Contacts of the helix formed by residues 153 - 164 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F GLU* 5.4 4.0 - - - +
150F ASN* 3.4 16.3 + - - +
151F LEU 4.2 0.8 - - - +
152F GLN* 1.3 80.9 - - + +
154F PRO* 1.3 69.0 - - - +
155F TYR 3.3 0.7 + - - -
156F PHE* 3.4 30.5 + - + -
157F THR* 3.6 11.6 + - - -
344F ARG* 3.1 29.2 + - - -
1P GLC 3.7 20.3 + - - +
2P GLC 2.7 30.0 + - - +
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Residues in contact with PRO 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU 5.6 0.2 - - - +
152F GLN 3.8 6.7 - - - +
153F GLU* 1.3 85.1 - - - +
155F TYR* 1.3 54.4 + - - +
156F PHE 3.1 3.5 + - - -
157F THR* 3.1 9.4 + - - +
158F TRP* 2.7 35.9 + - - +
340F TRP* 3.6 29.6 - - + +
343F VAL* 3.7 27.1 - - + -
344F ARG* 3.8 32.8 - - + +
347F VAL* 4.9 4.7 - - + -
2P GLC 3.4 11.2 - - - +
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Residues in contact with TYR 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F GLU* 3.9 23.0 + - - +
112F ALA* 4.1 7.8 - - - -
113F LEU* 3.3 44.4 + - + +
153F GLU 3.2 0.4 - - - -
154F PRO* 1.3 76.7 - - - +
156F PHE* 1.3 69.0 + + + +
158F TRP* 4.0 2.1 - - - +
159F PRO* 3.5 11.1 - - - +
230F TRP* 4.1 17.2 - + - -
258F PHE* 3.5 34.0 + - + +
260F GLY 4.2 4.0 + - - -
330F MET* 4.3 9.9 - - + -
340F TRP* 3.7 18.2 - + - -
1P GLC 4.0 32.9 + - - -
2P GLC 3.2 35.7 + - - +
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Residues in contact with PHE 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LEU* 3.7 35.0 - - + +
129F TRP* 6.1 0.3 - - - -
149F PHE* 3.8 19.8 - + + -
150F ASN* 3.3 50.3 - - + +
153F GLU* 3.7 12.1 - - + +
154F PRO 3.1 0.6 - - - -
155F TYR* 1.3 83.7 - + + +
157F THR* 1.3 62.4 + - - +
159F PRO* 3.2 15.8 - - - +
160F LEU* 5.8 0.3 - - - +
210F TYR* 4.2 19.7 - + - -
226F ILE* 3.8 26.7 - - + +
227F ASN* 4.1 11.4 - - - -
230F TRP* 4.9 3.8 - + - -
1P GLC 3.3 31.0 - - - -
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Residues in contact with THR 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PHE* 4.4 8.5 - - - -
150F ASN 4.3 0.3 + - - -
151F LEU* 3.9 20.1 + - - +
153F GLU 3.6 11.4 + - - -
154F PRO* 3.1 10.3 + - - +
156F PHE* 1.3 78.0 - - - +
158F TRP* 1.3 63.7 + - - +
159F PRO* 3.3 1.1 - - - -
160F LEU* 3.3 17.4 + - + +
161F ILE* 3.5 22.1 + - + +
195F LEU* 3.3 36.2 - - + +
347F VAL* 3.9 17.5 - - + +
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Residues in contact with TRP 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F PRO 2.7 22.2 + - - +
155F TYR 4.0 4.5 - - - +
157F THR* 1.3 72.7 - - - +
159F PRO* 1.4 58.6 - - + +
161F ILE* 2.8 32.3 + - + +
162F ALA* 2.7 48.7 + - + +
166F GLY 4.1 5.4 - - - -
167F TYR* 3.7 40.4 - - - -
168F ALA 3.9 1.1 - - - -
182F GLY 4.7 1.3 - - - -
183F VAL* 4.1 13.2 - - + -
256F LYS 4.0 8.9 + - - -
258F PHE* 3.1 45.2 - + - +
339F PHE* 3.6 33.2 - + - -
340F TRP* 4.7 6.5 - + + -
