Contacts of the helix formed by residues 132 - 138 (chain R) in PDB entry 3EXG
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 PHE 132 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83R PHE* 3.3 37.5 - - + -
84R ASN* 3.6 13.7 - - - -
86R SER* 4.9 1.3 - - - -
87R MET* 3.7 27.1 - - + -
90R ILE* 5.2 0.4 - - + -
118R ASN* 2.8 23.8 - - - +
130R GLN* 3.5 46.9 - - + -
131R CYS* 1.3 73.7 - - - +
133R ALA* 1.3 64.8 + - - +
134R ALA* 3.1 3.8 - - - -
135R TRP* 3.1 29.3 + + + +
136R TYR* 3.0 49.5 + + + -
170R LEU* 4.7 4.0 - - + -
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Residues in contact with ALA 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131R CYS* 3.7 15.8 - - - -
132R PHE* 1.3 75.6 - - - +
134R ALA* 1.3 57.9 + - - +
137R GLY* 2.9 29.3 + - - -
144R VAL* 4.4 1.8 - - - +
170R LEU* 3.6 27.3 - - + +
212R HIS* 4.3 7.0 - - + +
241R ILE* 3.5 23.3 - - + +
271R VAL* 3.8 20.2 - - + -
269T PHE* 4.9 0.2 - - - -
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Residues in contact with ALA 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R CYS* 5.4 1.0 - - - +
132R PHE 3.1 0.9 - - - -
133R ALA* 1.3 77.4 - - - +
135R TRP* 1.3 68.3 + - + +
138R HIS* 3.3 21.5 + - - +
263R GLU* 5.7 0.9 - - - +
269R PHE 3.8 13.9 - - - +
270R GLY* 4.2 9.6 - - - -
271R VAL* 4.3 6.2 - - + +
135T TRP* 4.9 0.9 - - - -
138T HIS* 3.7 32.1 - - + +
269T PHE* 4.0 18.3 - - + +
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Residues in contact with TRP 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87R MET* 3.9 26.5 - - + -
90R ILE* 3.9 19.1 - - + -
130R GLN* 4.3 9.4 - - - -
131R CYS 5.9 0.4 - - - -
132R PHE* 3.1 33.7 + + + +
134R ALA* 1.3 80.1 - - + +
136R TYR* 1.3 63.7 + - + +
138R HIS* 3.2 9.2 - - - +
139R CYS* 3.9 1.7 - - - -
90T ILE* 3.7 29.8 - - + -
94T ILE* 3.9 16.2 - - + -
135T TRP* 3.0 80.2 + + + +
136T TYR* 5.4 0.2 - - - -
138T HIS* 3.7 24.4 - + - -
139T CYS* 3.9 21.8 - - - -
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Residues in contact with TYR 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80R PHE* 5.1 0.2 - - - -
83R PHE* 3.8 20.8 - + - -
86R SER* 2.6 30.7 + - - -
90R ILE* 3.6 30.2 - - + +
93R VAL* 4.1 22.4 - - + +
94R ILE* 4.4 6.3 - - + -
132R PHE* 3.0 47.0 + + + +
135R TRP* 1.3 75.7 - - + +
137R GLY* 1.3 62.5 + - - +
138R HIS 3.2 0.9 + - - -
139R CYS* 3.2 13.5 + - - +
142R LEU* 3.4 33.3 - - + +
144R VAL* 3.4 24.6 - - + +
168R VAL* 4.2 15.7 - - + -
170R LEU* 4.5 3.6 - - + -
242R ARG* 4.7 0.3 - - - -
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Residues in contact with GLY 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133R ALA 2.9 22.6 + - - -
136R TYR* 1.3 75.6 - - - +
138R HIS* 1.3 55.6 + - - +
139R CYS 3.1 0.2 - - - -
144R VAL* 3.9 4.7 - - - +
241R ILE* 4.3 3.4 - - - -
242R ARG* 3.0 46.8 + - - +
269T PHE* 3.5 22.8 - - - -
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Residues in contact with HIS 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134R ALA 3.3 13.6 + - - +
135R TRP 3.2 17.3 - - - +
137R GLY* 1.3 76.2 - - - +
139R CYS* 1.4 54.8 + - - +
140R PRO* 3.6 9.4 - - - +
242R ARG* 3.9 6.4 + - - +
130T GLN* 5.1 2.0 - - - -
131T CYS* 4.7 10.7 + - - +
132T PHE* 6.1 0.4 - - - -
134T ALA* 4.1 13.8 - - + +
135T TRP* 3.6 25.5 + + + +
265T GLY* 5.6 1.5 - - - -
266T TRP* 3.6 70.0 + + + +
268T GLN* 2.8 29.8 + - - +
269T PHE* 3.5 17.1 + - - -
270T GLY* 4.1 1.3 - - - -
299T ASP* 4.4 0.5 - - - +
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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