Contacts of the helix formed by residues 176 - 194 (chain B) in PDB entry 5TWF
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 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B PHE* 4.4 16.7 - - + -
170B VAL* 3.9 10.1 - - + +
171B MET* 4.1 38.2 - - + +
173B LEU 4.9 1.8 - - - +
174B GLU 3.7 5.0 + - - +
175B GLU* 1.3 75.0 - - - +
177B ALA* 1.3 60.0 + - - +
178B HIS 3.0 4.1 - - - +
179B LEU* 2.9 22.0 + - - +
180B ASN* 2.7 29.3 + - - +
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Residues in contact with ALA 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 1.3 78.0 - - - +
178B HIS* 1.3 64.2 + - - +
180B ASN* 3.3 11.6 + - - -
181B THR* 2.2 38.2 + - - +
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Residues in contact with HIS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN* 2.8 38.4 + - + +
70B MET* 5.4 5.8 - - + -
71B LEU* 3.4 37.4 - - + +
74B THR* 6.3 0.8 - - - +
175B GLU* 4.8 10.4 - - + +
176B GLU 3.9 8.9 - - - +
177B ALA* 1.3 78.1 - - - +
179B LEU* 1.3 58.1 + - - +
181B THR* 3.9 2.5 - - - -
182B SER* 2.8 29.8 + - - -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.5 34.5 - - + -
159B TYR* 4.2 8.6 - - + -
162B ILE* 3.4 42.2 - - + -
163B TYR* 3.3 43.5 - - + +
167B PHE* 5.4 6.5 - - + -
170B VAL* 4.7 17.7 - - + -
175B GLU 5.2 0.4 - - - +
176B GLU* 2.9 9.8 + - - +
178B HIS* 1.3 76.4 - - - +
180B ASN* 1.3 66.5 + - - +
183B PHE* 2.9 32.2 + - - +
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Residues in contact with ASN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR* 3.0 35.1 + - - +
167B PHE* 4.8 11.3 - - - -
176B GLU* 2.7 41.1 + - - +
177B ALA* 3.3 7.9 + - - +
179B LEU* 1.3 79.9 - - - +
181B THR* 1.3 57.3 + - - +
183B PHE* 3.8 2.8 - - - +
184B LYS* 2.9 30.0 + - - +
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Residues in contact with THR 181 (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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36B LEU* 6.5 0.4 - - + -
41B LEU* 4.4 10.3 - - + +
177B ALA* 2.2 32.8 + - - +
178B HIS* 3.9 2.9 - - - -
180B ASN* 1.3 75.4 - - - +
182B SER* 1.3 65.1 + - - +
184B LYS* 3.1 10.0 + - + +
185B HIS* 2.9 23.4 + - - +
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Residues in contact with SER 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 4.5 5.7 - - - -
67B GLN* 3.3 35.6 - - - +
71B LEU* 3.9 10.3 - - - +
159B TYR* 2.7 26.3 + - - -
178B HIS* 2.8 25.1 + - - -
181B THR* 1.3 72.2 - - - +
183B PHE* 1.3 57.6 + - - +
185B HIS* 3.4 8.8 + - - +
186B PHE* 2.9 22.3 + - - +
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Residues in contact with PHE 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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156B PHE* 3.7 20.4 - + - -
159B TYR* 3.2 51.2 + + + -
160B ALA* 6.2 0.2 - - - -
163B TYR* 3.8 24.9 - + + +
179B LEU 2.9 22.8 + - - +
180B ASN 3.8 2.9 - - - +
182B SER* 1.3 74.8 - - - +
184B LYS* 1.3 62.8 + - - +
186B PHE* 3.2 1.6 + - - +
187B ILE* 2.9 61.4 + - + +
204B LEU* 3.9 23.1 - - + -
207B LEU* 3.8 25.4 - - + -
208B ILE* 4.2 4.9 - - + -
211B LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 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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39B GLY 3.9 19.4 + - - -
41B LEU* 3.7 18.1 - - + +
180B ASN 2.9 19.4 + - - +
181B THR* 3.1 10.5 + - + +
183B PHE* 1.3 81.6 - - - +
185B HIS* 1.3 57.7 + - - +
187B ILE* 4.0 1.1 - - - +
188B PHE* 2.9 68.1 + - + -
211B LEU* 4.5 25.4 - - + -
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Residues in contact with HIS 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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32B ALA* 4.9 6.3 - - + +
33B GLU* 5.9 0.2 - - - -
36B LEU* 3.6 41.4 - - + +
41B LEU* 3.6 15.3 - - + +
44B ALA 5.8 0.6 + - - -
45B VAL* 3.8 23.0 - - + +
60B ASN* 3.8 24.2 + - - -
63B ASP* 5.9 4.5 - - + -
64B PHE* 3.7 21.7 - + - -
181B THR 2.9 13.1 + - - +
182B SER* 3.5 11.3 - - - +
184B LYS* 1.3 75.0 - - - +
186B PHE* 1.3 63.1 + - - +
188B PHE* 3.9 1.6 - - - +
189B PHE* 3.0 21.1 + - + +
