Contacts of the helix formed by residues 185 - 201 (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 ASN 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165F GLY 2.7 27.7 + - - +
167F TYR* 3.5 19.6 - - + +
182F GLY* 3.5 20.1 + - - -
183F VAL 3.4 1.2 - - - -
184F ASP* 1.3 82.4 - - - +
186F ALA* 1.3 64.2 + - - +
187F GLY 3.0 5.8 + - - -
188F ALA* 2.8 22.7 + - - +
189F LYS* 3.0 19.6 + - - +
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Residues in contact with ALA 186 (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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164F ASP* 4.8 1.6 - - - +
185F ASN* 1.3 74.5 - - - +
187F GLY* 1.3 53.2 + - - +
189F LYS* 3.1 12.0 + - - +
190F ALA* 2.7 37.2 + - - +
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Residues in contact with GLY 187 (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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161F ILE 3.5 10.6 - - - +
164F ASP* 3.5 44.2 + - - +
165F GLY* 3.9 2.7 - - - -
185F ASN* 3.0 7.5 + - - -
186F ALA* 1.3 78.9 - - - +
188F ALA* 1.3 56.0 + - - +
190F ALA* 3.6 2.3 - - - +
191F GLY* 3.0 23.2 + - - -
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Residues in contact with ALA 188 (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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161F ILE* 3.6 30.3 + - + +
166F GLY* 4.0 10.2 - - - +
182F GLY 4.1 1.1 - - - +
183F VAL* 3.2 29.8 - - - +
185F ASN* 2.8 17.1 + - - +
187F GLY* 1.3 74.5 - - - +
189F LYS* 1.3 59.6 + - - +
191F GLY 3.4 0.3 + - - -
192F LEU* 2.9 31.9 + - - +
361F LEU* 4.0 3.1 - - + +
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Residues in contact with LYS 189 (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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184F ASP* 3.1 40.2 + - - +
185F ASN 3.0 15.8 + - - +
186F ALA* 3.4 9.6 - - - +
188F ALA* 1.3 74.1 - - - +
190F ALA* 1.3 55.0 + - - +
192F LEU* 3.3 0.7 + - - +
193F THR* 2.6 41.3 + - - -
357F VAL* 4.0 2.3 - - + +
358F ASP* 3.6 48.2 + - - +
361F LEU* 3.9 19.5 - - + +
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Residues in contact with ALA 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F ASP* 4.0 8.5 - - - +
186F ALA 2.7 20.2 + - - +
187F GLY 3.6 5.2 - - - +
189F LYS* 1.3 73.5 - - - +
191F GLY* 1.3 56.9 + - - +
193F THR* 3.2 11.0 - - - +
194F PHE* 3.0 30.0 + - - +
250F PHE* 3.6 6.8 - - + -
251F LYS* 3.8 28.5 - - - +
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Residues in contact with GLY 191 (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* 3.6 33.1 - - - +
161F ILE* 4.3 4.0 - - - -
187F GLY 3.0 14.9 + - - -
188F ALA 3.8 1.1 - - - -
190F ALA* 1.3 77.0 - - - +
192F LEU* 1.3 61.5 + - - +
194F PHE* 3.5 3.6 + - - +
195F LEU 3.2 16.3 + - - -
250F PHE* 3.7 17.4 - - - -
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Residues in contact with LEU 192 (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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161F ILE* 4.1 24.4 - - + +
188F ALA 2.9 17.8 + - - +
189F LYS 3.9 1.6 - - - +
191F GLY* 1.3 72.2 - - - +
193F THR* 1.3 65.9 + - - +
195F LEU* 3.1 29.8 + - + +
196F VAL* 2.9 35.9 + - + +
346F ALA 4.7 7.0 - - - +
347F VAL* 4.3 18.2 - - + +
350F ALA* 4.1 15.3 - - + -
351F ALA* 6.5 0.2 - - + -
357F VAL* 3.8 15.3 - - + +
360F ALA* 5.4 0.9 - - + -
361F LEU* 3.6 32.3 - - + -
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Residues in contact with THR 193 (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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189F LYS* 2.6 21.9 + - - +
