Contacts of the strand formed by residues 184 - 192 (chain B) in PDB entry 2HCK
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 TYR 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143B LEU* 4.4 20.1 - - + +
149B PHE* 4.3 14.4 - + - -
151B LYS* 4.5 9.2 + - - -
174B ILE* 4.3 11.4 - - + -
175B ARG 3.3 13.2 - - - +
176B ASP* 3.2 26.7 - - - -
177B SER* 3.2 10.9 + - - -
182B GLY* 4.6 12.9 + - - -
183B SER* 1.4 94.4 - - - +
185B SER* 1.3 57.1 + - - +
204B ILE* 3.0 42.0 + - + +
206B THR* 5.0 11.7 - - + +
212B PHE* 5.2 6.5 - + - -
223B LEU* 4.1 26.9 - - + -
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Residues in contact with SER 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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174B ILE* 3.3 6.9 - - - +
175B ARG* 2.8 62.2 + - - +
177B SER* 2.9 20.8 + - - +
184B TYR* 1.3 70.4 + - - +
186B LEU* 1.3 61.9 + - - +
202B TYR 3.3 13.1 + - - -
203B LYS* 4.3 2.3 - - - +
204B ILE* 3.5 6.1 - - - -
527B PTR 3.1 25.0 + - - -
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Residues in contact with LEU 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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172B PHE* 3.7 23.3 - - + -
173B MET 3.3 16.2 - - - +
174B ILE* 3.8 12.6 - - + -
185B SER* 1.3 75.2 - - - +
187B SER* 1.3 71.7 + - - +
188B VAL* 3.9 19.3 - - + -
200B LYS 3.8 0.5 - - - +
201B HIS* 3.3 3.5 - - - +
202B TYR* 2.8 47.6 + - + +
204B ILE* 3.7 15.0 - - + +
214B ILE* 5.0 7.2 - - + -
226B LEU* 5.3 9.0 - - + -
227B VAL* 6.4 0.2 - - + -
230B TYR* 5.9 0.9 - - + -
237B LEU* 4.2 13.7 - - + -
241B LEU* 4.0 16.2 - - + -
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Residues in contact with SER 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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158B ALA* 4.0 3.7 - - - +
162B LEU* 3.7 20.4 - - - -
172B PHE* 3.4 5.0 - - - +
173B MET* 2.9 36.7 + - - +
175B ARG* 3.1 22.0 + - - -
185B SER 4.2 0.2 - - - -
186B LEU* 1.3 77.1 - - - +
188B VAL* 1.4 58.1 + - - +
199B VAL* 4.0 1.6 - - - -
200B LYS 3.4 5.8 - - - -
201B HIS* 2.8 30.3 + - - -
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Residues in contact with VAL 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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162B LEU* 4.5 1.1 - - - -
170B GLY* 3.6 25.4 - - - +
171B SER 3.8 3.1 - - - -
172B PHE* 3.7 8.5 - - + -
186B LEU* 3.9 23.3 - - + -
187B SER* 1.4 75.5 - - - +
189B ARG* 1.3 68.7 + - - +
190B ASP* 4.8 0.5 - - - +
199B VAL* 3.2 6.3 - - - +
200B LYS* 2.8 34.9 + - - +
202B TYR* 4.2 21.8 - - + -
237B LEU* 4.7 5.6 - - + -
238B CYS* 4.8 10.3 - - - -
239B GLN* 4.8 8.7 - - + +
241B LEU* 3.9 10.5 - - + -
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Residues in contact with ARG 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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162B LEU* 3.2 29.2 + - + +
163B LEU* 3.6 23.9 + - + +
164B ALA 3.4 13.5 + - - -
165B PRO* 5.4 0.2 - - - +
166B GLY 5.2 0.2 - - - +
167B ASN* 2.9 34.4 + - - +
168B MET* 3.6 25.5 + - - +
169B LEU* 4.4 8.2 - - - +
170B GLY* 3.6 16.4 + - - -
171B SER* 3.0 21.9 + - - +
188B VAL* 1.3 76.4 - - - +
190B ASP* 1.4 66.7 + - - +
197B ASP* 3.2 29.5 + - + -
198B THR 3.4 10.8 - - - +
199B VAL* 4.2 7.0 - - + -
239B GLN* 4.2 6.4 - - - +
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Residues in contact with ASP 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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169B LEU* 5.5 8.1 - - - -
188B VAL 4.8 1.8 - - - +
189B ARG* 1.4 75.8 - - - +
191B TYR* 1.3 77.2 + - - +
192B ASP* 3.9 3.3 + - - +
197B ASP* 3.3 10.8 - - - +
198B THR* 2.7 51.6 + - - +
200B LYS* 3.4 28.2 + - + -
238B CYS* 4.0 17.6 - - - +
239B GLN* 3.5 31.5 + - + +
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Residues in contact with TYR 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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169B LEU* 5.0 13.5 - - + +
190B ASP* 1.3 85.9 + - - +
192B ASP* 1.3 78.8 + - - +
193B PRO* 3.6 29.2 + - + -
195B GLN 3.4 15.7 + - - -
196B GLY* 3.2 30.3 - - - -
197B ASP* 4.2 10.3 - - - +
198B THR* 3.8 1.1 - - - -
239B GLN* 5.6 1.0 + - - -
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Residues in contact with ASP 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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190B ASP* 3.9 10.2 + - - +
191B TYR* 1.3 77.5 - - - +
193B PRO* 1.4 64.4 - - + -
194B ARG* 2.9 16.1 + - - +
195B GLN* 3.0 20.7 + - - +
196B GLY 4.3 0.6 + - - -
198B THR* 4.4 7.3 + - + +
200B LYS* 4.6 12.1 - - - +
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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