Contacts of the helix formed by residues 137 - 145 (chain G) in PDB entry 2HAK
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 VAL 137 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136G GLU* 1.3 69.5 - - - +
138G PHE* 1.3 72.9 + - + +
140G TYR* 3.4 5.7 + - - +
141G LEU* 3.0 43.0 + - + +
147G MET* 6.0 1.3 - - + -
155G LYS* 5.9 0.7 - - + -
159G ILE* 5.8 1.3 - - + -
178G ALA 5.4 0.4 + - - -
181G LEU* 2.7 30.0 + - + +
183G LEU* 3.7 22.9 - - + -
189G ILE* 3.4 33.7 - - + -
239G ILE* 5.1 11.4 - - + -
242G THR* 5.5 0.2 - - + -
243G LEU* 4.1 16.2 - - + -
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Residues in contact with PHE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G GLU* 3.6 7.6 - - - +
137G VAL* 1.3 80.2 - - + +
139G ASP* 1.3 53.2 + - - +
141G LEU* 3.0 9.1 + - + +
142G VAL* 2.7 42.2 + - + +
178G ALA* 3.9 34.3 - - + -
181G LEU* 4.9 6.7 - - + -
215G TYR* 4.2 20.0 - + + -
238G VAL* 4.4 10.3 - - + -
239G ILE* 4.0 28.7 - - + -
242G THR* 3.4 31.6 - - + -
248G LEU* 3.9 28.7 - - + -
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Residues in contact with ASP 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G GLY* 6.0 0.4 - - - -
136G GLU* 3.6 42.3 + - + +
137G VAL 3.3 0.8 - - - -
138G PHE* 1.3 74.4 - - - +
140G TYR* 1.3 65.0 + - - +
142G VAL* 3.4 12.3 + - - +
143G ALA* 3.2 24.1 + - - +
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Residues in contact with TYR 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G GLY* 4.5 13.2 - - - +
136G GLU 3.1 18.0 + - - +
137G VAL 3.7 3.8 - - - +
138G PHE 3.2 0.2 - - - -
139G ASP* 1.3 75.8 - - - +
141G LEU* 1.3 68.2 + - + +
143G ALA* 3.1 1.8 + - - -
144G HIS* 2.9 81.6 + + + +
145G GLY 5.1 1.8 - - - -
147G MET* 3.8 22.0 - - + -
151G GLU* 4.6 5.7 + - - -
183G LEU* 3.8 19.1 - - + -
187G MET* 3.4 36.3 - - + +
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Residues in contact with LEU 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G VAL* 3.0 24.5 + - + +
138G PHE* 3.0 11.0 + - + +
140G TYR* 1.3 76.1 - - + +
142G VAL* 1.3 65.0 + - - +
143G ALA 2.9 3.0 + - - -
145G GLY* 3.0 42.6 + - - +
147G MET* 4.1 28.3 - - + -
242G THR* 3.5 51.4 - - + +
243G LEU* 3.8 20.6 - - + +
246G GLY* 4.5 11.7 - - - +
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Residues in contact with VAL 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G PHE* 2.7 24.1 + - + +
139G ASP* 3.4 12.8 + - - +
141G LEU* 1.3 72.3 - - - +
143G ALA* 1.3 59.9 + - + +
145G GLY 5.0 0.3 + - - -
246G GLY 5.4 3.6 - - - +
248G LEU* 6.1 5.8 - - + -
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Residues in contact with ALA 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ASP 3.2 14.7 + - - +
140G TYR* 3.1 4.1 + - - +
141G LEU 2.9 0.6 - - - -
142G VAL* 1.3 82.5 - - + +
144G HIS* 1.3 72.8 + - + +
145G GLY 3.8 0.4 - - - -
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Residues in contact with HIS 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G TYR* 2.9 70.5 + + + +
143G ALA* 1.3 89.0 + - + +
145G GLY* 1.3 62.7 + - - +
146G ARG 4.3 3.5 - - - +
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Residues in contact with GLY 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G TYR* 5.1 1.7 - - - -
141G LEU* 3.0 33.7 + - - +
142G VAL 4.8 0.2 - - - -
143G ALA 3.8 0.6 - - - -
144G HIS* 1.3 80.7 - - - +
146G ARG* 1.3 68.7 + - - +
147G MET* 4.8 0.7 - - - +
246G GLY* 4.2 8.3 - - - -
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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