Contacts of the strand formed by residues 184 - 191 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.8 25.2 - - + +
149A PHE* 4.6 10.3 - + - -
151A LYS* 5.0 6.4 + - - -
174A ILE* 4.5 11.4 - - + -
175A ARG 3.3 13.2 - - - +
176A ASP* 3.1 27.1 - - - -
177A SER* 3.0 10.8 + - - -
182A GLY* 3.9 18.1 + - - -
183A SER* 1.3 93.2 - - - +
185A SER* 1.3 58.9 + - - +
203A LYS* 4.8 0.2 - - - +
204A ILE* 2.8 43.9 + - + +
206A THR* 5.1 5.4 + - + -
212A PHE* 4.9 18.6 - + - -
223A LEU* 4.7 18.4 - - + -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.4 4.5 - - - -
175A ARG* 3.1 58.9 + - - +
177A SER* 2.6 23.3 + - - -
184A TYR* 1.3 71.0 + - - +
186A LEU* 1.3 60.0 + - - +
202A TYR 3.5 10.3 - - - -
203A LYS* 4.1 4.2 - - - +
204A ILE* 3.6 9.0 - - - +
527A PTR 3.1 24.3 + - - -
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 4.5 12.8 - - + -
173A MET 3.4 17.5 - - - +
174A ILE* 4.0 15.9 - - + -
185A SER* 1.3 75.4 - - - +
187A SER* 1.3 67.0 + - - +
188A VAL* 3.5 25.4 - - + -
200A LYS 3.8 0.2 - - - +
201A HIS* 3.0 5.7 - - - -
202A TYR* 2.7 61.7 + - + +
204A ILE* 3.9 12.8 - - + -
214A ILE* 4.5 11.7 - - + -
226A LEU* 5.6 8.5 - - + -
230A TYR* 6.4 0.7 - - + -
237A LEU* 4.2 13.7 - - + -
241A LEU* 4.8 6.5 - - + -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ALA* 3.8 4.6 - - - +
162A LEU* 3.9 19.9 - - - +
172A PHE* 3.2 9.0 - - - +
173A MET* 3.0 39.1 + - - +
175A ARG* 2.8 26.6 + - - -
186A LEU* 1.3 71.8 - - - +
188A VAL* 1.3 61.0 + - - +
199A VAL* 4.1 0.4 - - - -
200A LYS 3.3 5.2 - - - -
201A HIS* 2.8 29.6 + - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY* 4.2 12.8 - - - +
171A SER 3.8 1.6 - - - -
186A LEU* 3.5 31.6 - - + -
187A SER* 1.3 77.9 - - - +
189A ARG* 1.3 72.4 - - - +
190A ASP* 4.6 0.3 - - - +
199A VAL* 3.4 4.8 - - - -
200A LYS* 2.8 34.0 + - - +
202A TYR* 3.8 22.0 - - + -
237A LEU* 4.3 7.4 - - + -
238A CYS* 4.9 6.7 - - - -
239A GLN* 4.7 14.4 - - + +
241A LEU* 4.1 19.7 - - + -
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 2.9 36.2 + - + +
163A LEU* 4.2 7.5 + - + +
164A ALA 2.9 20.2 + - - -
165A PRO* 4.6 2.4 - - - +
167A ASN* 3.0 32.6 + - - +
168A MET* 3.0 31.7 + - - +
169A LEU* 4.0 6.6 - - - +
170A GLY* 3.2 20.5 + - - +
171A SER* 3.0 18.5 + - - +
188A VAL* 1.3 78.3 - - - +
190A ASP* 1.3 62.7 + - - +
197A ASP* 4.4 32.0 + - + +
198A THR 3.3 13.9 - - - +
199A VAL* 4.4 8.3 - - + +
239A GLN* 4.2 4.3 - - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.5 8.0 - - - +
188A VAL 4.6 3.4 - - - +
189A ARG* 1.3 76.2 - - - +
191A TYR* 1.4 74.5 + - - +
192A ASP* 4.6 1.6 - - - +
197A ASP* 3.6 7.8 - - - +
198A THR* 2.8 39.4 + - + +
200A LYS* 3.2 32.5 + - + -
238A CYS* 3.7 28.2 - - - +
239A GLN* 3.7 23.0 + - - +
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Residues in contact with TYR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 4.2 19.3 - - + +
190A ASP* 1.4 85.3 + - - +
192A ASP* 1.4 82.7 + - - +
193A PRO* 3.3 33.6 + - + +
195A GLN 3.4 9.6 - - - -
196A GLY* 3.6 23.2 - - - +
197A ASP* 4.4 13.9 - - - -
198A THR* 4.1 1.8 - - - -
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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