Contacts of the helix formed by residues 153 - 164 (chain G) in PDB entry 5TJ4
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 GLU 153 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G GLU* 5.5 2.6 - - - +
150G ASN* 3.4 19.9 + - - +
151G LEU 4.4 1.6 - - - -
152G GLN* 1.3 80.7 - - + +
154G PRO* 1.3 68.8 - - - +
155G TYR 3.3 0.7 + - - -
156G PHE* 3.5 26.6 + - + -
157G THR* 3.6 10.7 + - - -
344G ARG* 3.1 29.0 + - - -
1Q GLC 3.6 21.5 + - - +
2Q GLC 2.8 21.2 + - - +
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Residues in contact with PRO 154 (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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152G GLN 3.8 6.7 - - - +
153G GLU* 1.3 84.4 - - - +
155G TYR* 1.3 55.3 + - - -
156G PHE 3.1 3.1 + - - -
157G THR* 3.7 9.9 - - - +
158G TRP* 2.7 35.9 + - - +
340G TRP* 3.6 24.9 - - + +
343G VAL* 3.7 27.1 - - + -
344G ARG* 3.8 33.4 - - + +
347G VAL* 4.9 4.7 - - + -
2Q GLC 3.1 16.6 - - - +
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Residues in contact with TYR 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G GLU* 3.9 20.8 + - - +
112G ALA* 4.1 7.3 - - - -
113G LEU* 3.3 44.7 - - + +
153G GLU 3.3 0.2 - - - -
154G PRO* 1.3 76.0 - - - +
156G PHE* 1.3 68.6 - + + +
158G TRP* 4.0 2.8 + - - +
159G PRO* 3.5 10.6 - - - +
230G TRP* 4.1 16.8 - + - -
258G PHE* 3.5 34.3 + - + -
260G GLY 4.2 3.1 + - - -
330G MET* 4.3 8.3 - - + -
340G TRP* 3.8 17.2 - + - -
1Q GLC 3.7 39.9 + - - +
2Q GLC 2.9 37.2 + - - +
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Residues in contact with PHE 156 (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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113G LEU* 3.7 30.3 - - + +
129G TRP* 6.1 0.3 - - - -
149G PHE* 3.7 19.7 - + + -
150G ASN* 3.3 46.7 - - + +
153G GLU* 3.8 18.8 - - + +
154G PRO 3.1 0.6 - - - -
155G TYR* 1.3 79.7 - + + +
157G THR* 1.3 62.6 + - - +
158G TRP 3.4 0.2 - - - -
159G PRO* 3.2 15.6 - - - +
160G LEU* 5.3 0.5 + - - +
210G TYR* 4.1 22.0 - + - -
226G ILE* 3.7 31.1 - - + +
227G ASN* 4.0 12.1 - - - -
230G TRP* 4.9 4.9 - + - -
1Q GLC 3.8 29.2 - - - -
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Residues in contact with THR 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G PHE* 4.4 8.0 - - - -
150G ASN 4.3 0.7 + - - -
151G LEU* 3.9 19.8 + - - -
153G GLU 3.6 11.4 + - - -
154G PRO* 3.1 10.6 + - - +
156G PHE* 1.3 77.1 - - - +
158G TRP* 1.3 67.2 + - - +
160G LEU* 3.3 18.5 + - + +
161G ILE* 3.5 21.9 + - + +
195G LEU* 3.3 37.3 - - + +
347G VAL* 3.9 16.6 - - + +
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Residues in contact with TRP 158 (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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154G PRO* 2.7 22.8 + - - +
155G TYR 4.0 4.3 - - - +
157G THR* 1.3 72.0 - - - +
159G PRO* 1.4 59.6 - - + +
161G ILE* 2.8 31.7 + - + -
162G ALA* 2.7 48.8 + - + +
166G GLY 4.1 5.8 - - - -
167G TYR* 3.7 40.6 - - - -
168G ALA 3.9 1.8 - - - -
182G GLY 4.7 0.9 - - - -
183G VAL* 4.1 13.0 - - + -
256G LYS 4.0 8.9 + - - -
258G PHE* 3.1 43.9 - + - +
339G PHE* 3.6 31.9 - + - -
340G TRP* 4.7 6.3 - + + -
343G VAL* 4.4 18.8 - - + -
361G LEU* 6.2 0.4 - - + -
