Contacts of the helix formed by residues 214 - 226 (chain B) in PDB entry 5W5T
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 THR 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ILE* 4.5 4.9 - - + -
123B GLU* 6.5 0.7 - - - -
126B ALA* 5.6 0.9 - - - -
127B PRO* 2.7 38.2 + - + +
128B GLU 3.1 8.1 + - - -
129B TYR 3.2 21.8 + - - -
130B MET* 3.2 25.9 - - + +
212B PHE 3.7 1.4 + - - -
213B HIS* 1.3 70.9 - - - +
215B LYS* 1.3 63.8 + - - +
217B LEU* 3.1 3.8 + - - +
218B MET* 3.0 43.4 + - + +
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Residues in contact with LYS 215 (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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213B HIS* 3.3 2.8 - - + +
214B THR* 1.3 78.4 - - - +
216B PHE* 1.3 63.5 + - - +
218B MET* 3.3 17.4 + - - +
219B GLU* 3.3 30.8 + - - +
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Residues in contact with PHE 216 (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 ASP* 3.5 53.2 - - + -
212B PHE* 3.9 10.5 - + - -
213B HIS* 3.1 22.1 + - + +
215B LYS* 1.3 78.8 - - - +
217B LEU* 1.3 65.7 + - - +
219B GLU* 3.3 10.9 + - + +
220B ALA* 3.2 22.1 + - + +
223B ARG* 5.5 12.4 + - - -
242B ILE* 3.7 33.0 - - + -
246B GLY* 6.2 0.2 - - - -
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Residues in contact with LEU 217 (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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115B VAL* 4.8 1.8 - - + -
130B MET* 3.6 27.4 - - + -
132B ILE* 4.0 14.8 - - + -
212B PHE* 3.5 59.9 - - + -
213B HIS 3.0 6.5 + - - +
214B THR* 3.1 9.2 + - - +
216B PHE* 1.3 77.9 - - - +
218B MET* 1.3 68.9 + - + +
220B ALA* 3.2 7.2 + - + +
221B LEU* 3.1 52.4 + - + +
234B PHE* 3.9 8.3 - - + -
238B ILE* 5.3 0.4 - - + -
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Residues in contact with MET 218 (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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115B VAL* 4.2 20.4 - - + -
119B ILE* 3.9 31.8 - - - +
122B ILE* 4.3 18.8 - - + -
123B GLU* 4.6 12.3 - - + +
130B MET* 4.8 1.1 - - + -
214B THR* 3.0 39.4 + - + +
215B LYS* 3.3 10.3 + - - +
217B LEU* 1.3 93.1 - - + +
219B GLU* 1.3 63.2 + - - +
221B LEU* 3.5 4.6 + - + +
222B ARG* 3.1 43.2 + - - +
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Residues in contact with GLU 219 (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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215B LYS* 3.3 28.1 + - - +
216B PHE* 3.7 13.7 - - + +
217B LEU 3.2 0.4 - - - -
218B MET* 1.3 75.7 - - - +
220B ALA* 1.3 65.6 + - - +
222B ARG* 3.3 12.2 + - + +
223B ARG* 2.9 38.3 + - - +
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Residues in contact with ALA 220 (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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216B PHE* 3.2 18.7 + - + +
217B LEU* 3.2 15.3 + - + +
219B GLU* 1.3 77.3 - - - +
221B LEU* 1.3 52.5 + - + +
223B ARG* 2.9 26.4 + - - +
224B ASP* 2.7 35.2 + - - +
238B ILE* 4.1 28.1 - - + +
242B ILE* 5.4 2.5 - - + -
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Residues in contact with LEU 221 (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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112B ALA* 3.5 35.0 - - + +
115B VAL* 3.4 34.1 - - + -
116B TYR* 3.4 24.7 - - + +
119B ILE* 5.2 2.0 - - + -
217B LEU* 3.1 38.2 + - + +
218B MET* 4.1 6.7 - - + +
220B ALA* 1.3 75.0 - - - +
222B ARG* 1.3 55.7 + - - +
224B ASP* 3.8 5.0 - - - +
225B ALA* 2.9 27.5 + - - +
232B ARG* 4.5 1.0 + - - -
234B PHE* 4.0 10.5 - - + -
238B ILE* 3.6 15.0 - - + -
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Residues in contact with ARG 222 (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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116B TYR* 4.0 21.1 - - + -
119B ILE* 3.8 24.7 - - + +
123B GLU* 3.1 28.3 + - - -
218B MET* 3.1 32.1 + - - +
219B GLU* 3.6 10.5 - - + +
221B LEU* 1.3 75.3 - - - +
223B ARG* 1.3 58.7 + - - +
225B ALA* 3.2 4.0 + - - +
226B ALA* 3.0 28.4 + - - +
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Residues in contact with ARG 223 (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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216B PHE* 5.5 12.3 + - - -
219B GLU* 2.9 26.1 + - + +
220B ALA* 3.2 30.1 - - - +
222B ARG* 1.3 73.6 - - - +
224B ASP* 1.3 66.0 + - - +
226B ALA* 3.3 7.5 + - - +
227B ASP* 3.2 21.6 + - + +
241B TYR* 3.2 55.2 + - + -
242B ILE* 5.5 5.1 - - - +
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Residues in contact with ASP 224 (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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112B ALA* 3.8 7.9 - - - +
220B ALA 2.7 11.0 + - - +
221B LEU* 3.8 5.8 - - - +
223B ARG* 1.3 71.9 - - - +
225B ALA* 1.3 65.0 + - - +
227B ASP* 3.3 23.4 + - - +
230B SER* 2.5 23.7 + - - -
232B ARG* 2.7 43.4 + - - -
237B ASP* 3.3 16.1 - - - +
238B ILE* 3.4 29.8 - - + +
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Residues in contact with ALA 225 (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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116B TYR* 3.6 30.5 - - + +
221B LEU 2.9 20.1 + - - +
222B ARG 3.2 6.3 + - - +
224B ASP* 1.3 77.6 + - - +
226B ALA* 1.3 59.8 + - - +
227B ASP 3.2 4.4 + - - +
232B ARG* 3.8 27.2 + - - +
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Residues in contact with ALA 226 (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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222B ARG 3.0 16.7 + - - +
223B ARG* 3.3 8.5 + - - +
224B ASP 3.2 0.4 - - - -
225B ALA* 1.3 75.6 - - - +
227B ASP* 1.3 58.8 + - - +
228B PRO* 3.3 14.3 - - - +
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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