343F VAL* 4.4 18.2 - - + -
361F LEU* 6.2 0.4 - - + -
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Residues in contact with PRO 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F LEU* 4.2 7.9 - - + -
129F TRP* 6.0 2.2 - - + -
155F TYR 3.5 13.9 - - - +
156F PHE 3.2 18.8 - - - +
157F THR 3.3 2.0 - - - +
158F TRP* 1.4 90.4 - - + +
160F LEU* 1.3 55.6 + - - +
162F ALA 3.6 0.3 + - - -
163F ALA* 3.1 24.8 + - - +
226F ILE* 5.7 2.7 - - + -
247F LEU* 4.2 9.6 - - + -
255F SER* 3.6 16.0 - - - -
256F LYS 3.3 25.4 + - - +
257F PRO* 3.7 32.1 - - + -
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Residues in contact with LEU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F TRP* 3.8 48.6 - - + +
149F PHE* 5.9 1.1 - - + -
156F PHE 5.3 0.9 + - - +
157F THR* 3.3 10.0 + - - +
158F TRP 3.1 0.6 - - - -
159F PRO* 1.3 77.1 - - - +
161F ILE* 1.3 66.5 + - + +
163F ALA* 3.3 17.9 + - - +
164F ASP 4.5 0.3 + - - -
191F GLY* 3.6 29.2 - - - +
194F PHE* 4.2 10.1 - - + -
195F LEU* 3.9 29.4 - - + +
250F PHE* 3.7 34.1 - - + -
255F SER* 4.6 4.0 - - - -
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Residues in contact with ILE 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F THR* 3.6 24.9 - - + +
158F TRP* 2.8 41.8 + - + +
160F LEU* 1.3 74.6 - - + +
162F ALA* 1.3 59.5 + - - +
163F ALA 3.4 0.7 + - - -
164F ASP 4.3 0.2 + - - -
166F GLY* 3.5 11.7 + - - -
187F GLY 3.5 13.9 - - - +
188F ALA* 3.6 28.8 - - + +
191F GLY* 4.3 8.3 - - - -
192F LEU* 4.1 26.7 - - + +
343F VAL* 4.9 3.1 - - + -
347F VAL* 3.9 27.1 - - + -
361F LEU* 5.3 7.4 - - + -
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Residues in contact with ALA 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F TRP* 2.7 41.5 + - + +
159F PRO 3.8 0.9 - - - +
161F ILE* 1.3 70.8 - - - +
163F ALA* 1.3 66.0 + - - +
164F ASP 3.6 0.4 - - - -
165F GLY* 3.3 9.2 + - - -
166F GLY* 3.4 26.3 + - - +
256F LYS* 3.6 35.9 + - + +
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Residues in contact with ALA 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F PRO 3.1 12.7 + - - +
160F LEU* 3.4 14.4 - - - +
161F ILE 3.3 1.8 - - - -
162F ALA* 1.3 79.3 - - - +
164F ASP* 1.3 62.4 + - - +
165F GLY* 3.2 1.2 + - - -
250F PHE* 4.0 24.5 - - + +
253F GLN* 4.0 18.2 + - - +
254F PRO* 3.6 23.9 - - - +
255F SER* 4.2 4.3 - - - +
256F LYS* 4.5 7.6 - - - +
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Residues in contact with ASP 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160F LEU 4.5 1.2 + - - -
161F ILE 4.3 2.8 + - - -
162F ALA 3.6 0.2 - - - -
163F ALA* 1.3 77.4 - - - +
165F GLY* 1.3 55.1 + - - +
186F ALA* 4.8 1.2 - - - +
187F GLY* 3.5 31.8 + - - +
190F ALA* 4.0 3.1 - - - +
250F PHE* 4.3 17.5 - - + -
251F LYS* 3.6 32.2 - - + +
253F GLN* 3.3 26.3 + - - +
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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