Contacts of the strand formed by residues 179 - 184 (chain E) in PDB entry 2HU4
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 179 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 3.8 2.8 - - - +
177E ALA* 3.5 2.4 - - - +
178E TRP* 1.3 102.4 - - - +
180E ALA* 1.3 64.1 + - - +
194E ILE* 3.1 35.9 + - - +
224E ARG* 3.6 5.2 - - - +
225E THR* 3.1 28.6 + - - +
227E GLU* 3.5 19.6 + - - -
804E G39 4.4 3.1 - - - -
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Residues in contact with ALA 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E PHE* 4.6 5.6 - - + -
134E LEU* 4.2 15.8 - - + +
158E LEU* 4.2 24.0 - - + -
177E ALA* 4.7 0.4 - - + -
179E SER* 1.3 77.1 + - - +
181E SER* 1.3 59.5 + - - +
192E ILE 3.0 17.7 - - - +
193E GLY* 4.5 1.8 - - - -
225E THR* 3.6 9.2 - - - +
227E GLU* 2.7 49.6 + - - +
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Residues in contact with SER 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E PHE* 4.0 5.8 - - - -
158E LEU* 4.8 0.9 - - - +
180E ALA* 1.3 79.1 - - - +
182E ALA* 1.3 63.3 + - - +
192E ILE* 2.7 42.9 + - - +
225E THR* 4.1 14.7 - - - +
226E GLN* 3.2 22.6 + - - -
228E SER 3.0 21.1 + - - -
230E CYS* 3.3 11.8 + - - +
239E THR* 4.1 3.1 - - - -
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Residues in contact with ALA 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E PHE* 3.7 10.3 - - + -
123E SER* 3.5 4.0 + - - -
132E PHE* 3.8 38.1 - - + -
158E LEU* 5.0 2.0 - - + -
181E SER* 1.3 77.3 + - - +
183E CYS* 1.3 67.6 + - - +
189E TRP* 4.5 0.2 - - - -
190E LEU* 3.1 14.8 - - - +
191E THR* 4.2 7.0 - - + -
229E GLU* 3.1 23.6 - - - +
230E CYS* 3.4 5.6 - - - -
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Residues in contact with CYS 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E SER* 3.7 6.3 - - - +
182E ALA* 1.3 75.8 - - - +
184E HIS* 1.3 57.8 + - - +
185E ASP 4.1 0.9 + - - -
189E TRP* 3.4 12.9 - - - -
190E LEU* 2.8 43.3 + - - +
229E GLU* 5.3 0.4 - - - +
230E CYS* 2.0 58.6 - - - +
231E ALA* 5.1 0.2 - - - -
232E CYS* 3.4 25.7 - - - -
237E CYS* 3.8 7.9 - - - -
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Residues in contact with HIS 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 3.7 15.7 - - + +
123E SER* 4.6 0.2 + - - -
124E CYS 3.6 22.7 + - - +
125E SER* 3.5 25.9 - - - -
126E HIS* 3.7 11.5 + + - -
183E CYS* 1.3 74.6 - - - +
185E ASP* 1.3 60.4 + - - +
186E GLY* 2.9 40.4 + - - -
187E THR 3.3 19.4 + - - -
188E SER* 3.4 29.4 - - - -
189E TRP* 3.5 31.1 - + + -
232E CYS* 3.5 11.0 - - - +
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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
------------------------------------------------------------
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