Contacts of the strand formed by residues 172 - 176 (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 ARG 172 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E GLU* 4.3 5.7 + - - -
130E ARG* 3.3 49.6 - - - +
132E PHE* 5.3 1.0 - - - -
159E MET* 3.2 7.8 - - - +
160E SER* 2.6 38.3 + - - +
170E ASN 4.0 1.4 + - - -
171E SER* 1.3 72.7 - - - +
173E PHE* 1.3 67.6 + - - +
174E GLU* 2.7 32.4 + - - +
189E TRP* 3.9 24.2 - - - +
165H GLU* 3.9 7.9 - - - +
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Residues in contact with PHE 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E THR* 3.7 13.2 - - + -
159E MET* 3.6 25.3 - - + +
171E SER 3.9 0.4 + - - -
172E ARG* 1.3 84.3 - - - +
174E GLU* 1.3 66.0 + - - +
175E SER* 3.3 39.7 - - - -
176E VAL* 3.8 2.0 - - + -
206E LYS* 4.3 2.2 - - - -
100H TYR 3.3 20.2 - - - -
101H SER* 3.6 24.0 - - - -
102H LYS 3.5 19.7 - - - -
163H VAL* 3.5 27.2 - - + +
164H GLY* 3.6 23.1 - - - -
165H GLU* 4.3 6.5 + - + +
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Residues in contact with GLU 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PHE* 4.0 19.5 - - + -
158E LEU* 2.9 38.8 + - + +
159E MET* 3.9 18.2 - - - -
160E SER* 3.0 12.7 + - - +
172E ARG* 2.7 41.8 + - - +
173E PHE* 1.3 82.1 - - - +
175E SER* 1.3 62.3 + - - +
189E TRP* 5.9 1.1 - - - +
191E THR* 3.5 20.4 + - + +
206E LYS* 3.1 23.4 + - - +
209E GLY* 6.0 2.1 - - - -
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Residues in contact with SER 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E THR* 3.4 3.6 - - - -
158E LEU* 2.7 45.5 + - - +
173E PHE* 3.3 20.2 - - - -
174E GLU* 1.3 82.0 + - - +
176E VAL* 1.3 66.8 + - - +
191E THR* 4.9 3.6 - - - -
193E GLY* 4.4 17.2 + - - -
204E VAL* 4.5 11.3 + - - +
206E LYS* 3.7 20.6 - - - +
99H VAL 4.8 2.3 + - - -
100H TYR 4.7 0.3 + - - -
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Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E PRO 4.1 6.3 - - - +
156E ARG 3.7 13.7 - - - +
157E THR* 4.3 3.8 - - + -
173E PHE* 4.1 0.7 - - + -
175E SER* 1.3 78.1 + - - +
177E ALA* 1.3 68.7 + - - +
193E GLY 4.0 6.1 - - - +
195E SER* 3.6 25.8 - - - +
204E VAL* 5.7 2.1 - - - +
99H VAL* 3.6 31.8 + - + +
100H TYR 4.3 1.7 + - - +
101H SER* 3.7 33.0 - - - +
102H LYS* 3.9 10.1 - - + +
458H TRP* 3.9 21.1 - - + +
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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