Contacts of the helix formed by residues 128 - 139 (chain A) in PDB entry 1FUU
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A THR* 1.3 68.7 + - - +
129A PHE* 1.3 59.2 + - - +
130A VAL* 2.5 37.8 + - - +
131A GLU* 2.7 32.9 + - - +
132A ASP 2.9 9.9 + - - -
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Residues in contact with PHE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A THR 2.9 8.2 + - - +
128A SER* 1.3 72.8 - - - +
130A VAL* 1.3 78.6 + - + +
132A ASP* 4.0 10.6 - - - +
133A ALA* 3.4 22.3 + - - +
155A ARG* 4.0 31.4 + - - +
157A ARG* 5.6 1.2 - - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A SER* 2.5 17.0 + - - +
129A PHE* 1.3 99.3 - - + +
131A GLU* 1.3 63.2 + - + +
133A ALA* 3.2 7.0 + - - +
134A GLU* 3.0 28.3 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A HIS* 4.0 3.0 + - - -
127A THR* 4.8 6.4 + - - +
128A SER* 2.7 21.6 + - - +
130A VAL* 1.3 77.3 - - + +
132A ASP* 1.3 57.2 + - - +
134A GLU* 3.7 12.2 - - + +
135A GLY* 2.7 33.3 + - - -
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A HIS* 2.9 29.6 - - - -
123A CYS* 3.9 10.3 - - - -
127A THR* 4.0 26.9 + - + +
128A SER 2.9 13.7 + - - +
129A PHE* 4.0 10.9 - - - +
131A GLU* 1.3 78.0 - - - +
133A ALA* 1.3 62.6 + - - +
136A LEU* 3.0 35.3 + - - +
148A ARG* 5.7 1.0 - - - +
152A ASN* 2.7 38.5 + - - +
155A ARG* 4.3 2.9 + - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE 3.4 14.8 + - - +
130A VAL* 3.2 11.8 + - - +
132A ASP* 1.3 79.2 - - - +
134A GLU* 1.3 62.8 + - - +
136A LEU* 3.3 3.5 + - - +
137A ARG* 3.1 22.6 + - - +
157A ARG* 4.3 25.3 - - + +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 4.3 0.7 + - - -
130A VAL* 3.0 17.9 + - + +
131A GLU* 3.8 12.1 - - - +
133A ALA* 1.3 76.6 - - - +
135A GLY* 1.3 62.5 + - - +
137A ARG* 3.4 19.7 + - + +
138A ASP* 3.7 13.5 - - - +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS* 2.8 27.2 + - - -
121A HIS* 3.3 30.3 - - - +
131A GLU 2.7 17.4 + - - -
134A GLU* 1.3 74.9 - - - +
136A LEU* 1.3 56.9 + - - +
139A ALA* 3.0 15.1 + - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A PRO* 3.5 21.7 - - - +
121A HIS* 3.7 19.3 - - + +
123A CYS* 4.4 7.0 - - + -
132A ASP* 3.0 25.5 + - - +
133A ALA 3.3 0.6 + - - +
135A GLY* 1.3 74.4 - - - +
137A ARG* 1.3 68.0 + - - +
138A ASP 3.4 0.2 - - - -
139A ALA* 3.7 5.6 + - - -
142A VAL* 4.0 22.9 - - + -
152A ASN* 3.5 29.8 - - - +
157A ARG* 3.4 32.7 - - + +
158A PHE* 3.8 27.1 - - + -
159A ARG 5.4 2.1 + - - -
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS 3.6 7.6 - - - +
89A ALA* 4.2 2.8 - - - +
90A PRO* 4.2 7.1 - - - +
133A ALA 3.1 13.6 + - - +
134A GLU* 3.5 15.7 - - + +
135A GLY 3.4 0.8 - - - -
136A LEU* 1.3 79.2 - - - +
138A ASP* 1.3 63.4 + - + +
157A ARG 4.7 2.4 + - - -
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 3.2 31.0 - - + +
119A LYS* 2.9 44.3 + - + +
134A GLU* 3.7 10.8 - - - +
137A ARG* 1.3 77.9 - - + +
139A ALA* 1.3 66.9 + - - +
140A GLN* 3.5 7.6 + - - +
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 2.9 3.3 - - - -
90A PRO* 2.7 34.9 - - - +
119A LYS* 4.0 11.7 - - - +
121A HIS* 3.5 27.4 - - + +
135A GLY 3.0 24.3 + - - +
136A LEU* 3.7 3.1 + - - +
137A ARG 3.6 1.6 - - - -
138A ASP* 1.3 77.9 - - - +
140A GLN* 1.3 53.8 + - - +
141A ILE 4.3 0.2 - - - +
142A VAL* 4.0 16.4 - - + -
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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