Contacts of the helix formed by residues 127 - 136 (chain P) in PDB entry 3E8E
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 127 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49P LEU 5.1 1.9 - - - +
126P GLY* 1.3 71.4 - - - -
128P MET* 1.3 65.1 + - - +
129P PHE* 3.9 9.6 - - + +
130P SER* 2.6 32.4 + - - +
131P HIS* 3.3 7.1 - - - -
169P PRO 4.1 0.9 - - - +
170P GLU* 3.4 37.0 - - - +
172P LEU 3.5 5.8 - - - -
173P LEU* 3.6 13.7 - - + -
326P ASN 4.5 1.0 + - - -
327P PHE* 4.5 12.5 - - + -
330P TYR* 5.0 2.1 + - - -
351P G98 4.3 15.8 - - - +
18Q ARG* 2.5 41.5 + - - +
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Residues in contact with MET 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P GLY 3.8 1.6 + - - -
127P GLU* 1.3 69.6 - - - +
129P PHE* 1.3 58.1 + - - +
131P HIS* 3.2 12.4 + - - +
132P LEU* 2.8 28.9 + - + +
138P PHE* 3.8 20.4 - - + -
146P TYR* 3.5 29.6 - - + -
169P PRO* 3.5 18.6 - - + +
172P LEU* 2.7 42.4 + - + +
174P ILE* 4.3 11.1 - - + +
180P ILE* 3.4 33.0 - - + -
227P LEU* 4.5 1.3 - - - -
231P MET* 3.7 23.8 - - - +
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Residues in contact with PHE 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P GLU* 3.9 3.8 - - - +
128P MET* 1.3 78.6 - - - +
130P SER* 1.3 63.5 - - - +
132P LEU* 3.7 3.6 - - - +
133P ARG* 2.9 75.2 + - + +
169P PRO* 3.2 14.7 + - + +
170P GLU* 3.6 47.1 - - + +
328P ASP* 5.8 0.7 - - - -
16Q THR 3.4 7.6 - - - -
17Q GLY* 3.4 16.2 - - - -
18Q ARG* 3.2 51.8 - - + -
19Q ARG* 4.3 4.9 - - - -
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Residues in contact with SER 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P GLU* 2.6 33.3 + - - +
129P PHE* 1.3 87.7 - - - +
131P HIS* 1.3 63.2 + - - +
133P ARG* 3.5 4.1 + - - +
134P ARG* 3.0 33.3 + - - +
326P ASN 3.9 14.3 + - - -
328P ASP* 5.5 6.7 - - - -
18Q ARG* 5.5 4.0 - - - -
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Residues in contact with HIS 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P GLY 2.7 30.1 + - - -
127P GLU 3.3 26.4 + - - -
128P MET* 3.2 5.0 + - - +
130P SER* 1.3 79.6 + - - +
132P LEU* 1.3 57.7 + - - +
134P ARG* 3.0 33.1 + - - +
135P ILE* 2.8 37.7 + - + +
138P PHE* 4.6 11.4 - - + -
174P ILE* 4.2 16.8 - - + +
314P PHE* 3.2 35.8 - + + -
316P PRO* 4.4 3.6 - - + +
317P LYS 5.9 0.2 - - - -
326P ASN* 4.3 14.6 - - + -
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Residues in contact with LEU 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P MET* 2.8 16.9 + - + +
129P PHE 3.7 4.3 - - - +
131P HIS* 1.3 74.9 - - - +
133P ARG* 1.3 80.2 + - - +
135P ILE* 4.6 0.7 - - - -
136P GLY* 2.7 52.0 + - - +
137P ARG* 3.8 15.3 - - - -
138P PHE* 4.0 26.9 - - + +
169P PRO* 4.2 18.4 - - + -
230P GLU* 3.9 23.1 - - + +
231P MET* 3.8 23.3 - - + +
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Residues in contact with ARG 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P PHE* 2.9 61.2 + - + +
130P SER* 3.9 5.6 - - - +
132P LEU* 1.3 90.3 - - - +
134P ARG* 1.3 62.5 + - - +
136P GLY* 3.8 7.3 + - - -
230P GLU* 2.8 33.5 + - - +
234P GLY 3.1 24.2 + - - -
7Q TYR* 5.6 0.3 + - - -
10Q PHE* 3.8 21.8 - - - -
11Q ILE* 6.4 2.0 - - - -
15Q ARG 5.0 0.4 + - - -
16Q THR* 3.3 28.1 + - - -
19Q ARG* 4.3 4.9 - - - +
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Residues in contact with ARG 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P SER* 3.0 21.2 + - - +
131P HIS* 3.0 50.2 + - - +
133P ARG* 1.3 80.3 - - - +
135P ILE* 1.3 77.3 + - - +
314P PHE* 3.4 23.6 - - - -
326P ASN* 5.4 2.6 + - - -
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Residues in contact with ILE 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P HIS* 2.8 20.7 + - + +
132P LEU 4.4 1.1 - - - +
134P ARG* 1.3 100.7 - - - +
136P GLY* 1.3 58.3 + - - +
137P ARG* 3.2 31.6 + - - +
138P PHE* 3.4 28.7 - - + -
142P HIS* 5.2 5.6 - - + +
314P PHE* 5.8 2.2 - - + -
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Residues in contact with GLY 136 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P LEU* 2.7 26.9 + - - +
133P ARG* 4.3 6.4 + - - -
134P ARG 3.4 3.2 - - - -
135P ILE* 1.3 69.6 - - - +
137P ARG* 1.3 60.3 + - - -
234P GLY* 3.0 26.7 - - - +
7Q TYR* 3.9 24.1 - - - -
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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