Contacts of the helix formed by residues 173 - 189 (chain B) in PDB entry 5TKM
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 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B GLU* 3.9 18.6 - - - +
171B TRP* 3.2 3.7 - - + +
172B TYR* 1.3 78.8 - - + +
174B PHE* 1.3 65.3 + - - +
175B ASP 3.2 2.6 + - - -
176B GLU* 3.3 33.4 + - - +
177B ASN* 2.9 42.1 + - - +
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.5 28.0 + - - -
148B MET 4.3 3.1 - - - -
149B ASP 3.9 1.6 - - - -
150B TYR* 3.6 39.0 - + + -
153B PHE* 3.4 48.9 - + + -
168B PHE* 5.0 2.0 - + - -
170B PRO* 4.4 12.8 - - + -
171B TRP* 2.9 37.5 + + - +
172B TYR 3.2 1.6 - - - -
173B LYS* 1.3 75.3 - - - +
175B ASP* 1.3 72.8 + - - +
178B TYR* 2.9 37.3 + + + +
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ALA* 6.4 1.6 - - + -
183A ARG* 3.8 28.7 + - - +
150B TYR* 6.1 0.3 - - - +
172B TYR 4.8 2.5 + - - +
173B LYS 3.3 0.8 - - - -
174B PHE* 1.3 96.8 - - - +
176B GLU* 1.3 63.0 + - - +
178B TYR* 3.4 5.5 + - - +
179B ALA* 3.0 22.9 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 3.3 32.9 - - + +
173B LYS* 3.3 46.9 + - + +
175B ASP* 1.3 77.7 - - - +
177B ASN* 1.3 72.9 + - - +
179B ALA* 3.8 6.0 - - - +
180B PHE* 3.1 23.7 + - - +
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 5.6 1.0 + - - +
23B ASN* 3.1 37.8 + - - +
24B GLU* 3.1 31.9 + - - +
25B PRO* 3.4 18.5 - - + +
171B TRP* 5.9 1.6 - - - +
173B LYS* 2.9 32.4 + - - +
174B PHE 3.7 3.4 - - - +
176B GLU* 1.3 79.3 - - - +
178B TYR* 1.3 65.0 + - - +
180B PHE* 3.3 3.1 + - - +
181B LEU* 2.9 30.2 + - - +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.8 10.0 - - - +
146B LYS* 5.6 1.6 + - - -
147B ILE* 3.6 26.9 + - + -
148B MET 3.4 25.4 - - - -
149B ASP* 3.8 28.0 + - + +
174B PHE* 2.9 27.9 + + + +
175B ASP* 3.7 6.3 - - - +
177B ASN* 1.3 76.3 - - - +
179B ALA* 1.3 62.8 + - + +
181B LEU* 3.2 5.8 + - - +
182B HIS* 2.8 58.9 + + + +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP* 5.7 3.8 - - + +
179A ALA* 4.6 19.7 - - + -
175B ASP 3.0 17.0 + - - +
176B GLU* 3.8 7.4 - - - +
178B TYR* 1.3 85.0 - - + +
180B PHE* 1.3 63.0 + - - +
182B HIS* 3.6 4.3 + - - +
183B ARG* 3.2 38.9 + - - +
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B PRO* 3.5 38.1 - - + -
176B GLU 3.1 17.6 + - - +
177B ASN* 3.8 3.1 - - - +
179B ALA* 1.3 77.3 - - - +
181B LEU* 1.3 65.5 + - + +
183B ARG* 3.4 25.6 + - - +
184B THR* 2.8 49.8 + - + -
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ASN* 3.5 27.6 - - + +
25B PRO* 4.1 26.2 - - + +
121B ALA 3.3 25.6 - - - +
122B ARG* 4.5 1.8 - - - -
123B LEU* 4.1 37.2 - - + +
147B ILE* 3.8 23.3 - - + +
177B ASN 2.9 19.5 + - - +
178B TYR 3.7 3.8 - - - +
180B PHE* 1.3 81.5 - - + +
182B HIS* 1.3 56.4 + - - +
184B THR* 3.3 3.5 + - - -
185B LEU* 2.9 31.2 + - - +
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Residues in contact with HIS 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.9 16.1 - - + +
178B TYR* 2.8 55.3 + + + +
179B ALA* 4.0 4.7 - - - +
181B LEU* 1.3 72.9 - - - +
183B ARG* 1.3 59.6 + - - +
185B LEU* 4.0 2.1 - - + +
186B LYS* 3.0 57.0 + - + +
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ASP* 3.8 29.2 + - - +
179B ALA* 3.2 24.9 + - - +
180B PHE* 3.8 33.3 + - - +
182B HIS* 1.3 78.3 + - - +
184B THR* 1.3 65.3 + - - +
186B LYS* 3.4 11.2 + - + +
187B GLU* 3.1 21.2 + - + +
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Residues in contact with THR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 3.8 20.9 - - + -
131B TYR* 3.2 29.4 - - + +
180B PHE* 2.8 44.0 + - + -
181B LEU* 3.7 4.9 - - - -
183B ARG* 1.3 75.8 - - - +
185B LEU* 1.3 65.1 + - - +
187B GLU* 3.2 10.6 + - - +
188B ILE* 3.0 23.5 + - + +
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.2 9.6 - - + +
135B LEU* 3.8 28.9 - - + -
145B VAL* 3.6 29.6 - - + +
146B LYS* 3.6 22.4 - - - -
147B ILE* 3.9 18.2 - - + +
181B LEU 2.9 16.9 + - - +
182B HIS* 4.0 3.6 - - + +
184B THR* 1.3 72.5 - - - +
186B LYS* 1.3 66.8 + - - +
188B ILE* 3.0 8.2 + - + +
189B LEU* 2.9 45.0 + - + +
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Residues in contact with LYS 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B HIS* 3.0 44.6 + - + +
183B ARG* 3.6 9.6 - - + +
185B LEU* 1.3 76.1 - - - +
187B GLU* 1.3 61.9 + - - +
189B LEU* 3.4 5.6 + - - +
190B ARG 3.0 38.2 + - - +
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Residues in contact with GLU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 2.9 37.1 + - + -
132B ARG* 3.1 33.2 + - - +
183B ARG* 3.1 13.0 + - + +
184B THR* 3.5 12.7 - - - +
185B LEU 3.1 0.6 - - - -
186B LYS* 1.3 76.7 - - - +
188B ILE* 1.3 62.3 + - - +
190B ARG* 3.2 11.5 + - - -
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 4.4 20.6 - - + -
126B TYR* 4.7 11.9 - - + -
131B TYR* 3.5 62.1 - - + +
132B ARG* 4.1 8.1 - - - +
135B LEU* 3.8 35.7 - - + -
136B CYS* 4.0 12.3 - - - +
184B THR 3.0 16.1 + - - +
185B LEU* 3.0 11.1 + - + +
187B GLU* 1.3 77.0 - - - +
189B LEU* 1.3 62.1 + - + +
190B ARG* 3.6 13.9 + - - -
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 3.7 42.6 - - + +
136B CYS* 4.0 9.2 - - - +
139B SER* 4.2 18.6 - - - +
145B VAL* 3.9 22.2 - - + +
185B LEU* 2.9 39.8 + - + +
186B LYS* 4.1 4.9 - - - +
187B GLU 3.2 0.4 - - - -
188B ILE* 1.3 75.2 - - - +
190B ARG* 1.3 78.3 + - - +
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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