Contacts of the helix formed by residues 127 - 136 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E GLY* 1.3 73.6 - - - -
128E MET* 1.3 63.1 + - - +
129E PHE* 3.1 10.5 + - + +
130E SER* 2.8 31.2 + - - +
131E HIS* 3.3 7.5 - - - -
169E PRO 4.0 0.4 - - - +
170E GLU* 3.1 36.3 - - - +
172E LEU 3.6 4.9 - - - -
173E LEU* 3.8 13.0 - - + -
326E ASN 4.9 2.6 + - - +
327E PHE* 4.8 11.1 - - + -
351E G98 4.2 16.8 - - - +
18F ARG* 2.4 43.5 + - - -
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Residues in contact with MET 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E GLY 3.9 0.6 + - - -
127E GLU* 1.3 71.2 - - - +
129E PHE* 1.3 62.7 + - - +
131E HIS* 3.1 6.5 + - + +
132E LEU* 2.8 23.7 + - + +
138E PHE* 3.9 18.4 - - + -
146E TYR* 3.6 33.9 - - + -
169E PRO* 3.5 24.4 + - + +
172E LEU* 2.7 40.2 + - + +
174E ILE* 4.2 16.7 - - + +
180E ILE* 3.8 10.8 - - + -
227E LEU* 4.5 1.3 - - - -
231E MET* 3.7 31.0 - - - +
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Residues in contact with PHE 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E GLU* 3.0 10.5 - - - +
128E MET* 1.3 78.8 - - - +
130E SER* 1.3 64.6 + - - +
132E LEU* 3.4 3.5 + - - +
133E ARG* 2.9 70.5 + - + +
169E PRO* 3.3 15.0 + - + -
170E GLU* 3.6 42.4 - - + +
16F THR 3.4 10.1 - - - -
17F GLY* 3.3 14.1 - - - -
18F ARG* 3.3 47.6 - - + -
19F ARG* 4.2 4.5 - - - -
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Residues in contact with SER 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E GLY 5.1 0.2 + - - -
127E GLU* 2.8 26.9 + - - +
129E PHE* 1.3 87.1 - - - +
131E HIS* 1.3 73.1 + - - +
133E ARG* 3.5 5.1 + - - +
134E ARG* 3.0 34.8 + - - +
326E ASN* 4.5 15.4 + - - -
18F ARG* 6.0 2.7 - - - -
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Residues in contact with HIS 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E GLY 2.7 28.7 + - - -
127E GLU 3.3 25.6 - - - -
128E MET* 3.1 5.8 + - + +
130E SER* 1.3 83.8 + - - +
132E LEU* 1.3 59.4 + - - +
134E ARG* 3.0 36.3 + - - +
135E ILE* 2.9 38.6 + - + +
138E PHE* 4.7 8.7 - - + -
174E ILE* 4.3 11.0 - - + -
314E PHE* 3.5 34.5 - + + -
316E PRO* 4.6 7.4 - - + +
326E ASN* 3.8 16.4 - - - -
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E MET* 2.8 17.3 + - - +
129E PHE* 3.7 4.5 - - - +
131E HIS* 1.3 75.4 - - - +
133E ARG* 1.3 77.7 + - - +
135E ILE* 4.4 0.4 - - - -
136E GLY 2.9 38.9 + - - +
137E ARG* 3.7 16.2 - - - -
138E PHE* 3.8 26.2 - - + -
169E PRO* 4.2 26.5 - - + -
230E GLU* 4.0 9.2 - - - +
231E MET* 3.7 45.8 - - + +
234E GLY* 5.1 0.2 - - - -
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Residues in contact with ARG 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE* 2.9 63.3 + - + +
130E SER* 3.9 5.2 - - - +
132E LEU* 1.3 88.8 + - - +
134E ARG* 1.3 63.7 - - - +
136E GLY* 3.9 6.5 + - - -
230E GLU* 2.7 34.3 + - - +
234E GLY 3.5 24.7 + - - -
10F PHE* 3.8 20.5 - - - -
15F ARG 4.9 0.4 + - - -
16F THR* 3.2 27.0 + - - +
17F GLY 5.1 0.2 + - - -
19F ARG* 4.5 5.9 - - - +
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Residues in contact with ARG 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E SER* 3.0 23.7 + - - +
131E HIS* 3.0 49.6 + - - +
133E ARG* 1.3 78.8 - - - +
135E ILE* 1.3 77.7 + - - +
136E GLY* 4.4 0.7 - - - -
314E PHE* 4.0 14.8 - - - -
326E ASN* 5.1 3.0 + - - -
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Residues in contact with ILE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E HIS* 2.9 23.3 + - + +
132E LEU 4.1 1.6 - - - +
134E ARG* 1.3 91.3 - - - +
136E GLY* 1.3 59.2 + - - +
137E ARG 3.3 20.9 + - - +
138E PHE* 2.9 42.0 - - + -
142E HIS* 4.7 7.4 - - + +
314E PHE* 6.1 3.1 - - + -
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Residues in contact with GLY 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU* 2.9 19.7 + - - +
133E ARG* 4.3 7.1 + - - -
134E ARG 3.3 2.5 - - - -
135E ILE* 1.3 76.6 - - - +
137E ARG* 1.3 71.1 + - - +
234E GLY* 3.1 24.1 - - - +
7F TYR* 6.4 2.5 - - - -
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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