Contacts of the helix formed by residues 138 - 143 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137H GLY* 1.3 71.6 - - - +
139H SER* 1.3 60.7 + - - +
140H PHE 3.3 3.1 - - - -
141H ALA* 3.2 24.8 + - - +
142H HIS* 4.2 7.2 - - - -
173H ASP* 2.8 27.3 + - - +
174H HIS* 3.0 9.4 - - - +
175H ARG* 2.9 36.7 + - - +
177H TYR* 2.9 28.0 + - - -
242H TYR* 4.1 10.7 - - + -
283H TYR* 4.1 17.2 - - + +
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Residues in contact with SER 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLU* 3.3 29.6 + - - +
16G GLY 4.4 1.1 - - - -
64H ALA* 3.5 28.9 + - - +
117H TRP* 3.3 10.1 - - - -
135H CYS* 4.6 3.9 - - - -
136H LEU 3.4 14.8 + - - -
137H GLY 3.0 4.7 + - - -
138H ASN* 1.3 72.6 - - - +
140H PHE* 1.3 65.7 + - - +
141H ALA 3.0 2.5 - - - -
142H HIS* 3.1 31.3 + - - +
173H ASP* 4.4 1.0 + - - -
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Residues in contact with PHE 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H TRP* 3.7 18.6 - + - -
135H CYS* 4.4 6.6 + - - -
138H ASN 3.2 1.2 + - - -
139H SER* 1.3 79.3 - - - +
141H ALA* 1.3 58.1 + - - +
142H HIS 2.9 6.5 + - - -
143H LEU* 3.0 27.9 + - + +
153H HIS* 3.9 19.5 - + + -
156H ALA* 3.6 25.4 - - + -
157H LEU* 3.4 36.6 - - + -
160H ILE* 4.3 8.3 - - + -
172H ILE* 4.2 26.5 - - + -
173H ASP 4.8 7.7 + - - +
174H HIS* 6.2 1.1 - - + -
245H HIS* 3.7 29.6 - + - -
250H PHE* 3.7 17.9 - + + -
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Residues in contact with ALA 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H ASN* 3.2 37.5 + - - +
139H SER 3.0 0.4 - - - -
140H PHE* 1.3 79.6 - - - +
142H HIS* 1.3 60.9 + - - +
143H LEU 3.3 1.6 - - - -
173H ASP 5.7 0.2 + - - -
174H HIS* 5.4 1.9 - - + +
177H TYR* 3.9 9.4 - - + +
242H TYR* 3.2 7.2 - - + -
243H TYR* 2.7 48.1 + - - +
245H HIS* 4.2 11.0 + - - +
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Residues in contact with HIS 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ALA* 3.6 14.1 - - + +
15G GLU* 3.0 39.0 + - + -
16G GLY* 3.0 20.4 + - - +
17G LEU* 2.9 39.3 - - + +
137H GLY 5.3 1.7 + - - -
138H ASN 4.2 5.7 + - - -
139H SER* 3.2 22.7 + - - +
140H PHE 2.9 0.4 + - - -
141H ALA* 1.3 75.7 - - - +
143H LEU* 1.3 60.5 + - - +
144H PRO* 3.0 11.7 - - - +
240H LEU* 6.1 1.4 - - - +
241H SER 4.4 10.5 - - - +
242H TYR* 3.7 31.8 + + - -
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Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F VAL 6.0 0.9 - - - +
17G LEU* 3.6 8.7 - - + +
116H ASN* 6.2 0.2 - - - +
117H TRP* 3.9 22.2 - - + -
118H LEU* 4.6 20.6 - - + -
139H SER 4.4 0.2 + - - -
140H PHE* 3.0 18.8 + - + +
141H ALA 4.6 0.7 - - - -
142H HIS* 1.3 78.0 - - - +
144H PRO* 1.3 79.0 - - + +
152H GLU* 4.0 17.9 - - + +
153H HIS* 2.9 28.7 + - + -
156H ALA* 3.6 30.5 - - + -
243H TYR* 3.9 8.3 - - - +
245H HIS* 4.9 0.3 - - - -
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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
------------------------------------------------------------
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