Contacts of the helix formed by residues 138 - 143 (chain G) in PDB entry 1R8Y
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 ASN 138 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G GLY* 1.3 76.0 - - - +
139G SER* 1.3 61.7 + - - +
140G PHE 3.3 3.4 - - - -
141G ALA* 3.4 19.6 + - - +
142G HIS* 4.1 8.5 + - - -
173G ASP* 2.9 21.4 + - - -
174G HIS* 3.0 12.3 - - - +
175G ARG* 2.8 41.6 + - - +
177G TYR* 2.8 29.2 + - - -
242G TYR* 4.1 9.7 - - + -
283G TYR* 4.1 13.2 - - + +
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Residues in contact with SER 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ALA* 3.6 28.7 + - - +
117G TRP* 3.3 10.3 - - - -
135G CYS* 4.6 3.5 + - - -
136G LEU 3.6 13.9 + - - -
137G GLY 3.2 4.6 + - - -
138G ASN* 1.3 74.1 - - - +
140G PHE* 1.3 65.1 + - - +
141G ALA 3.1 2.7 - - - -
142G HIS* 3.0 30.2 + - - +
173G ASP* 4.5 1.0 + - - -
15H GLU* 3.5 32.4 + - - +
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Residues in contact with PHE 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G TRP* 3.7 17.6 - + - -
135G CYS* 4.4 6.6 - - - -
138G ASN 3.3 1.2 - - - -
139G SER* 1.3 77.7 - - - +
141G ALA* 1.3 58.7 + - - +
142G HIS 3.0 5.1 + - - -
143G LEU* 3.1 24.6 + - + +
153G HIS* 3.8 24.0 - + + -
156G ALA* 3.6 23.1 - - + -
157G LEU* 3.5 39.5 - - + -
160G ILE* 4.2 10.5 - - + -
172G ILE* 4.2 24.0 - - + -
173G ASP 4.8 7.5 + - - +
174G HIS* 6.1 1.1 - - + -
245G HIS* 3.6 31.4 - + - -
250G PHE* 3.8 16.2 - + + -
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Residues in contact with ALA 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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138G ASN* 3.4 36.2 + - - +
139G SER 3.1 0.6 - - - -
140G PHE* 1.3 78.9 - - - +
142G HIS* 1.3 61.4 + - - +
143G LEU 3.2 1.3 + - - -
173G ASP 5.7 0.2 + - - -
174G HIS* 5.3 2.8 - - + +
177G TYR* 4.0 9.6 - - + +
242G TYR* 3.3 6.7 - - + -
243G TYR* 2.7 48.5 + - - +
245G HIS* 4.1 11.4 - - - +
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Residues in contact with HIS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G GLY 5.3 2.1 + - - -
138G ASN 4.1 7.4 + - - -
139G SER* 3.2 28.9 + - - +
140G PHE 3.0 1.0 - - - -
141G ALA* 1.3 77.2 - - - +
143G LEU* 1.3 62.5 + - - +
144G PRO* 3.2 10.9 - - - +
240G LEU* 6.1 1.6 - - - +
241G SER 4.5 10.8 - - - +
242G TYR* 3.7 32.9 + + - -
14H ALA* 3.3 23.5 - - + +
15H GLU* 2.9 45.7 + - - +
16H GLY* 4.4 3.4 - - - +
17H LEU* 3.4 18.3 - - + +
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Residues in contact with LEU 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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117G TRP* 4.0 21.5 - - + -
118G LEU* 4.6 21.5 - - + -
139G SER 4.4 0.2 + - - -
140G PHE* 3.1 17.2 + - + +
141G ALA 4.5 0.2 - - - -
142G HIS* 1.3 75.9 - - - +
144G PRO* 1.3 83.1 - - + +
152G GLU* 3.9 18.6 - - + +
153G HIS* 2.9 29.1 + - + -
156G ALA* 3.6 31.0 - - + -
243G TYR* 3.9 9.2 - - - +
245G HIS* 4.8 0.2 - - - -
16H GLY 6.0 0.2 - - - -
17H LEU* 3.8 14.4 - - + -
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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