Contacts of the helix formed by residues 131 - 137 (chain R) in PDB entry 6QX2
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 ILE 131 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101R TYR* 4.1 24.7 - - + +
102R PRO 3.6 13.2 - - - +
103R LEU* 4.1 13.9 - - + -
129R THR* 3.1 14.3 + - - +
130R LYS* 1.3 75.6 - - - +
132R THR* 1.3 62.0 + - - +
133R LEU 3.2 0.2 - - - -
134R GLU* 3.0 25.0 + - + +
135R LEU 3.5 3.6 + - - -
164R PHE* 3.5 32.1 - - + -
188R LEU* 4.1 10.8 - - + -
476R ILE* 6.0 0.2 - - + -
480R PHE* 3.7 48.5 - - + -
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Residues in contact with THR 132 (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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50R LEU* 4.0 24.0 - - + -
103R LEU* 2.6 49.6 + - - +
128R MET* 3.8 20.2 - - + -
129R THR* 3.0 13.9 + - - -
131R ILE* 1.3 75.8 - - - +
133R LEU* 1.3 63.1 + - - +
135R LEU* 3.1 19.1 + - + +
136R LEU* 3.2 24.8 + - + +
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Residues in contact with LEU 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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54R ASN* 5.5 2.2 - - - +
59R THR* 4.4 10.5 - - + -
60R PRO* 4.0 30.5 - - + -
128R MET* 3.6 25.6 - - + -
129R THR 3.7 2.7 + - - +
130R LYS* 3.2 21.3 - - + +
132R THR* 1.3 78.6 - - - +
134R GLU* 1.3 57.4 + - - +
136R LEU* 3.2 6.6 + - + +
137R ARG* 2.8 36.4 + - - +
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Residues in contact with GLU 134 (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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130R LYS 4.7 0.7 - - - +
131R ILE* 3.0 13.2 + - + +
133R LEU* 1.3 81.1 - - - +
135R LEU* 1.3 62.3 + - - +
136R LEU 3.5 0.2 + - - -
137R ARG* 2.7 41.9 + - - -
163R ARG* 3.0 39.6 + - + +
164R PHE* 4.0 14.8 - - + -
476R ILE* 3.6 15.8 - - + +
479R ARG* 3.3 28.7 + - - -
480R PHE* 3.7 25.8 - - + -
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Residues in contact with LEU 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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40R ASP* 4.5 6.3 - - + +
42R LEU* 4.5 5.6 - - + -
50R LEU* 3.6 27.6 - - + -
103R LEU* 3.9 26.7 - - + -
131R ILE 3.5 2.3 + - - +
132R THR* 3.1 14.8 + - + +
134R GLU* 1.3 77.1 - - - +
136R LEU* 1.3 59.3 + - + +
160R LEU* 3.5 15.0 - - + +
161R PRO* 3.4 11.4 - - - +
162R ALA* 2.9 45.4 + - + +
164R PHE* 3.6 22.7 - - + +
166R ASN* 3.9 22.7 - - + +
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Residues in contact with LEU 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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50R LEU* 3.7 16.6 - - + +
51R TYR* 4.4 5.4 - - - -
54R ASN* 3.7 33.0 - - + +
128R MET* 3.7 26.7 - - - -
132R THR* 3.2 23.6 + - + +
133R LEU* 3.2 5.6 + - + +
135R LEU* 1.3 77.7 - - + +
137R ARG* 1.3 67.8 + - - +
138R ASP 3.2 0.3 + - - -
139R ILE* 3.0 38.2 + - + +
160R LEU* 3.9 31.9 - - + -
161R PRO* 4.2 3.8 - - - -
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Residues in contact with ARG 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 LEU 2.8 15.3 + - - +
134R GLU* 2.7 41.0 + - - +
135R LEU 3.5 1.8 - - - -
136R LEU* 1.3 73.4 - - - +
138R ASP* 1.3 83.0 + - - +
161R PRO* 3.2 22.3 - - - +
163R ARG* 3.5 25.5 - - + +
366R ARG* 3.9 4.9 - - - +
472R GLU* 3.3 39.0 + - - +
475R GLU* 4.4 9.1 + - - -
476R ILE* 4.0 16.2 - - - +
479R ARG* 4.8 1.0 - - - +
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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