Contacts of the helix formed by residues 183 - 188 (chain B) in PDB entry 1YZ3
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 CYS 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.0 14.4 - - - +
79B GLY* 3.8 16.4 - - - +
159B VAL* 4.6 3.6 - - - -
180B SER* 3.7 18.5 + - - +
181B ALA 3.2 3.5 - - - +
182B PHE* 1.3 78.4 - - - +
184B LEU* 1.3 63.4 + - + +
185B GLU* 3.3 3.9 + - - -
186B ALA* 2.7 26.9 + - - -
187B VAL* 3.2 16.5 + - - +
213B LEU* 6.1 1.0 - - - +
2001B SAH 3.6 45.3 - - - +
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Residues in contact with LEU 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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78B ILE* 5.0 1.8 - - + -
159B VAL* 4.1 23.3 - - + -
180B SER* 4.7 3.3 + - - +
183B CYS* 1.3 82.0 - - + +
185B GLU* 1.3 64.4 + - - +
187B VAL* 3.4 5.1 + - - +
188B SER* 2.9 29.2 + - - -
194B PHE* 3.7 26.2 - - + +
197B ALA* 3.9 23.1 - - + -
198B LEU* 4.0 38.1 - - + +
201B ILE* 4.2 16.8 - - + -
213B LEU* 4.2 23.1 - - + +
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Residues in contact with GLU 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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182B PHE* 3.3 23.8 - - - +
183B CYS 3.9 8.5 + - - -
184B LEU* 1.3 78.4 + - - +
186B ALA* 1.3 65.8 + - + +
187B VAL 3.3 0.6 + - - -
188B SER 4.1 0.7 + - - -
194B PHE* 3.4 24.3 - - + -
213B LEU* 5.9 1.7 - - - +
214B ILE 4.5 1.4 - - - +
215B GLY* 3.9 8.6 - - - -
216B ALA* 2.9 44.7 + - + +
219B GLU* 5.2 0.9 - - - +
231B VAL* 3.0 28.1 - - + +
232B VAL* 3.3 27.7 + - + +
234B VAL* 4.3 10.1 - - + -
273B PHE* 4.6 4.7 - - + -
3002B SKA 5.8 0.3 - - - -
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Residues in contact with ALA 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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23B VAL* 4.8 0.5 - - - +
27B TYR* 2.8 34.8 + - - +
182B PHE* 3.6 18.4 - - + +
183B CYS 2.7 14.1 + - - +
185B GLU* 1.3 79.4 - - + +
187B VAL* 1.3 60.7 + - + +
188B SER 3.8 0.2 - - - -
219B GLU* 5.1 2.0 - - - +
222B TYR* 4.0 18.4 - - + +
229B LEU* 5.7 0.5 - - - +
230B THR 4.5 6.1 - - - +
231B VAL* 4.0 18.5 - - + +
2001B SAH 4.5 1.1 - - + -
3002B SKA 5.7 2.0 - - - -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.5 26.7 - - + +
27B TYR* 3.9 5.6 - - + +
159B VAL* 3.8 29.4 - - + -
160B HIS* 2.8 26.3 + - - +
183B CYS* 3.5 18.2 - - - +
184B LEU* 3.7 8.1 - - - +
186B ALA* 1.3 86.7 - - + +
188B SER* 1.3 61.3 + - - +
2001B SAH 3.4 50.3 - - + +
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Residues in contact with SER 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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23B VAL* 4.9 0.7 - - - -
160B HIS* 3.8 8.8 - - - -
184B LEU 2.9 21.6 + - - -
185B GLU 4.1 1.0 + - - +
186B ALA 3.8 0.6 - - - -
187B VAL* 1.3 79.3 - - - +
189B PRO* 1.3 63.5 - - - +
190B ASP 3.8 4.0 - - - -
193B SER* 3.8 6.3 + - - -
194B PHE* 3.4 38.0 + - - -
197B ALA* 4.1 3.8 - - - +
231B VAL* 5.4 0.7 - - - -
232B VAL* 2.9 36.4 + - - +
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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