Contacts of the helix formed by residues 186 - 198 (chain B) in PDB entry 5SY1
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 SER 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.7 13.6 - - - +
168B LYS* 4.7 9.1 + - - +
182B ALA* 3.1 19.6 + - - +
183B LEU 3.4 5.1 + - - -
184B PHE 3.2 0.8 - - - -
185B GLY* 1.3 76.9 - - - +
187B LEU* 1.3 58.6 + - - +
188B PRO 3.5 2.5 - - - -
189B GLN* 3.2 18.7 + - - -
190B ILE* 2.9 43.8 + - - +
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Residues in contact with LEU 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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183B LEU* 3.5 22.0 - - + +
184B PHE* 3.6 34.3 - - + +
185B GLY 3.4 0.4 - - - -
186B SER* 1.3 74.9 - - - +
188B PRO* 1.3 72.0 - - + +
190B ILE* 4.2 13.3 - - + +
191B ALA* 3.5 22.5 + - - +
287B TYR* 3.4 22.0 - - + +
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Residues in contact with PRO 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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95B GLY 5.6 0.2 - - - -
99B CYS* 4.1 15.7 - - - -
185B GLY 4.2 2.7 - - - +
186B SER 3.9 1.6 - - - -
187B LEU* 1.3 90.8 - - + +
189B GLN* 1.3 59.4 + - - +
191B ALA* 3.3 3.4 + - + +
192B CYS* 2.9 35.0 + - - +
284B ILE* 4.4 22.9 - - + -
287B TYR* 3.6 33.7 - - + -
288B GLN* 3.8 13.7 - - - +
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Residues in contact with GLN 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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95B GLY 5.3 0.4 - - - -
96B VAL* 4.4 23.2 + - + +
99B CYS* 4.1 30.8 - - + +
100B LYS* 5.1 10.1 - - - +
131B TYR* 6.1 0.8 - - - -
135B TYR* 4.1 17.8 + - - -
164B LEU* 4.0 20.5 - - + +
185B GLY 5.5 1.0 - - - +
186B SER* 3.2 21.6 + - - +
188B PRO* 1.3 79.4 - - - +
190B ILE* 1.3 64.6 + - - +
192B CYS* 4.5 4.1 - - - +
193B LEU* 3.5 26.7 + - + +
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Residues in contact with ILE 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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161B PHE* 4.1 20.9 - - + -
164B LEU* 3.7 25.1 - - + +
165B VAL* 4.5 13.0 - - + -
168B LYS* 4.8 15.9 - - + -
183B LEU* 5.3 8.5 - - + -
186B SER* 2.9 31.2 + - - +
187B LEU* 4.2 15.0 - - + +
189B GLN* 1.3 77.5 - - - +
191B ALA* 1.3 67.4 + - + +
192B CYS 3.2 1.2 + - - -
193B LEU* 3.2 14.7 + - - +
194B ALA* 3.3 9.8 + - + +
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Residues in contact with ALA 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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187B LEU 3.5 14.6 + - - +
188B PRO* 3.3 3.8 + - + +
190B ILE* 1.3 82.4 - - + +
192B CYS* 1.3 60.8 + - - +
193B LEU 3.4 0.2 - - - -
194B ALA* 3.4 18.0 + - + +
195B PHE* 3.5 10.9 + - - +
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Residues in contact with CYS 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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91B VAL 4.6 0.7 - - - -
92B ALA* 3.2 46.1 - - - +
95B GLY* 4.4 13.2 - - - +
96B VAL* 4.1 13.2 - - + +
188B PRO* 2.9 19.8 + - + +
189B GLN* 4.5 0.4 - - - +
191B ALA* 1.3 76.7 - - - +
193B LEU* 1.3 63.1 + - - +
194B ALA 3.2 0.4 - - - -
195B PHE* 3.4 17.9 + - - +
196B LEU* 3.7 4.9 + - - +
284B ILE* 5.4 4.9 - - + -
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Residues in contact with LEU 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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96B VAL* 4.1 22.0 - - + -
135B TYR* 4.8 9.2 - - + +
138B LEU* 5.2 2.2 - - + -
157B SER* 4.7 7.7 - - - +
160B HIS* 3.7 42.8 - - + +
161B PHE* 4.0 16.7 - - + +
164B LEU* 4.3 12.6 - - + -
189B GLN* 3.5 21.4 + - + +
190B ILE 3.2 7.4 + - - +
192B CYS* 1.3 74.8 - - - +
194B ALA* 1.3 60.8 + - - +
195B PHE 3.2 0.7 - - - -
196B LEU* 3.1 41.8 + - + +
197B SER* 3.1 12.3 + - - -
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Residues in contact with ALA 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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161B PHE* 4.2 19.2 - - + -
190B ILE 3.3 11.0 + - - +
191B ALA* 3.5 16.2 - - + +
192B CYS 3.2 0.8 - - - -
193B LEU* 1.3 78.9 - - - +
195B PHE* 1.3 57.8 + - - +
197B SER* 2.6 25.5 + - - +
198B PHE* 3.2 17.9 + - + +
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Residues in contact with PHE 195 (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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86B HIS* 4.9 3.6 - + - -
88B GLY* 3.2 42.8 - - - -
92B ALA* 4.2 10.3 - - + -
191B ALA 3.5 8.3 + - - +
192B CYS* 3.4 14.7 + - - +
193B LEU 3.2 0.6 - - - -
194B ALA* 1.3 76.7 - - - +
196B LEU* 1.3 66.4 + - + +
198B PHE* 3.4 8.3 + - + +
199B GLN* 3.3 45.5 + - + +
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Residues in contact with LEU 196 (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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89B LEU* 4.8 8.5 - - + +
92B ALA* 4.2 19.1 - - + -
93B VAL* 4.5 16.4 - - + -
96B VAL* 5.5 3.1 - - + -
138B LEU* 4.2 22.2 - - + -
157B SER* 3.6 24.0 + - - -
192B CYS 3.7 8.0 + - - +
193B LEU* 3.1 35.9 + - + +
195B PHE* 1.3 80.0 - - + +
197B SER* 1.3 61.1 + - - +
199B GLN* 4.6 4.7 - - + -
200B TYR* 3.4 50.4 + - + +
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Residues in contact with SER 197 (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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157B SER* 4.1 15.9 + - - -
158B TRP* 4.6 29.2 - - - -
161B PHE* 5.2 8.8 - - - -
193B LEU 3.1 9.8 + - - -
194B ALA* 2.6 28.5 + - - +
196B LEU* 1.3 78.7 - - - +
198B PHE* 1.3 73.3 + - - +
199B GLN 3.4 0.7 - - - -
201B PRO* 3.3 23.6 - - - +
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Residues in contact with PHE 198 (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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158B TRP* 5.7 7.2 - + - -
194B ALA* 3.2 16.0 + - + +
195B PHE* 3.4 8.8 + - + +
196B LEU 3.3 0.4 - - - -
197B SER* 1.3 94.1 + - - +
199B GLN* 1.3 60.6 + - - +
201B PRO* 4.8 0.4 - - - -
202B LEU* 3.3 29.8 - - - +
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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