Contacts of the helix formed by residues 171 - 184 (chain G) in PDB entry 5T0G
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 171 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G THR* 4.1 18.8 + - + +
170G VAL* 1.3 91.1 - - + +
172G GLN* 1.3 65.8 + - - +
173G THR 3.2 3.1 - - - -
174G GLU* 2.9 45.2 + - - +
175G SER 3.6 6.2 + - - -
205G VAL* 3.5 36.4 - - + +
206G LEU* 5.4 6.5 - - + -
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Residues in contact with GLN 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ILE* 6.1 0.4 - - - +
37G LEU 4.2 1.2 + - - -
38G THR* 3.2 21.9 + - + +
39G SER* 2.8 46.0 + - - +
40G VAL* 5.2 0.9 - - + -
81G THR* 4.7 4.0 - - - +
167G ALA* 3.3 21.5 - - + +
168G ALA* 3.2 22.0 + - - +
169G GLY* 3.4 19.9 - - - +
170G VAL 2.9 18.6 + - - +
171G LYS* 1.3 72.0 + - - +
173G THR* 1.3 65.8 + - - +
174G GLU 3.2 0.2 - - - -
175G SER* 3.2 8.3 + - - -
176G THR* 2.9 27.5 + - - +
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Residues in contact with THR 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G GLY 4.5 13.0 - - - +
170G VAL 4.4 6.7 + - - +
172G GLN* 1.3 76.5 - - - +
174G GLU* 1.3 87.2 + - - +
176G THR* 2.2 26.6 + - - -
177G SER* 3.8 6.2 + - - -
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Residues in contact with GLU 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170G VAL 4.6 0.3 - - - +
171G LYS* 2.9 42.8 + - - +
173G THR* 1.3 100.2 + - - +
175G SER* 1.3 66.4 + - - +
177G SER* 3.1 19.3 + - - -
178G PHE* 3.4 9.4 + - - +
205G VAL* 4.2 14.3 - - + +
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Residues in contact with SER 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G THR* 5.8 2.0 - - - -
40G VAL* 3.7 19.2 - - - +
167G ALA* 4.9 2.9 - - - -
171G LYS 3.6 3.0 + - - -
172G GLN* 3.2 16.2 + - - -
174G GLU* 1.3 76.6 - - - +
176G THR* 1.3 64.8 + - - +
178G PHE* 3.2 7.8 + - - +
179G LEU* 2.9 29.2 + - - +
201G CYS* 3.2 25.8 + - - +
205G VAL* 3.8 19.6 - - - +
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Residues in contact with THR 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G THR* 5.8 0.9 - - + -
167G ALA* 3.3 29.4 - - + +
172G GLN 2.9 16.8 + - - +
173G THR* 2.2 35.2 + - - -
175G SER* 1.3 73.2 - - - +
177G SER* 1.3 55.9 + - - -
179G LEU* 2.7 30.8 + - - +
180G GLU* 2.9 25.8 + - - +
56H LEU* 4.1 10.0 - - + +
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Residues in contact with SER 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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173G THR 4.1 5.0 + - - -
174G GLU* 3.1 18.4 + - - -
176G THR* 1.3 81.0 + - - +
178G PHE* 1.3 59.8 + - - +
179G LEU 3.6 0.2 + - - -
180G GLU* 3.6 23.5 + - - +
181G LYS* 3.8 11.4 + - - +
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Residues in contact with PHE 178 (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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174G GLU 3.4 8.7 + - - +
175G SER* 3.2 8.5 + - - +
176G THR 3.1 0.8 - - - -
177G SER* 1.3 83.5 + - - +
179G LEU* 1.3 65.8 + - + +
180G GLU 3.5 0.2 + - - -
181G LYS* 3.6 5.5 + - + +
182G LYS* 3.5 24.0 + - + +
200G THR* 3.6 19.3 - - - -
201G CYS* 3.5 44.0 - - + -
204G THR* 3.5 33.0 - - + +
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Residues in contact with LEU 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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40G VAL* 4.0 22.2 - - + -
41G ALA 5.0 1.1 - - - +
42G VAL* 4.4 17.7 - - + -
165G ALA* 4.9 7.6 - - + -
167G ALA* 4.7 9.4 - - + +
175G SER* 2.9 25.0 + - - +
176G THR* 2.7 16.5 + - - +
178G PHE* 1.3 76.1 - - + +
180G GLU* 1.3 64.5 + - - +
182G LYS* 2.9 10.6 + - + +
183G VAL* 2.9 34.4 + - + +
189G TRP* 6.1 2.9 - - + -
197G THR* 5.2 7.9 - - - +
201G CYS* 3.7 27.4 - - + -
56H LEU* 4.2 15.0 - - + -
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Residues in contact with GLU 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G THR* 2.9 21.9 + - - +
177G SER* 3.9 18.2 + - - +
178G PHE 3.3 0.6 - - - -
179G LEU* 1.3 76.9 - - - +
181G LYS* 1.3 59.4 + - - +
183G VAL* 3.8 1.0 + - - +
184G LYS* 3.2 36.8 + - - +
54H SER* 3.3 29.9 - - - -
55H ILE* 4.5 10.3 + - + +
56H LEU* 3.6 29.8 - - + +
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Residues in contact with LYS 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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177G SER 3.8 7.6 + - - +
178G PHE* 3.6 8.8 + - + +
179G LEU 3.2 0.8 - - - -
180G GLU* 1.3 76.3 - - - +
182G LYS* 1.3 63.3 + - - +
184G LYS 3.0 20.8 + - - +
185G LYS* 4.2 10.7 - - - +
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Residues in contact with LYS 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178G PHE* 3.5 18.6 + - + +
179G LEU* 2.9 15.2 + - + +
181G LYS* 1.3 77.4 - - - +
183G VAL* 1.3 64.2 + - - +
185G LYS* 4.3 8.6 - - + +
187G PHE* 3.4 26.4 - - + +
189G TRP* 3.4 30.7 - - + -
193G GLN* 3.3 28.7 + - - +
197G THR* 3.8 18.6 - - + -
200G THR* 5.9 0.4 - - - +
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Residues in contact with VAL 183 (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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42G VAL* 6.4 0.7 - - + -
164G LYS* 4.7 20.0 - - - -
165G ALA* 5.0 10.3 - - + -
179G LEU* 2.9 26.2 + - + +
180G GLU 4.2 4.0 - - - +
181G LYS 3.4 0.2 - - - -
182G LYS* 1.3 77.4 - - + +
184G LYS* 1.3 70.3 + - + +
186G LYS 4.3 0.3 - - - -
187G PHE* 3.2 25.9 + - - +
189G TRP* 3.7 29.6 - - + +
56H LEU* 3.8 21.3 - - + -
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Residues in contact with LYS 184 (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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180G GLU* 3.2 22.7 + - - +
181G LYS* 3.0 16.2 - - - +
182G LYS 3.3 2.2 - - - -
183G VAL* 1.3 88.8 - - + +
185G LYS* 1.3 76.7 + - - +
186G LYS* 5.0 0.4 - - - -
55H ILE* 3.3 38.7 + - - +
56H LEU* 5.4 3.4 - - - +
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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