2 35.9 - - - +
349H ASN* 3.5 18.2 - - - +
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Residues in contact with GLU 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LYS* 3.4 23.4 + - - +
34G ARG* 3.3 28.3 + - - -
167G ASN* 3.6 21.5 + - - +
168G ASP* 1.3 76.2 - - - +
170G ILE* 1.3 85.4 + - + +
171G PHE 3.4 0.2 + - - -
172G VAL* 3.4 6.2 + - - +
173G GLU* 3.2 32.6 + - - +
335H LYS* 5.1 11.4 - - + +
349H ASN* 4.3 8.6 - - - +
350H VAL 4.5 4.8 - - - +
351H THR* 4.7 11.1 + - - +
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Residues in contact with ILE 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G TYR* 4.3 19.1 - - + -
26G LEU* 5.4 9.5 - - + +
27G ARG* 4.3 19.5 - - + +
30G LYS* 4.7 14.1 - - + +
165G PHE* 3.8 15.5 - - + -
166G ILE* 3.7 19.1 - - + +
167G ASN* 3.3 24.6 + - + +
169G GLU* 1.3 103.0 - - + +
171G PHE* 1.3 57.8 + - - +
173G GLU* 4.4 7.9 - - + +
174G LEU* 3.2 26.3 + - + +
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Residues in contact with PHE 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G ILE* 3.8 17.5 - - + +
167G ASN 2.6 22.0 + - - +
168G ASP* 3.6 8.5 - - - +
169G GLU 3.2 0.2 - - - -
170G ILE* 1.3 72.6 - - - +
172G VAL* 1.3 68.2 + - + +
174G LEU* 3.2 6.0 + - + +
175G VAL* 3.0 45.1 + - + +
224G PHE* 4.5 3.1 - + - -
227G ILE* 3.5 23.6 - - + -
240G LEU* 3.8 33.4 - - + -
243G LYS* 4.3 17.9 - - + -
244G TYR* 4.1 26.7 - + + -
247G LEU* 4.4 15.3 - - + -
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Residues in contact with VAL 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G ASP 3.1 18.7 + - - +
169G GLU* 3.4 5.6 + - - +
171G PHE* 1.3 76.3 - - + +
173G GLU* 1.3 54.4 + - + +
175G VAL* 3.7 5.8 - - - +
176G ASN* 2.8 40.1 + - + +
244G TYR* 4.4 12.0 - - + -
247G LEU* 3.2 30.7 - - + -
248G THR* 3.9 26.5 - - + -
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Residues in contact with GLU 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 3.9 22.5 - - + +
29G LEU* 6.1 1.2 - - - +
30G LYS* 3.1 43.2 + - - +
169G GLU* 3.2 19.3 + - - +
170G ILE* 4.4 7.2 - - + +
172G VAL* 1.3 77.2 - - + +
174G LEU* 1.3 55.0 + - - +
176G ASN* 3.7 7.4 - - - +
177G ALA* 2.7 36.4 + - - +
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Residues in contact with LEU 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G VAL* 3.8 42.4 - - + +
22G GLU* 4.2 6.5 - - + -
23G TYR* 4.0 23.3 - - + +
26G LEU* 3.8 15.0 - - + +
166G ILE* 4.7 15.3 - - + -
170G ILE* 3.2 22.7 + - + +
171G PHE* 3.2 10.7 + - + +
173G GLU* 1.3 72.1 - - - +
175G VAL* 1.3 57.1 + - + +
177G ALA 3.7 0.2 - - - -
178G LEU* 2.7 40.7 + - + +
227G ILE* 4.4 15.7 - - + -
231G PHE* 4.7 12.1 - - + -
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Residues in contact with VAL 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G PHE* 3.0 51.1 + - + +
172G VAL 3.9 4.0 - - - +
174G LEU* 1.3 77.7 - - + +
176G ASN* 1.3 57.5 + - - +
178G LEU* 3.8 7.8 - - - +
179G GLY* 3.0 23.0 + - - -
223G ILE* 4.5 12.8 - - + +
224G PHE* 4.3 17.7 - - + -
227G ILE* 4.5 8.1 - - + -
244G TYR* 4.0 36.6 - - + -
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Residues in contact with ASN 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G VAL* 2.8 27.1 + - + +
173G GLU* 3.7 8.5 - - - +
175G VAL* 1.3 74.4 - - - +
177G ALA* 1.3 57.7 + - - +
179G GLY* 3.2 4.3 + - - -
180G GLN* 2.9 25.5 + - - +
244G TYR* 5.8 3.6 - - + +
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Residues in contact with ALA 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G GLU* 3.7 15.9 - - + +
25G ARG* 4.9 4.6 + - - +
26G LEU* 3.8 29.2 - - + -
173G GLU 2.7 22.4 + - - +
174G LEU 3.9 0.7 - - - +
176G ASN* 1.3 72.9 - - - +
178G LEU* 1.3 57.9 + - - +
180G GLN* 3.4 11.0 + - + +
181G TYR* 3.0 26.9 + - - +
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Residues in contact with LEU 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G TRP* 4.1 25.6 - - + +
18G ARG* 5.2 4.7 - - + +
19G VAL* 3.5 25.6 - - + +
22G GLU* 4.9 2.9 - - + +
174G LEU* 2.7 25.8 + - + +
175G VAL* 3.8 6.1 - - - +
177G ALA* 1.3 70.2 - - - +
179G GLY* 1.3 61.7 - - - +
181G TYR* 4.0 11.4 - - + +
182G ASN* 3.5 16.6 + - - -
223G ILE* 3.5 37.5 - - + +
227G ILE* 3.4 33.7 - - + -
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Residues in contact with GLY 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175G VAL 3.0 15.1 + - - -
176G ASN* 3.2 5.3 + - - -
178G LEU* 1.3 75.3 - - - +
180G GLN* 1.3 61.7 + - - +
181G TYR 3.7 0.2 + - - -
182G ASN* 3.7 16.5 + - - +
220G SER 6.2 2.0 - - - -
223G ILE* 5.8 1.7 - - - +
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Residues in contact with GLN 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ARG* 6.3 0.9 - - - +
176G ASN 2.9 12.9 + - - +
177G ALA* 3.4 14.3 + - + +
179G GLY* 1.3 75.5 - - - +
181G TYR* 1.3 65.3 + - - +
182G ASN* 3.5 4.3 + - - +
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Residues in contact with TYR 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G TRP* 5.4 6.1 - + - -
18G ARG* 2.8 72.1 + - + +
22G GLU* 3.2 33.4 - - - +
25G ARG* 6.2 0.2 - - - -
177G ALA 3.0 10.8 + - - +
178G LEU* 4.1 10.8 - - + +
179G GLY 3.4 0.2 - - - -
180G GLN* 1.3 75.4 - - - +
182G ASN* 1.3 79.3 + - - +
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Residues in contact with ASN 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G TRP* 3.3 31.2 - - - -
18G ARG* 5.7 2.5 - - - -
178G LEU 3.5 12.1 + - - -
179G GLY 4.1 11.6 - - - +
180G GLN 3.4 7.9 - - - +
181G TYR* 1.3 97.9 - - - +
211G GLU* 2.8 52.3 + - - +
212G SER* 3.5 14.6 + - - -
214G PRO* 5.0 6.6 - - - +
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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
------------------------------------------------------------
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