Contacts of the helix formed by residues 127 - 139 (chain F) in PDB entry 4S0H
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 SER 127 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126F LEU* 1.3 75.4 - - - +
128F ALA* 1.3 66.5 + - - +
129F PRO* 3.3 21.9 - - - +
130F GLU* 2.3 34.9 + - - +
131F ARG* 3.2 23.7 + - - +
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Residues in contact with ALA 128 (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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127F SER* 1.3 72.1 - - - +
129F PRO* 1.3 64.3 - - + +
131F ARG* 3.6 26.0 + - - +
132F ASP* 2.6 34.6 + - - +
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Residues in contact with PRO 129 (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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127F SER* 3.3 17.9 - - - +
128F ALA* 1.3 92.5 - - + +
130F GLU* 1.3 63.9 + - + +
132F ASP* 3.5 11.5 + - + +
133F GLN* 3.3 21.3 + - - +
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Residues in contact with GLU 130 (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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119F ARG* 3.2 38.3 + - - +
123F GLN* 3.3 17.2 + - - +
125F TYR 5.3 0.2 - - - +
126F LEU* 4.1 9.2 - - + -
127F SER* 2.3 46.4 + - - +
129F PRO* 1.3 77.9 - - + +
131F ARG* 1.3 64.0 + - - +
133F GLN* 3.2 12.3 + - - +
134F LEU* 3.0 25.4 + - - +
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Residues in contact with ARG 131 (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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126F LEU* 3.8 31.8 + - + +
127F SER 3.2 6.6 + - - +
128F ALA* 3.6 34.6 + - - +
130F GLU* 1.3 75.9 - - - +
132F ASP* 1.3 57.0 + - - +
134F LEU* 3.4 5.5 + - - +
135F ALA* 2.8 37.1 + - - +
142F SER* 3.8 17.0 + - - +
145F VAL* 4.1 16.1 - - + +
146F LYS* 3.4 57.5 - - - +
149F PHE* 5.9 0.4 - - + -
153F ARG* 5.8 3.6 - - - +
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Residues in contact with ASP 132 (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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128F ALA* 2.6 25.5 + - - +
129F PRO* 3.5 10.2 - - + +
130F GLU 3.4 0.2 - - - -
131F ARG* 1.3 75.5 - - - +
133F GLN* 1.3 65.0 + - - +
135F ALA* 3.4 2.8 - - - +
136F SER* 3.4 18.7 + - - -
142F SER* 2.8 31.6 + - - -
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Residues in contact with GLN 133 (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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119F ARG* 4.9 8.8 + - - -
129F PRO 3.3 8.9 + - - +
130F GLU* 3.2 16.1 + - - +
131F ARG 3.1 0.4 - - - -
132F ASP* 1.3 74.6 - - - +
134F LEU* 1.3 69.1 + - - +
135F ALA 2.9 1.9 + - - -
136F SER* 2.9 20.7 + - - +
137F VAL* 3.2 20.5 + - + +
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Residues in contact with LEU 134 (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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115F GLU* 5.4 5.8 - - + +
116F LEU* 4.1 13.7 - - + -
119F ARG* 4.1 31.2 - - + +
126F LEU* 3.8 24.2 - - + -
130F GLU 3.0 15.7 + - - +
131F ARG* 3.7 5.2 - - - +
133F GLN* 1.3 75.4 - - - +
135F ALA* 1.3 62.9 + - - +
137F VAL* 3.5 11.3 + - + +
138F LEU* 2.9 51.6 + - + +
145F VAL* 3.9 15.5 - - + -
149F PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 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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131F ARG 2.8 21.2 + - - +
132F ASP* 3.4 10.1 - - - +
133F GLN 2.9 2.2 + - - -
134F LEU* 1.3 69.1 - - - +
136F SER* 1.3 52.6 + - - +
138F LEU* 2.8 5.4 + - - -
139F LYS 2.6 33.3 + - - -
140F LEU* 3.1 26.2 + - - +
141F THR* 4.0 16.6 - - - +
142F SER* 4.1 5.6 - - - +
145F VAL* 4.3 9.9 - - + +
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Residues in contact with SER 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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132F ASP 3.4 8.1 + - - -
133F GLN* 2.9 14.7 + - - -
135F ALA* 1.3 76.8 - - - +
137F VAL* 1.3 63.1 + - - +
139F LYS* 3.6 18.9 + - - +
140F LEU 4.7 1.3 - - - -
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Residues in contact with VAL 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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133F GLN* 3.2 23.9 + - + +
134F LEU* 3.5 14.6 - - + +
135F ALA 3.0 0.4 + - - -
136F SER* 1.3 81.7 - - - +
138F LEU* 1.3 72.4 + - + +
139F LYS* 3.2 10.8 + - - +
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Residues in contact with LEU 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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111F ALA 4.8 0.7 - - - +
112F GLN* 2.7 52.9 + - + +
115F GLU* 3.6 33.2 - - + -
116F LEU* 3.7 29.8 - - + -
134F LEU* 2.9 44.1 + - + +
135F ALA 2.8 6.5 + - - +
137F VAL* 1.3 82.2 - - + +
139F LYS* 1.3 61.3 + - - +
140F LEU* 4.3 12.1 - - + -
145F VAL* 5.2 1.6 - - + -
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Residues in contact with LYS 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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112F GLN* 3.7 9.3 + - - +
135F ALA 2.6 14.0 + - - -
136F SER* 3.6 16.1 + - - +
137F VAL 3.2 8.2 - - - +
138F LEU* 1.3 79.2 - - - +
140F LEU* 1.3 60.1 - - - +
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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