190F ALA* 3.2 18.6 - - - +
192F LEU* 1.3 72.5 - - - +
194F PHE* 1.3 66.1 + - + +
196F VAL* 3.3 3.6 + - - +
197F ASP* 3.1 35.9 + - - +
357F VAL* 4.0 25.3 - - - +
358F ASP* 5.9 1.1 - - - -
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Residues in contact with PHE 194 (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* 3.4 49.6 - + + -
130F GLU* 4.0 17.5 - - + -
133F PRO* 4.4 13.5 - - + -
160F LEU* 4.2 12.3 - - + -
190F ALA 3.0 18.3 + - - +
191F GLY 3.5 4.3 - - - +
193F THR* 1.3 74.2 - - + +
195F LEU* 1.3 67.6 + - - +
197F ASP* 3.0 24.4 + - + +
198F LEU* 3.0 40.5 + - + +
250F PHE* 3.6 27.4 - + + -
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Residues in contact with LEU 195 (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* 5.6 0.4 - - + -
149F PHE* 4.1 20.2 - - + -
151F LEU* 4.4 12.3 - - + -
157F THR* 3.3 31.0 - - + +
160F LEU* 3.9 22.7 - - + -
191F GLY 3.2 4.6 + - - +
192F LEU* 3.1 25.0 + - + +
194F PHE* 1.3 79.1 - - - +
196F VAL* 1.3 63.8 + - + +
198F LEU* 3.2 19.3 + - + +
199F ILE* 3.4 21.8 + - + +
204F MET* 4.0 22.7 - - + -
347F VAL* 4.4 8.1 - - + -
351F ALA* 5.8 2.5 - - + -
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Residues in contact with VAL 196 (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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192F LEU* 2.9 25.2 + - + +
193F THR* 3.5 7.6 - - - +
195F LEU* 1.3 75.5 - - + +
197F ASP* 1.3 54.1 + - - +
199F ILE* 3.0 12.9 + - + +
200F LYS* 2.8 51.5 + - + +
350F ALA* 3.7 35.4 - - + +
351F ALA* 4.4 6.3 - - + +
357F VAL* 3.7 26.5 - - + -
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Residues in contact with ASP 197 (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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193F THR* 3.1 26.1 + - - +
194F PHE* 3.0 17.5 + - + +
196F VAL* 1.3 77.2 - - - +
198F LEU* 1.3 54.8 + - + +
200F LYS* 3.9 18.0 - - - +
201F ASN* 2.7 50.6 + - - +
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Residues in contact with LEU 198 (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* 4.7 11.2 - - + -
132F ILE* 4.7 20.0 - - + -
133F PRO* 5.0 6.7 - - + -
147F LEU* 5.5 0.7 - - + -
194F PHE* 3.0 66.2 - - + +
195F LEU* 3.2 11.1 + - - +
197F ASP* 1.3 76.4 - - + +
199F ILE* 1.3 58.1 + - - +
201F ASN 3.8 0.3 - - - -
202F LYS 3.6 1.2 + - - -
203F HIS* 2.9 53.8 + - + -
204F MET* 3.0 36.3 + - + -
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Residues in contact with ILE 199 (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* 3.8 26.9 - - + -
195F LEU* 3.4 22.9 - - + +
196F VAL* 3.0 9.4 + - + +
198F LEU* 1.3 76.3 - - - +
200F LYS* 1.3 64.1 + - - +
201F ASN 3.2 0.2 - - - -
202F LYS* 3.1 17.5 + - - +
204F MET* 3.4 18.5 - - + +
205F ASN* 4.4 0.4 - - - +
206F ALA* 3.6 28.7 - - + +
351F ALA* 3.6 40.4 - - + +
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Residues in contact with LYS 200 (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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196F VAL* 2.8 38.1 + - + +
197F ASP* 3.6 19.1 - - - +
199F ILE* 1.3 73.8 - - - +
201F ASN* 1.3 63.0 + - - +
202F LYS* 3.5 4.3 + - - +
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Residues in contact with ASN 201 (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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197F ASP* 2.7 39.7 + - - +
199F ILE 3.2 0.4 - - - -
200F LYS* 1.3 76.2 - - - +
202F LYS* 1.3 56.0 + - - +
203F HIS* 2.8 46.0 + - + +
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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