Contacts of the helix formed by residues 127 - 136 (chain C) in PDB entry 3E8C
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C GLY* 1.3 73.2 - - - -
128C MET* 1.3 64.6 + - - +
129C PHE* 3.2 16.6 + - + +
130C SER* 2.9 26.6 + - - +
131C HIS* 3.2 10.4 - - - -
169C PRO 4.1 0.4 - - - +
170C GLU* 3.1 32.7 - - - +
172C LEU 3.5 5.4 - - - -
173C LEU* 3.8 14.1 - - + -
326C ASN 4.8 1.4 + - - +
327C PHE* 4.7 11.2 - - + -
351C G96 4.1 17.7 - - - +
18I ARG* 3.1 41.6 + - - -
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Residues in contact with MET 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLY 3.8 1.2 + - - -
127C GLU* 1.3 70.9 - - - +
129C PHE* 1.3 62.9 + - - +
131C HIS* 3.1 6.7 + - - +
132C LEU* 2.8 23.3 + - + +
138C PHE* 3.8 19.3 - - + -
146C TYR* 3.8 22.0 - - + -
169C PRO* 3.5 18.8 - - + +
172C LEU* 2.7 41.2 + - + +
174C ILE* 4.1 15.1 - - + +
180C ILE* 3.3 30.1 - - + -
227C LEU* 4.5 1.3 - - - -
231C MET* 3.7 31.0 - - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C GLU* 3.9 9.0 - - - +
128C MET* 1.3 78.5 - - - +
130C SER* 1.3 64.6 + - - +
132C LEU* 3.7 2.8 - - - +
133C ARG* 2.9 72.5 + - + +
169C PRO* 3.2 15.5 + - + -
170C GLU* 3.3 53.2 - - + +
16I THR 3.3 22.4 - - - -
17I GLY* 3.4 17.9 - - - -
18I ARG* 3.5 23.1 - - + -
19I ARG* 4.1 6.1 - - - -
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Residues in contact with SER 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C GLY 4.9 0.2 - - - -
127C GLU* 2.9 23.4 + - - +
129C PHE* 1.3 87.7 - - - +
131C HIS* 1.3 68.1 + - - +
133C ARG* 3.6 5.0 + - - +
134C ARG* 3.1 31.7 + - - +
326C ASN* 3.9 19.0 + - - +
328C ASP* 5.9 3.1 - - - -
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Residues in contact with HIS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLY 2.7 27.7 + - - -
127C GLU 3.2 25.7 + - - -
128C MET* 3.1 5.3 + - - +
130C SER* 1.3 77.5 + - - +
132C LEU* 1.3 60.8 + - - +
134C ARG* 3.1 33.8 + - - +
135C ILE* 3.0 41.2 + - + +
138C PHE* 4.8 6.1 - - + -
174C ILE* 4.1 17.3 - - + +
314C PHE* 3.6 29.1 - + + -
316C PRO* 4.1 9.2 - - + +
326C ASN* 3.9 16.6 - - - -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C MET* 2.8 19.8 + - - +
129C PHE* 3.7 4.0 - - - +
131C HIS* 1.3 71.3 - - - +
133C ARG* 1.3 68.7 + - - +
136C GLY 2.8 44.7 + - - +
137C ARG* 3.7 26.2 - - - -
138C PHE* 3.6 23.5 - - + -
169C PRO* 4.1 20.2 - - + -
230C GLU* 3.9 33.9 - - + +
231C MET* 3.8 25.6 - - + +
234C GLY* 4.5 0.4 - - - -
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Residues in contact with ARG 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PHE* 2.9 65.1 + - + +
130C SER* 3.8 5.8 - - - +
132C LEU* 1.3 86.8 - - - +
134C ARG* 1.3 60.7 + - - +
136C GLY* 3.9 4.4 + - - -
230C GLU* 2.8 31.4 + - - +
234C GLY 3.4 23.0 + - - -
7I TYR* 4.1 17.4 + - - -
10I PHE* 3.5 28.8 - - - -
15I ARG 4.7 0.6 + - - -
16I THR* 3.4 25.7 + - - +
19I ARG* 4.3 5.3 - - - +
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Residues in contact with ARG 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C SER* 3.1 30.3 + - - +
131C HIS* 3.1 41.2 + - - +
133C ARG* 1.3 77.5 - - - +
135C ILE* 1.3 75.3 + - - +
136C GLY* 3.2 0.9 + - - -
314C PHE* 4.0 14.6 - - - -
326C ASN* 5.4 2.6 + - - -
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C HIS* 3.0 33.6 + - + +
132C LEU 4.5 0.7 - - - +
134C ARG* 1.3 91.7 - - - +
136C GLY* 1.3 57.5 + - - +
137C ARG 3.5 18.4 + - - +
138C PHE* 4.0 18.8 - - + -
142C HIS* 5.2 4.0 - - + -
314C PHE* 4.5 19.7 - - + -
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Residues in contact with GLY 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C LEU* 2.8 20.4 + - - +
133C ARG* 4.3 6.6 + - - -
134C ARG 3.2 3.7 - - - -
135C ILE* 1.3 76.2 - - - +
137C ARG* 1.3 59.4 + - - -
234C GLY* 3.2 24.0 - - - +
7I TYR* 4.1 18.4 + - - -
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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