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Residues in contact with PHE 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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64B PHE* 3.5 33.8 - + + -
68B ILE* 5.2 0.7 - - + -
152B LEU* 3.3 45.8 - - + -
155B LEU* 4.4 11.0 - - + -
156B PHE* 3.8 31.9 - + + -
159B TYR* 3.3 31.4 - + + +
182B SER 2.9 10.9 + - - +
183B PHE 3.2 7.2 + - - +
185B HIS* 1.3 76.0 - - - +
187B ILE* 1.3 78.3 + - + +
189B PHE* 3.2 2.4 + - - +
190B VAL* 3.0 32.8 + - + +
196B ILE* 3.6 17.3 - - + -
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Residues in contact with ILE 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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156B PHE* 4.1 6.7 - - + -
183B PHE* 2.9 59.0 + - + +
184B LYS* 4.1 3.8 - - - +
186B PHE* 1.3 93.0 - - + +
188B PHE* 1.3 59.7 + - + +
190B VAL* 3.3 4.7 - - + +
191B GLN* 2.9 61.9 + - + +
201B LEU* 4.5 9.4 - - + -
208B ILE* 4.0 28.7 - - + -
211B LEU* 5.1 6.7 - - + -
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.7 18.6 - - + -
42B ARG* 3.1 60.8 - - + -
45B VAL* 4.1 16.4 - - + +
184B LYS* 2.9 61.9 + - + +
185B HIS 3.9 2.7 - - - +
187B ILE* 1.3 78.8 - - + +
189B PHE* 1.3 62.5 + - - +
191B GLN* 3.7 15.5 - - + +
192B GLU* 3.0 24.6 + - - +
211B LEU* 4.1 19.7 - - + -
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Residues in contact with PHE 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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45B VAL* 4.0 21.7 - - + +
56B TRP* 3.2 32.3 - + - -
57B ILE* 3.4 26.7 - - + -
60B ASN* 3.5 37.5 - - + -
61B THR 5.1 0.4 - - - -
64B PHE* 3.6 23.3 - + + -
152B LEU* 4.9 3.4 - - + -
185B HIS 3.0 18.7 + - - +
186B PHE 3.6 3.4 - - - +
188B PHE* 1.3 78.6 - - - +
190B VAL* 1.3 66.9 + - + +
192B GLU* 3.2 2.4 + - - +
193B PHE* 3.1 38.8 + + - -
195B LEU* 3.6 26.5 - - + -
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Residues in contact with VAL 190 (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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152B LEU* 4.3 18.4 - - + -
186B PHE* 3.0 31.8 + - + +
187B ILE* 3.3 17.5 - - - +
189B PHE* 1.3 80.7 - - + +
191B GLN* 1.3 61.0 + - - +
194B ASN* 2.8 26.9 + - - -
195B LEU* 3.1 15.7 + - + -
196B ILE* 3.9 46.2 + - + +
201B LEU* 4.5 12.1 - - + -
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Residues in contact with GLN 191 (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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42B ARG* 5.1 5.2 + - - -
187B ILE* 2.9 46.7 + - + +
188B PHE* 3.7 23.5 - - - +
190B VAL* 1.3 80.8 - - + +
192B GLU* 1.3 64.0 + - - +
193B PHE 3.2 0.3 + - - -
194B ASN* 3.1 19.3 - - - +
196B ILE 5.9 1.1 - - - -
201B LEU* 5.3 7.0 - - + +
208B ILE* 3.7 17.2 - - - +
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Residues in contact with GLU 192 (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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42B ARG 4.2 6.4 - - - +
45B VAL* 4.0 9.9 - - + -
46B MET* 3.4 35.9 - - - +
47B LEU 4.9 0.5 + - - -
188B PHE 3.0 17.4 + - - +
189B PHE 3.2 3.8 + - - +
191B GLN* 1.3 77.6 - - - +
193B PHE* 1.3 88.3 + - + +
194B ASN* 3.8 7.3 + - - +
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Residues in contact with PHE 193 (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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45B VAL 3.0 28.7 - - - -
47B LEU* 3.8 17.0 - - + -
53B LEU* 3.3 38.6 - - + -
56B TRP* 3.5 12.3 - + - -
57B ILE* 3.8 6.1 - - + -
145B MET* 4.9 4.8 - - - +
149B LYS* 5.2 0.7 - - - -
189B PHE* 3.1 46.2 + + - +
192B GLU* 1.3 96.5 - - + +
194B ASN* 1.3 74.4 + - - +
195B LEU* 3.2 27.1 + - + +
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Residues in contact with ASN 194 (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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149B LYS* 3.4 18.1 - - - -
190B VAL 2.8 15.6 + - - -
191B GLN* 3.1 14.7 + - - +
192B GLU 4.1 6.1 + - - +
193B PHE* 1.3 75.6 + - - +
195B LEU* 1.3 61.4 + - - +
196B ILE* 3.3 9.2 + - - +
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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
------------------------------------------------------------
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