Contacts of the helix formed by residues 127 - 136 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126I GLY* 1.3 70.6 - - - -
128I MET* 1.3 62.6 + - - +
129I PHE* 4.0 10.2 - - + +
130I SER* 2.7 33.9 + - - +
131I HIS* 3.2 6.6 - - - -
169I PRO 4.0 1.6 - - - +
170I GLU* 3.2 36.5 - - - +
172I LEU 3.5 4.9 - - - -
173I LEU* 3.6 16.2 - - + -
326I ASN 5.0 2.0 + - - -
327I PHE* 4.7 11.5 - - + -
351I G98 4.1 18.9 - - - +
18J ARG* 2.6 38.0 + - - -
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Residues in contact with MET 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I GLY 3.9 1.2 + - - -
127I GLU* 1.3 70.5 - - - +
129I PHE* 1.3 64.7 + - - +
131I HIS* 3.2 6.4 + - - +
132I LEU* 2.8 23.9 + - + +
138I PHE* 3.7 20.9 - - + -
146I TYR* 3.4 32.1 - - + -
169I PRO* 3.5 18.1 + - + +
172I LEU* 2.7 40.5 + - + +
174I ILE* 4.2 17.6 - - + +
180I ILE* 3.5 27.8 - - + -
227I LEU* 4.7 0.4 - - - -
231I MET* 3.7 26.0 - - - +
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Residues in contact with PHE 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I GLU* 4.1 5.2 - - - +
128I MET* 1.3 79.0 - - - +
130I SER* 1.3 62.2 + - - +
132I LEU* 3.7 2.7 - - - +
133I ARG* 2.9 73.4 + - + +
169I PRO* 3.2 14.3 + - + +
170I GLU* 3.4 52.9 - - + +
16J THR 3.4 11.0 - - - -
17J GLY* 3.3 28.7 - - - -
18J ARG* 3.4 28.7 - - + -
19J ARG* 4.2 5.4 - - - -
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Residues in contact with SER 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I GLY 5.0 0.3 + - - -
127I GLU* 2.7 26.3 + - - +
129I PHE* 1.3 85.2 - - - +
131I HIS* 1.3 74.5 + - - +
133I ARG* 3.4 4.6 + - - +
134I ARG* 3.1 46.0 + - - +
326I ASN* 4.6 14.8 + - - +
328I ASP* 6.1 0.9 - - - -
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Residues in contact with HIS 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I GLY 2.8 28.5 + - - -
127I GLU 3.2 26.2 - - - -
128I MET* 3.2 8.6 + - - +
130I SER* 1.3 84.4 + - - +
132I LEU* 1.3 64.5 + - - +
134I ARG* 3.4 25.2 + - - +
135I ILE* 3.1 34.6 + - + +
138I PHE* 4.4 11.4 - - + -
174I ILE* 4.4 6.5 - - + +
314I PHE* 3.4 42.4 - + + -
316I PRO* 4.6 5.6 - - + +
326I ASN* 4.0 12.3 - - - -
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Residues in contact with LEU 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I MET* 2.8 17.4 + - - +
129I PHE* 3.7 3.4 - - - +
131I HIS* 1.3 75.0 - - - +
133I ARG* 1.3 75.8 + - - +
135I ILE* 3.9 0.6 - - - +
136I GLY 3.0 34.3 + - - +
137I ARG* 3.8 24.5 - - - -
138I PHE* 3.8 26.6 - - + +
169I PRO* 4.1 19.1 - - + -
230I GLU* 4.0 35.2 - - + +
231I MET* 3.9 25.8 - - + +
234I GLY* 4.6 0.2 - - - -
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Residues in contact with ARG 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I PHE* 2.9 63.0 + - + +
130I SER* 3.8 5.6 - - - +
132I LEU* 1.3 89.2 - - - +
134I ARG* 1.3 63.0 + - - +
136I GLY* 3.7 8.1 + - - -
230I GLU* 2.7 33.6 + - - +
234I GLY 3.5 21.2 + - - -
7J TYR* 4.4 10.8 + - - -
10J PHE* 3.7 26.6 - - - -
15J ARG 4.9 0.6 + - - -
16J THR* 3.3 27.5 + - - +
19J ARG* 4.3 6.1 - - - +
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Residues in contact with ARG 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I SER* 3.1 25.7 + - - +
131I HIS* 3.4 43.3 + - - +
132I LEU 3.2 0.4 - - - -
133I ARG* 1.3 79.6 - - - +
135I ILE* 1.3 65.1 + - + +
136I GLY* 4.7 0.2 - - - -
326I ASN* 4.9 4.9 + - - -
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Residues in contact with ILE 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I HIS* 3.1 19.9 + - + +
132I LEU 3.9 2.5 - - - +
134I ARG* 1.3 82.0 - - + +
136I GLY* 1.3 59.0 + - - +
137I ARG 3.4 21.8 + - - +
138I PHE* 3.1 39.9 - - + -
142I HIS* 4.9 5.6 - - + +
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Residues in contact with GLY 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I LEU* 3.0 21.3 + - - +
133I ARG* 3.7 2.5 + - - -
134I ARG 3.4 3.0 + - - -
135I ILE* 1.3 76.9 - - - +
137I ARG* 1.3 59.5 + - - -
234I GLY* 3.1 23.7 - - - +
7J TYR* 4.1 23.6 + - - -
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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