Contacts of the helix formed by residues 120 - 132 (chain A) in PDB entry 6U81
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 GLY 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLY 3.4 17.9 - - - -
20A ARG* 5.4 0.4 - - - -
116A ASP* 5.1 0.8 + - - -
118A PHE 3.5 3.0 + - - -
119A PRO* 1.3 75.2 - - - +
121A ILE* 1.3 67.3 + - - -
122A ALA* 3.1 4.3 - - - -
123A ALA* 3.2 7.2 + - - +
124A ARG* 2.9 27.9 + - - +
201A EDO 6.1 0.2 - - - -
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Residues in contact with ILE 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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19A GLY 3.0 17.3 + - - +
20A ARG* 3.5 17.6 - - - +
21A ARG* 3.7 52.0 - - + +
22A ARG 5.2 0.7 - - - +
120A GLY* 1.3 72.9 - - - -
122A ALA* 1.3 67.6 + - + +
124A ARG* 3.7 16.7 - - - +
125A GLU* 3.0 55.4 + - + +
135A GLU* 3.8 5.4 - - + +
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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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19A GLY 4.5 0.6 + - - +
120A GLY* 3.1 1.5 - - - -
121A ILE* 1.3 86.9 - - + +
123A ALA* 1.3 63.7 + - - +
125A GLU* 3.4 6.1 + - - +
126A GLU* 3.3 20.1 + - - +
129A ARG* 5.2 1.0 + - - -
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Residues in contact with ALA 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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116A ASP* 5.8 1.6 - - + +
119A PRO* 3.5 25.6 - - + -
120A GLY* 3.2 9.8 + - - +
122A ALA* 1.3 78.8 - - - +
124A ARG* 1.3 63.8 + - - +
126A GLU* 3.3 7.8 + - - +
127A LEU* 3.2 27.7 + - + +
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Residues in contact with ARG 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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119A PRO* 2.9 43.7 + - + -
120A GLY* 2.9 22.3 + - - +
121A ILE* 3.7 18.6 - - - +
123A ALA* 1.3 75.6 - - - +
125A GLU* 1.3 62.4 + - - +
127A LEU* 3.1 12.6 + - - +
128A ALA* 3.1 21.3 + - - +
135A GLU* 2.9 35.1 + - + +
138A ILE* 4.0 12.4 - - + +
139A GLN* 3.5 46.3 - - - +
142A PHE* 5.5 0.7 - - - -
7B T 2.9 39.0 + - - -
8B C 5.0 4.6 + - - -
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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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21A ARG* 4.8 6.4 + - - -
121A ILE* 3.0 47.0 + - + +
122A ALA* 4.0 5.8 - - - +
124A ARG* 1.3 77.9 - - - +
126A GLU* 1.3 59.1 + - - +
128A ALA* 3.6 9.3 + - - +
129A ARG* 3.4 35.1 + - - +
135A GLU* 4.2 11.7 - - + -
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Residues in contact with GLU 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 ALA 3.3 10.3 + - - +
123A ALA* 3.3 9.4 + - - +
124A ARG 3.2 0.8 - - - -
125A GLU* 1.3 73.9 - - - +
127A LEU* 1.3 61.8 + - + +
128A ALA 3.1 1.1 - - - -
129A ARG* 3.0 28.7 + - + +
130A GLU* 2.6 53.6 + - + +
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Residues in contact with LEU 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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108A LEU* 4.5 14.4 - - + +
109A LEU* 4.1 9.0 - - + -
112A ALA* 3.8 27.8 - - + -
119A PRO* 5.2 3.8 - - + -
123A ALA* 3.2 17.4 + - + +
124A ARG* 3.1 11.5 + - - +
126A GLU* 1.3 76.6 - - + +
128A ALA* 1.3 52.7 + - - +
130A GLU* 3.2 19.0 + - - +
131A THR* 2.6 43.7 + - + +
138A ILE* 3.5 19.7 - - + -
142A PHE* 3.8 30.5 - - + -
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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 ARG 3.1 11.5 + - - +
125A GLU* 3.7 10.8 - - - +
126A GLU 3.1 0.2 - - - -
127A LEU* 1.3 76.4 - - - +
129A ARG* 1.3 59.1 + - + +
131A THR* 3.8 0.7 - - - -
132A GLY* 3.1 24.7 + - - -
133A LEU 3.1 26.2 - - - +
135A GLU* 3.9 17.9 - - + +
138A ILE* 3.3 7.5 - - + +
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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 ALA 5.2 1.4 + - - -
125A GLU* 3.4 28.0 + - - +
126A GLU* 3.0 39.9 + - + +
128A ALA* 1.3 78.3 - - - +
130A GLU* 1.3 60.2 + - + +
131A THR 3.1 9.5 + - - -
132A GLY* 3.7 4.9 + - - -
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Residues in contact with GLU 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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108A LEU* 3.1 31.9 - - + +
126A GLU* 2.6 51.5 + - + +
127A LEU* 3.2 20.8 + - - +
129A ARG* 1.3 74.8 - - + +
131A THR* 1.3 58.6 + - + +
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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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105A GLN* 2.8 41.6 + - - +
108A LEU* 3.7 24.7 - - + -
109A LEU* 5.1 5.4 - - + -
127A LEU* 2.6 31.4 + - + +
129A ARG 4.3 0.4 - - - -
130A GLU* 1.3 83.1 - - + +
132A GLY* 1.3 60.0 + - - +
133A LEU* 3.1 37.3 + - + +
138A ILE* 3.8 0.9 - - - +
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Residues in contact with GLY 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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105A GLN* 4.5 2.9 - - - -
128A ALA 3.1 15.3 + - - -
129A ARG 3.7 4.9 + - - -
131A THR* 1.3 78.0 - - - +
133A LEU* 1.3 61.6 + - - +
134A PRO* 3.9 3.8 - - - +
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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