Contacts of the helix formed by residues 173 - 189 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.9 19.5 - - - +
171A TRP* 3.2 4.6 - - + +
172A TYR* 1.3 79.5 - - + +
174A PHE* 1.3 65.4 + - - +
175A ASP 3.2 2.9 + - - -
176A GLU* 3.3 34.6 + - - +
177A ASN* 2.9 40.7 + - - +
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.5 28.3 + - - -
148A MET 4.3 2.9 - - - -
149A ASP 3.9 1.6 - - - -
150A TYR* 3.6 38.6 - + + -
153A PHE* 3.4 48.5 - + + -
168A PHE* 5.0 2.0 - + - -
170A PRO* 4.4 13.7 - - + -
171A TRP* 2.9 37.3 + + - +
172A TYR 3.2 1.6 + - - -
173A LYS* 1.3 76.7 - - - +
175A ASP* 1.3 75.0 + - - +
178A TYR* 2.9 38.2 + + + +
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Residues in contact with ASP 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A TYR* 6.1 0.2 - - - +
172A TYR 4.8 2.1 + - - +
173A LYS 3.3 0.8 - - - -
174A PHE* 1.3 97.8 - - - +
176A GLU* 1.3 63.5 + - - +
178A TYR* 3.4 6.1 + - - +
179A ALA* 3.0 22.3 + - - +
179B ALA* 6.4 1.8 - - + -
183B ARG* 3.8 29.3 + - - +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LYS* 3.3 45.6 - - + +
175A ASP* 1.3 76.6 - - - +
177A ASN* 1.3 74.2 + - - +
179A ALA* 3.8 6.8 - - - +
180A PHE* 3.1 24.1 + - - +
176B GLU* 3.3 32.4 - - + +
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A GLU* 5.6 1.4 + - - +
23A ASN* 3.1 38.4 + - - +
24A GLU* 3.1 31.9 + - - +
25A PRO* 3.4 18.4 - - + +
171A TRP* 5.9 1.8 - - - +
173A LYS* 2.9 32.6 + - - +
174A PHE 3.7 2.9 - - - +
176A GLU* 1.3 78.8 - - - +
178A TYR* 1.3 65.1 + - - +
180A PHE* 3.3 3.7 + - - +
181A LEU* 2.9 30.1 + - - +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.8 9.5 - - - +
146A LYS* 5.6 1.6 + - - -
147A ILE* 3.6 26.3 + - + -
148A MET 3.4 26.9 - - - -
149A ASP* 3.8 26.0 + - + +
174A PHE* 2.9 28.1 + + + +
175A ASP* 3.7 6.7 - - - +
177A ASN* 1.3 76.9 - - - +
179A ALA* 1.3 61.1 + - + +
181A LEU* 3.2 6.0 + - - +
182A HIS* 2.8 59.7 + + + +
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Residues in contact with ALA 179 (chain A).
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 3.0 17.2 + - - +
176A GLU* 3.8 7.6 - - - +
177A ASN 3.2 0.4 - - - -
178A TYR* 1.3 83.4 - - + +
180A PHE* 1.3 62.2 + - - +
182A HIS* 4.0 3.6 - - - +
183A ARG* 3.2 37.9 + - - +
175B ASP* 5.7 3.4 - - + +
179B ALA* 4.6 19.3 - - + -
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Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO* 3.5 37.5 - - + -
176A GLU 3.1 17.6 + - - +
177A ASN* 3.8 3.4 - - - +
179A ALA* 1.3 77.7 - - - +
181A LEU* 1.3 64.7 + - + +
183A ARG* 3.4 25.7 + - - +
184A THR* 2.8 49.0 + - + -
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 3.5 27.4 - - + +
25A PRO* 4.1 26.9 - - + -
121A ALA 3.3 25.4 - - - +
122A ARG* 4.5 1.3 - - - -
123A LEU* 4.1 38.2 - - + +
147A ILE* 3.8 23.4 - - + +
177A ASN 2.9 19.2 + - - +
178A TYR 3.7 2.7 - - - +
180A PHE* 1.3 80.8 - - + +
182A HIS* 1.3 57.1 + - - +
184A THR* 3.3 3.8 + - - -
185A LEU* 2.9 31.5 + - - +
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.9 16.1 - - + +
178A TYR* 2.8 54.7 + + + +
179A ALA* 4.0 4.9 + - - +
181A LEU* 1.3 73.7 - - - +
183A ARG* 1.3 59.2 + - - +
185A LEU* 3.6 2.7 + - + +
186A LYS* 3.0 57.6 + - + +
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Residues in contact with ARG 183 (chain A).
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* 3.2 24.7 + - - +
180A PHE* 3.8 32.6 - - + +
181A LEU 3.2 0.2 - - - -
182A HIS* 1.3 78.7 + - - +
184A THR* 1.3 65.4 + - - +
186A LYS* 3.4 11.3 + - + +
187A GLU* 3.1 21.4 + - + +
175B ASP* 3.8 29.9 + - - +
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.8 19.7 - - + -
131A TYR* 3.2 30.3 - - + +
180A PHE* 2.8 44.5 + - + -
181A LEU* 3.3 5.1 + - - -
183A ARG* 1.3 75.6 - - - +
185A LEU* 1.3 64.8 + - - +
187A GLU* 3.2 10.7 + - - +
188A ILE* 3.0 23.1 + - + +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.2 10.0 - - + +
135A LEU* 3.8 27.8 - - + -
145A VAL* 3.6 28.9 - - + +
146A LYS* 3.6 23.3 - - - +
147A ILE* 3.9 17.7 - - + +
181A LEU 2.9 17.1 + - - +
182A HIS* 4.0 3.1 - - + +
184A THR* 1.3 74.2 - - - +
186A LYS* 1.3 69.0 + - - +
188A ILE* 3.0 9.4 + - + +
189A LEU* 2.9 45.5 + - + +
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A HIS* 3.0 44.9 + - + +
183A ARG* 3.6 10.3 - - + +
185A LEU* 1.3 76.4 - - - +
187A GLU* 1.3 62.2 + - - +
189A LEU* 3.4 5.6 + - - -
190A ARG 3.0 38.6 + - - +
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Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR* 2.9 38.4 + - - -
132A ARG* 3.1 33.1 + - - +
183A ARG* 3.1 13.6 + - + +
184A THR* 3.5 12.3 - - - +
185A LEU 3.1 0.4 - - - -
186A LYS* 1.3 77.1 - - - +
188A ILE* 1.3 62.5 + - - +
190A ARG* 3.2 11.8 + - - -
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 4.4 20.4 - - + -
126A TYR* 4.7 12.8 - - + -
131A TYR* 3.5 60.8 - - + +
132A ARG* 4.1 8.5 - - - +
135A LEU* 3.8 35.7 - - + -
136A CYS* 4.0 11.5 - - - +
184A THR 3.0 16.1 + - - +
185A LEU* 3.0 10.2 + - + +
187A GLU* 1.3 76.4 - - - +
189A LEU* 1.3 62.1 + - + +
190A ARG* 3.6 13.9 + - - -
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.7 43.7 - - + +
136A CYS* 4.0 10.4 - - - +
139A SER* 4.2 18.4 - - - +
145A VAL* 3.9 22.0 - - + +
185A LEU* 2.9 38.9 + - + +
186A LYS* 3.4 6.0 + - - +
187A GLU 3.2 0.2 - - - -
188A ILE* 1.3 76.5 - - - +
190A ARG* 1.3 77.2 + - - +
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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