Contacts of the strand formed by residues 184 - 191 (chain B) in PDB entry 1HCS
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 ILE* 4.4 13.7 - - + +
149B TYR* 3.7 33.5 + + - -
174B VAL* 4.2 5.6 - - + -
175B ARG 3.5 18.6 - - - +
176B GLU* 4.6 7.6 - - + -
177B SER 4.0 0.7 - - - +
180B THR* 5.0 0.5 + - - -
182B GLY 5.3 0.9 - - - -
183B ALA* 1.3 90.7 - - - +
185B CYS* 1.3 75.4 + - - +
203B LYS* 4.2 0.9 - - - +
204B ILE* 3.0 29.6 + - + +
206B LYS* 5.0 9.9 - - + -
212B PHE* 4.8 12.1 - + - -
223B LEU* 3.3 50.4 - - + +
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Residues in contact with CYS 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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101A PTR 3.7 28.7 - - + +
173B LEU 3.4 5.0 - - - +
174B VAL* 4.4 0.4 - - - -
175B ARG* 3.2 57.0 + - + +
177B SER* 3.8 20.9 - - - -
178B GLU 4.6 0.2 - - - -
180B THR* 4.0 10.3 - - - -
184B TYR* 1.3 89.9 - - - +
186B LEU* 1.3 60.9 + - - +
187B SER* 3.6 2.8 + - - +
203B LYS* 4.2 7.2 - - - +
204B ILE* 3.9 5.8 - - - +
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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* 3.4 25.1 - - + -
173B LEU 3.8 2.5 - - - +
174B VAL* 3.4 27.1 - - + +
185B CYS* 1.3 71.8 - - - +
187B SER* 1.3 68.0 + - - +
188B VAL* 4.4 5.7 - - + +
202B TYR* 3.0 39.4 + - + +
204B ILE* 3.3 24.8 - - + +
214B ILE* 4.3 7.4 - - + -
226B LEU* 4.1 22.2 - - + -
227B VAL* 5.0 3.4 - - + -
230B TYR* 4.8 7.2 - - + -
237B LEU* 6.4 1.6 - - + -
241B LEU* 4.5 21.8 - - + -
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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 SER* 4.4 1.6 + - - -
162B LEU* 3.6 24.5 - - - -
172B PHE* 2.9 27.9 - - - +
173B LEU* 3.1 18.9 + - - -
175B ARG* 4.2 19.2 + - - -
185B CYS* 4.4 2.3 + - - +
186B LEU* 1.3 72.8 - - - +
188B VAL* 1.3 67.0 + - - +
199B VAL* 4.8 1.6 - - - -
200B LYS 3.6 9.6 - - - -
201B HIS* 4.1 19.9 + - - +
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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* 4.1 3.8 - - - -
170B GLY* 4.3 8.7 - - - +
171B THR 3.3 13.0 - - - +
172B PHE* 3.9 11.2 - - + -
186B LEU* 4.4 13.0 - - + +
187B SER* 1.3 83.8 - - - +
189B SER* 1.3 76.5 + - - +
199B VAL* 3.5 8.7 - - - +
200B LYS* 3.0 31.1 + - - +
202B TYR* 4.7 7.9 - - + -
237B LEU* 5.5 3.8 - - + -
238B CYS* 3.7 31.4 - - - -
239B HIS* 4.4 6.5 - - + +
241B LEU* 4.2 17.7 - - + -
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Residues in contact with SER 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* 3.9 29.6 - - - -
167B ASN* 5.5 1.6 - - - -
168B PRO 3.6 4.5 + - - -
169B ARG* 4.0 1.8 - - - +
170B GLY* 3.2 24.5 + - - -
171B THR* 2.6 47.2 + - - -
188B VAL* 1.3 81.7 - - - +
190B ASP* 1.3 63.4 + - - +
197B LEU* 6.1 1.8 - - - -
198B ASN 3.8 5.8 - - - -
238B CYS* 5.1 0.8 - - - -
239B HIS* 4.8 2.6 - - - +
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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 ARG* 3.7 12.0 - - - -
189B SER* 1.3 76.2 - - - +
191B PHE* 1.3 86.9 + - - +
192B ASP* 3.5 11.3 - - - +
197B LEU* 3.0 26.0 - - - +
198B ASN* 3.0 23.2 + - + +
199B VAL* 5.1 0.2 - - - +
200B LYS* 5.1 13.5 - - + +
238B CYS* 3.0 39.1 - - + +
239B HIS* 4.1 7.6 - - - +
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Residues in contact with PHE 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 ARG* 3.4 43.4 + - + +
190B ASP* 1.3 91.6 + - - +
192B ASP* 1.3 94.6 + - - +
193B ASN* 3.6 20.0 - - - -
195B LYS 5.2 0.4 - - - -
196B GLY* 3.2 28.5 - - - -
197B LEU* 3.8 12.6 - - + -
198B ASN* 5.2 0.4 - - - -
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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