Contacts of the helix formed by residues 126 - 138 (chain R) in PDB entry 4NYJ
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 GLU 126 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123R ARG* 3.7 33.7 - - - +
124R THR* 4.7 3.8 - - - +
125R VAL* 1.3 80.8 - - - +
127R SER* 1.3 67.9 + - - +
128R ARG* 3.1 9.7 + - + +
129R GLN* 3.0 34.8 + - + +
130R ALA* 3.4 8.0 + - - +
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Residues in contact with SER 127 (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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123R ARG* 3.8 10.0 + - - +
126R GLU* 1.3 73.3 + - - +
128R ARG* 1.3 53.9 + - - +
130R ALA* 3.0 8.7 + - - +
131R GLN* 2.8 52.3 + - - +
141R TYR* 4.3 2.9 - - - -
143R GLU* 3.0 28.5 + - - -
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Residues in contact with ARG 128 (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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126R GLU* 3.1 6.9 - - + -
127R SER* 1.3 79.2 - - - +
129R GLN* 1.3 64.6 + - + +
131R GLN* 3.2 22.7 + - - +
132R ASP* 3.0 60.6 + - - +
135R ARG* 5.8 4.9 - - - +
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Residues in contact with GLN 129 (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 THR* 6.3 1.2 - - - +
90R PHE* 3.8 26.5 - - + -
124R THR 3.8 7.6 + - - +
125R VAL* 3.8 9.6 - - + +
126R GLU* 3.0 41.7 + - + +
128R ARG* 1.3 76.6 - - + +
130R ALA* 1.3 57.5 + - - +
132R ASP* 3.5 7.9 + - - +
133R LEU* 3.0 28.8 + - - +
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Residues in contact with ALA 130 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R PHE* 4.1 14.8 - - + -
90R PHE* 4.0 13.2 - - + -
113R LEU* 3.8 3.7 - - + +
125R VAL* 4.7 0.7 - - + -
126R GLU 3.4 8.1 + - - +
127R SER* 3.0 9.1 + - - +
129R GLN* 1.3 77.5 - - - +
131R GLN* 1.3 60.5 + - - +
133R LEU* 3.3 1.9 + - - +
134R ALA* 2.9 30.7 + - - +
141R TYR* 3.4 36.1 - - + +
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Residues in contact with GLN 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R SER* 2.8 41.8 + - - +
128R ARG* 3.6 27.7 - - - +
130R ALA* 1.3 72.0 - - - +
132R ASP* 1.3 53.3 + - - +
134R ALA* 3.1 7.2 + - - +
135R ARG* 2.7 37.1 + - - +
141R TYR* 3.8 24.2 - - + +
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Residues in contact with ASP 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R ARG* 3.0 53.4 + - - +
129R GLN* 3.7 7.1 - - - +
131R GLN* 1.3 74.5 - - - +
133R LEU* 1.3 64.5 + - - +
135R ARG* 3.3 10.0 + - - +
136R SER* 3.0 24.9 + - - -
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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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90R PHE* 3.6 35.4 - - + +
93R ILE* 4.3 13.9 - - + -
94R HIS 5.8 0.4 - - - +
113R LEU* 4.1 11.9 - - + -
129R GLN 3.0 19.3 + - - +
130R ALA 3.7 3.4 - - - +
132R ASP* 1.3 76.3 - - - +
134R ALA* 1.3 62.4 + - - +
136R SER* 3.0 23.5 + - - +
137R TYR* 3.2 51.9 + - + +
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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
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113R LEU* 4.1 11.2 - - + +
130R ALA 2.9 17.2 + - - +
131R GLN 3.5 4.9 - - - +
133R LEU* 1.3 78.9 - - - +
135R ARG* 1.3 56.3 + - - +
137R TYR* 3.3 2.5 + - - -
138R GLY 3.0 22.2 + - - -
139R ILE* 3.0 40.1 + - + +
141R TYR* 3.8 21.5 - - + +
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Residues in contact with ARG 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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128R ARG* 5.8 4.4 - - - +
131R GLN 2.7 20.4 + - - +
132R ASP* 3.8 11.2 - - - +
133R LEU 3.3 0.2 - - - -
134R ALA* 1.3 73.6 - - - +
136R SER* 1.3 62.9 + - - +
138R GLY* 3.1 13.7 + - - +
139R ILE 5.0 0.7 - - - -
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Residues in contact with SER 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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132R ASP 3.0 14.6 + - - -
133R LEU* 3.0 19.7 + - - +
135R ARG* 1.3 77.9 - - - +
137R TYR* 1.3 72.1 + - - +
138R GLY 3.7 0.2 + - - -
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Residues in contact with TYR 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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93R ILE* 4.2 13.7 - - + -
94R HIS* 3.0 42.3 + + - +
97R ARG* 3.5 60.1 + - + +
98R GLU* 6.0 0.2 - - - -
113R LEU* 5.7 1.3 - - + -
133R LEU* 3.2 45.8 + - + +
134R ALA* 3.9 4.9 - - - +
135R ARG 3.2 0.4 - - - -
136R SER* 1.3 94.3 + - - +
138R GLY* 1.3 61.2 + - - +
139R ILE* 3.6 22.7 + - + +
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Residues in contact with GLY 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 3.0 5.0 + - - -
135R ARG* 3.1 13.4 + - - -
136R SER 3.4 0.4 + - - -
137R TYR* 1.3 79.3 - - - +
139R ILE* 1.3 60.7 + - - +
140R PRO* 4.7 1.0 - - - +
162R GLU* 4.8 4.7 - - - +
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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