Contacts of the helix formed by residues 119 - 129 (chain A) in PDB entry 3U78
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 THR 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A GLN* 2.9 44.2 + - + +
117A ALA 3.1 4.2 - - - +
118A GLY* 1.3 80.3 - - - +
120A ARG* 1.3 66.4 + - - +
121A THR* 3.5 9.5 + - - -
122A PHE* 3.0 13.7 + - - +
123A ILE* 2.9 19.5 + - - +
198A ALA* 3.9 21.1 - - + +
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Residues in contact with ARG 120 (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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118A GLY 3.9 0.8 + - - -
119A THR* 1.3 73.8 - - - +
121A THR* 1.3 56.7 + - - +
123A ILE* 3.3 11.1 + - - +
124A LYS* 3.0 25.9 + - + +
276A ASP* 3.6 21.6 + - - -
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Residues in contact with THR 121 (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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115A VAL* 3.7 22.4 - - + -
119A THR* 3.1 9.6 + - - -
120A ARG* 1.3 75.4 - - - +
122A PHE* 1.3 65.5 + - - +
124A LYS* 3.2 17.4 + - + +
125A GLU* 3.2 25.5 + - - +
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Residues in contact with PHE 122 (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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115A VAL* 3.3 23.6 - - + -
116A GLN 3.1 22.4 - - - +
117A ALA* 3.7 17.7 - - + -
118A GLY 3.3 12.1 - - - -
119A THR* 3.0 5.0 + - - +
121A THR* 1.3 81.2 - - - +
123A ILE* 1.3 65.3 + - + +
125A GLU* 3.4 6.8 + - - +
126A LEU* 3.0 33.3 + - + +
129A ARG* 5.0 4.0 + - - -
278A TYR* 3.4 52.9 - + - -
280A ASP* 5.0 1.1 - - - -
324A SER 5.6 0.4 - - - -
326A VAL 6.1 0.2 - - - -
327A PHE* 3.8 35.0 - + + -
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Residues in contact with ILE 123 (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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118A GLY 4.0 10.1 - - - +
119A THR 2.9 19.3 + - - +
120A ARG* 3.5 14.6 - - - +
121A THR 3.1 0.4 - - - -
122A PHE* 1.3 86.2 - - + +
124A LYS* 1.3 59.6 + - - +
126A LEU* 3.3 5.3 + - + +
127A ARG* 2.9 44.6 + - + +
276A ASP* 3.4 48.5 - - + +
278A TYR* 4.1 14.4 - - + -
357A LEU* 3.9 23.3 - - + -
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Residues in contact with LYS 124 (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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120A ARG* 3.0 13.7 + - + +
121A THR* 3.2 11.9 + - - +
123A ILE* 1.3 76.5 - - - +
125A GLU* 1.3 58.3 + - + +
127A ARG* 3.4 5.8 + - - +
128A SER* 2.7 33.7 + - - +
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Residues in contact with GLU 125 (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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115A VAL* 3.6 28.9 - - - +
121A THR* 3.2 29.3 + - - +
122A PHE* 3.8 7.3 - - + +
123A ILE 3.2 0.4 - - - -
124A LYS* 1.3 76.7 - - + +
126A LEU* 1.3 66.4 + - - +
128A SER* 2.9 15.5 + - - -
129A ARG* 3.0 34.9 + - - +
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Residues in contact with LEU 126 (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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122A PHE* 3.0 27.3 + - + +
123A ILE* 3.3 8.5 + - + +
125A GLU* 1.3 76.8 - - - +
127A ARG* 1.3 62.8 + - + +
128A SER 3.3 0.7 + - - -
129A ARG* 3.7 9.1 + - - +
131A PHE* 3.8 27.3 - - + -
278A TYR* 3.7 34.8 - - + -
302A TYR* 3.5 44.8 + - + +
327A PHE* 4.1 19.1 - - + -
337A LYS* 5.9 0.5 + - - -
357A LEU* 4.2 15.9 - - + -
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Residues in contact with ARG 127 (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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123A ILE* 2.9 26.2 + - + +
124A LYS* 3.9 5.6 - - - +
126A LEU* 1.3 78.2 - - + +
128A SER* 1.3 59.8 + - - +
129A ARG 4.4 2.8 - - - +
275A GLN* 3.8 6.6 - - - +
276A ASP* 3.1 28.7 + - - -
300A ILE* 5.7 1.6 - - - +
302A TYR* 5.6 0.2 - - - -
337A LYS* 5.5 4.2 + - - -
357A LEU* 4.2 20.0 - - + +
358A THR 4.5 0.2 + - - -
359A SER* 3.0 48.5 + - - +
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Residues in contact with SER 128 (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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124A LYS* 2.7 21.3 + - - +
125A GLU* 2.9 8.0 + - - -
127A ARG* 1.3 79.8 - - - +
129A ARG* 1.3 67.9 + - - +
130A VAL* 3.2 11.8 + - - +
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Residues in contact with ARG 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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122A PHE* 5.0 4.2 + - - -
125A GLU* 3.0 43.0 + - - +
126A LEU* 3.7 11.7 + - - +
127A ARG 3.8 2.8 - - - +
128A SER* 1.3 78.3 - - - +
130A VAL* 1.3 66.7 + - - +
131A PHE* 3.4 41.9 - - + -
327A PHE* 3.3 44.0 - - - +
330A ASP* 3.3 22.5 + - - -
337A LYS* 4.6 7.4 + - - -
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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