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Residues in contact with PRO 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G LEU* 4.2 7.6 - - + -
129G TRP* 6.1 2.0 - - + -
155G TYR 3.5 13.7 - - - +
156G PHE 3.2 19.5 - - - +
157G THR 3.2 1.8 - - - +
158G TRP* 1.4 90.4 - - + +
160G LEU* 1.3 59.6 + - - +
162G ALA 3.5 0.2 + - - -
163G ALA* 3.1 20.4 + - - +
226G ILE* 5.7 3.4 - - + -
247G LEU* 4.2 9.4 - - + -
255G SER* 3.6 17.6 - - - -
256G LYS 3.3 26.1 + - - +
257G PRO* 3.7 32.1 - - + -
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Residues in contact with LEU 160 (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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129G TRP* 3.8 44.1 - - + +
149G PHE* 5.9 1.1 - - + -
156G PHE 5.3 0.6 + - - +
157G THR* 3.3 11.1 + - + +
158G TRP 3.1 0.2 - - - -
159G PRO* 1.3 76.1 - - - +
161G ILE* 1.3 66.3 + - + +
163G ALA* 3.3 18.0 + - - +
164G ASP 4.5 0.7 + - - -
191G GLY* 3.6 29.0 - - - +
194G PHE* 4.2 9.4 - - + -
195G LEU* 3.8 29.4 - - + +
198G LEU* 6.2 0.2 - - + -
250G PHE* 3.7 37.8 - - + -
255G SER* 4.6 4.2 - - - -
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Residues in contact with ILE 161 (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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157G THR* 3.6 34.1 - - + +
158G TRP* 2.8 42.2 + - + +
160G LEU* 1.3 73.2 - - + +
162G ALA* 1.3 59.1 + - - +
163G ALA 3.4 0.9 + - - -
164G ASP 4.3 0.2 + - - -
166G GLY 3.5 11.3 + - - -
187G GLY 3.5 13.7 - - - +
188G ALA* 3.6 28.8 - - + +
191G GLY* 4.3 7.4 - - - -
192G LEU* 4.1 26.9 - - + +
195G LEU* 6.3 0.2 - - + -
343G VAL* 4.9 2.9 - - + -
347G VAL* 3.9 19.5 - - + -
361G LEU* 5.2 7.4 - - + -
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Residues in contact with ALA 162 (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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158G TRP* 2.7 41.3 + - + +
159G PRO 3.9 0.7 - - - +
161G ILE* 1.3 71.9 - - - +
163G ALA* 1.3 66.5 + - - +
164G ASP 3.6 0.4 - - - -
165G GLY* 3.3 8.8 + - - -
166G GLY* 3.5 26.3 + - - +
256G LYS* 3.7 33.8 - - + +
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Residues in contact with ALA 163 (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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159G PRO 3.1 14.6 + - - +
160G LEU* 3.4 15.3 - - - +
161G ILE 3.2 1.4 - - - -
162G ALA* 1.3 79.8 - - - +
164G ASP* 1.3 63.0 + - - +
165G GLY* 3.2 0.7 + - - -
250G PHE* 4.0 23.8 - - + +
253G GLN* 4.0 18.5 + - - +
254G PRO* 3.6 22.9 - - - +
255G SER* 4.2 4.9 - - - -
256G LYS* 4.6 7.6 - - - +
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Residues in contact with ASP 164 (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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160G LEU 4.5 1.2 + - - -
161G ILE 4.3 2.4 + - - -
162G ALA 3.6 0.2 - - - -
163G ALA* 1.3 79.0 - - - +
165G GLY* 1.3 56.5 + - - +
186G ALA* 4.8 1.2 - - - +
187G GLY* 3.5 31.5 + - - +
190G ALA* 4.0 5.2 - - - +
250G PHE* 4.3 18.4 - - + -
251G LYS* 3.6 28.4 - - + +
253G GLN* 3.3 26.7 + - - +
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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