Contacts of the helix formed by residues 134 - 146 (chain F) in PDB entry 4PIW
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 134 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101F ARG* 4.3 12.1 + - - +
109F GLU* 3.7 33.9 + - + +
133F CYS* 1.3 69.4 - - - +
135F MSE 1.3 62.4 + - - +
136F ASP* 4.3 4.0 - - - +
137F THR* 3.2 26.3 - - - +
138F ILE* 3.2 23.6 + - - +
161F TYR* 2.3 33.2 + - - -
162F LYS* 3.7 11.5 + - - -
283F PRO* 5.9 2.6 - - - +
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Residues in contact with MSE 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F PRO* 3.9 9.6 - - + -
127F HIS* 3.8 28.3 - - + -
133F CYS* 2.8 17.4 + - - +
134F GLU* 1.3 67.6 - - - +
136F ASP* 1.3 58.6 + - - +
137F THR 3.1 2.5 - - - -
138F ILE* 2.9 23.8 + - + -
139F MSE 2.7 60.3 + - - +
149F VAL* 3.9 14.1 - - + -
151F GLU* 4.2 7.6 - - + +
161F TYR* 3.4 26.2 + - + -
169F ILE* 3.3 39.3 - - + +
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Residues in contact with ASP 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F GLU* 4.3 2.0 - - - +
135F MSE 1.3 75.9 - - - +
137F THR* 1.3 60.6 + - - +
139F MSE 4.4 5.7 - - - +
140F ALA* 3.4 20.1 + - - +
161F TYR* 3.2 15.8 + - - +
162F LYS* 2.8 36.6 + - - +
164F ARG* 3.4 25.5 + - - -
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Residues in contact with THR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLU* 4.0 31.1 - - + +
110F THR* 5.6 2.9 - - + -
134F GLU* 3.2 28.8 + - - +
135F MSE 3.1 0.6 - - - -
136F ASP* 1.3 77.8 - - - +
138F ILE* 1.3 63.9 + - - +
140F ALA* 3.3 7.6 + - + +
141F LEU* 3.1 28.9 + - + +
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Residues in contact with ILE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ILE* 5.0 3.1 - - + +
109F GLU* 4.4 8.7 - - + -
112F ILE* 4.1 22.9 - - + -
123F ILE* 3.7 24.7 - - + +
125F PRO* 3.7 20.6 - - + -
133F CYS* 4.2 10.5 - - + -
134F GLU 3.2 14.1 - - - +
135F MSE 2.9 36.7 + - + +
137F THR* 1.3 74.7 - - - +
139F MSE 1.3 59.8 + - - +
141F LEU* 3.1 11.9 + - - +
142F ALA* 2.9 25.5 + - - +
149F VAL* 4.3 13.5 - - + -
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Residues in contact with MSE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F MSE 2.7 43.0 + - + +
136F ASP* 4.5 6.1 - - - +
138F ILE* 1.3 72.5 - - - +
140F ALA* 1.3 57.9 + - - +
142F ALA* 3.7 5.4 - - + +
143F LYS* 3.1 28.8 + - - +
149F VAL* 3.6 30.7 - - + -
164F ARG* 5.7 0.9 - - - +
169F ILE* 4.1 24.5 - - + +
170F GLY* 4.1 17.7 - - - +
171F HIS* 4.3 15.0 - - + -
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ASP 3.4 15.1 + - - +
137F THR* 3.3 13.9 + - + +
138F ILE 3.1 0.4 - - - -
139F MSE 1.3 77.2 - - - +
141F LEU* 1.3 61.4 + - + +
143F LYS* 3.6 5.0 + - - +
144F LYS* 3.1 29.0 + - - +
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F GLU 3.7 23.3 - - - +
112F ILE* 3.9 28.5 - - + -
113F GLU* 3.3 42.6 - - + +
116F ILE* 4.9 4.9 - - + -
123F ILE* 5.2 6.7 - - + -
137F THR* 3.1 23.9 + - + +
138F ILE* 3.1 8.9 + - + +
140F ALA* 1.3 77.4 - - + +
142F ALA* 1.3 62.3 + - - +
144F LYS* 4.3 7.0 - - + -
145F HIS* 3.1 34.8 + - + +
147F LEU* 4.7 3.0 - - - +
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Residues in contact with ALA 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F ILE* 4.5 3.1 - - + +
138F ILE 2.9 15.3 + - - +
139F MSE 3.7 11.2 - - + +
141F LEU* 1.3 76.5 - - - +
143F LYS* 1.3 59.5 + - - +
146F ASN* 2.9 12.5 + - - -
147F LEU* 2.8 53.0 + - + +
149F VAL* 3.6 21.1 - - + -
171F HIS* 5.1 2.0 - - + -
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Residues in contact with LYS 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MSE 3.1 18.6 + - - +
140F ALA* 4.0 4.9 - - - +
142F ALA* 1.3 76.7 - - - +
144F LYS* 1.3 62.7 + - - +
146F ASN* 3.9 13.5 + - - +
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Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLU* 2.7 26.4 + - - +
140F ALA 3.1 19.6 + - - +
141F LEU* 3.8 5.6 - - + +
143F LYS* 1.3 81.4 - - - +
145F HIS* 1.3 87.7 + - + +
146F ASN* 3.8 3.5 + - - +
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Residues in contact with HIS 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F GLU* 3.5 21.9 + - + +
116F ILE* 3.6 34.8 - - + +
141F LEU* 3.1 27.3 + - - +
144F LYS* 1.3 110.2 + - + +
146F ASN* 1.3 72.9 + - - +
147F LEU* 3.4 23.0 - - + +
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Residues in contact with ASN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ARG* 4.3 3.8 - - - +
142F ALA 2.9 9.4 + - - -
143F LYS* 3.9 11.2 - - - +
144F LYS 3.5 3.1 + - - -
145F HIS* 1.3 81.7 - - - +
147F LEU* 1.3 61.7 + - - +
148F PHE* 4.4 4.0 + - - -
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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