Contacts of the helix formed by residues 119 - 132 (chain A) in PDB entry 5OND
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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91A ALA* 3.7 12.2 - - - +
118A ILE* 1.3 79.0 + - - +
120A GLU* 1.3 72.4 + - + +
121A GLY 3.6 4.9 - - - +
122A ALA* 3.5 14.1 - - - +
123A PHE* 2.7 29.2 + - - +
149A GLU* 3.1 39.7 + - - +
152A HIS* 5.8 11.0 - - + +
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Residues in contact with GLU 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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119A THR* 1.3 77.6 - - + +
121A GLY* 1.3 66.4 + - - +
123A PHE* 3.0 7.6 + - - +
124A GLU* 2.8 63.8 + - + +
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Residues in contact with GLY 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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119A THR* 3.6 4.8 - - - +
120A GLU* 1.3 76.7 - - - +
122A ALA* 1.3 53.3 + - - +
124A GLU* 4.9 2.5 - - - -
125A GLY* 2.6 36.3 + - - -
145A LEU* 3.7 6.4 - - - +
148A LYS* 3.8 26.8 + - - -
149A GLU* 3.5 11.0 - - - -
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Residues in contact with ALA 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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91A ALA* 4.6 7.4 - - + +
92A VAL* 4.7 9.0 - - + -
95A GLN* 4.3 14.6 - - + -
119A THR* 3.5 27.8 + - - +
120A GLU 3.2 0.4 - - - -
121A GLY* 1.3 75.1 - - - +
123A PHE* 1.3 65.7 + - - +
125A GLY* 3.6 0.2 - - - -
126A PHE* 2.9 30.8 + - + -
145A LEU* 3.7 13.5 - - + -
149A GLU* 3.0 17.1 + - + +
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Residues in contact with PHE 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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95A GLN* 3.6 25.7 + - - +
118A ILE* 3.8 20.4 - - + -
119A THR 2.7 23.6 + - - +
120A GLU* 3.0 11.9 + - - +
122A ALA* 1.3 73.6 - - - +
124A GLU* 1.3 80.3 + - - +
126A PHE* 3.2 2.9 + - - +
127A GLN* 2.9 54.6 + - + +
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Residues in contact with GLU 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 GLU* 2.8 47.9 + - + +
121A GLY* 4.2 2.9 - - - +
123A PHE* 1.3 89.6 - - - +
125A GLY* 1.3 68.3 + - - +
127A GLN* 3.1 18.1 + - - +
128A ALA* 3.0 21.8 + - - +
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Residues in contact with GLY 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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121A GLY 2.6 24.0 + - - -
122A ALA 3.6 1.1 - - - -
124A GLU* 1.3 74.1 - - - +
126A PHE* 1.3 56.1 + - - +
128A ALA* 3.3 7.0 + - - +
129A ILE* 3.0 28.6 + - - +
141A LEU* 5.2 1.2 - - - +
145A LEU* 3.8 19.5 - - - -
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Residues in contact with PHE 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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51A PHE* 4.0 14.6 - + - -
56A PHE* 5.6 0.4 - + - -
92A VAL* 3.7 43.3 - - + -
95A GLN* 3.6 20.6 - - + +
96A LEU* 3.5 28.3 - - + -
122A ALA 2.9 25.0 + - - +
123A PHE 3.8 3.1 - - - +
125A GLY* 1.3 71.7 - - - +
127A GLN* 1.3 61.8 + - - +
128A ALA 3.1 1.3 - - - -
129A ILE* 3.9 9.6 - - + -
130A PHE* 2.7 69.3 + + + -
142A LEU* 4.4 11.9 - - + -
145A LEU* 3.6 19.3 - - + -
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Residues in contact with GLN 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 PHE* 2.9 49.2 + - + +
124A GLU* 3.5 19.1 - - - +
126A PHE* 1.3 76.8 - - - +
128A ALA* 1.3 59.0 + - - +
130A PHE* 3.5 13.0 + - - +
131A THR* 3.0 35.0 + - - +
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Residues in contact with ALA 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 GLU 3.0 11.5 + - - +
125A GLY* 3.6 9.9 - - - +
127A GLN* 1.3 74.5 - - - +
129A ILE* 1.3 65.2 + - - +
131A THR* 3.0 17.9 + - - -
132A GLU* 3.1 14.0 + - - +
141A LEU* 4.2 16.9 - - + +
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Residues in contact with ILE 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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50A LEU* 4.1 7.0 - - + -
51A PHE* 3.8 28.0 - - + -
125A GLY 3.0 18.7 + - - +
126A PHE* 3.1 26.0 + - + +
128A ALA* 1.3 76.2 - - - +
130A PHE* 1.3 76.3 + - + +
132A GLU 3.0 12.0 + - - -
138A ARG* 3.2 29.3 - - + +
141A LEU* 3.5 26.0 - - + -
142A LEU* 3.9 28.3 - - + +
145A LEU* 4.2 10.1 - - + -
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Residues in contact with PHE 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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33A ILE* 3.7 24.5 - - + +
35A LEU* 5.4 2.3 - - - +
50A LEU* 4.0 35.2 - - + -
95A GLN* 3.8 20.6 - - - -
96A LEU* 4.6 8.1 - - + -
126A PHE* 2.7 58.5 + + + +
127A GLN* 4.2 14.4 - - - +
129A ILE* 1.3 73.8 - - + +
131A THR* 1.3 63.2 + - + +
132A GLU 3.4 0.9 + - - +
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Residues in contact with THR 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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127A GLN* 3.0 25.1 + - - +
128A ALA* 3.0 10.0 + - - -
129A ILE 3.1 0.2 - - - -
130A PHE* 1.3 83.4 - - + +
132A GLU* 1.3 57.0 + - - +
133A PRO* 3.2 13.2 - - - +
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Residues in contact with GLU 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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35A LEU* 4.5 2.9 - - - +
128A ALA 3.1 10.6 + - - +
129A ILE 3.0 10.3 + - - +
130A PHE 4.8 0.7 - - - +
131A THR* 1.3 76.8 - - - +
133A PRO* 1.3 67.4 - - - +
134A ASP* 2.9 43.2 + - - +
137A ALA* 3.6 23.1 - - + +
138A ARG* 2.8 35.4 + - + +
141A LEU* 4.1 11.2 - - + +
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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