Contacts of the helix formed by residues 120 - 132 (chain A) in PDB entry 2DNO
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 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 3.8 16.4 - - - +
118A PHE* 3.2 6.2 - - - +
119A GLN* 1.3 95.0 - - + +
121A HIS* 1.3 65.1 + - - +
122A ALA* 4.3 6.8 + - - +
123A GLU* 3.2 29.6 + - - +
124A ALA* 3.1 15.9 + - - +
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Residues in contact with HIS 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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66A SER* 5.1 10.9 + - - -
68A GLY 4.2 9.9 - - - -
69A GLU* 3.7 32.3 + - - +
70A ASP 4.3 11.5 + - - -
71A ARG* 3.8 17.8 - - + +
120A THR* 1.3 70.8 - - - +
122A ALA* 1.3 66.4 + - - +
124A ALA* 2.5 37.7 + - - +
125A GLN* 3.1 16.8 + - + +
148A PHE* 3.8 32.1 - + - -
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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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120A THR* 3.5 7.5 - - - +
121A HIS* 1.3 87.0 - - - +
123A GLU* 1.3 65.1 + - + +
125A GLN* 3.7 4.1 + - - +
126A ALA* 3.3 19.6 + - - +
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Residues in contact with GLU 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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94A PHE 3.0 23.6 - - - +
95A GLY* 3.2 23.3 + - - -
96A THR 4.3 4.3 + - - +
118A PHE* 3.9 16.2 - - + -
119A GLN* 5.4 2.5 - - + -
120A THR* 3.2 27.7 + - - +
121A HIS 2.7 3.8 + - - -
122A ALA* 1.3 76.5 - - + +
124A ALA* 1.3 65.5 + - - +
126A ALA* 3.2 16.6 - - - +
127A ALA 3.4 1.7 + - - -
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Residues in contact with ALA 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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71A ARG* 3.6 24.2 - - - +
73A LEU* 3.7 21.0 - - + +
118A PHE* 3.7 16.6 - - + -
120A THR 3.1 11.5 + - - +
121A HIS* 2.5 21.1 + - - +
123A GLU* 1.3 73.7 - - - +
125A GLN* 1.3 63.4 + - - +
127A ALA* 3.3 12.1 + - - +
128A ILE* 3.5 10.0 + - - +
148A PHE* 4.4 6.1 - - + -
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Residues in contact with GLN 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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63A SER* 4.9 10.2 + - - -
64A SER* 5.7 5.0 - - - -
65A GLY 5.9 2.5 - - - +
66A SER* 4.1 19.7 + - - +
121A HIS* 3.1 15.8 + - + +
122A ALA* 4.0 7.2 - - - +
124A ALA* 1.3 78.5 - - - +
126A ALA* 1.3 67.2 + - - +
128A ILE* 3.1 12.6 + - - +
129A ASN* 2.8 53.1 + - - +
148A PHE* 4.0 26.1 - - + -
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Residues in contact with ALA 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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94A PHE* 4.0 19.3 - - + +
122A ALA 3.3 12.1 + - - +
123A GLU* 3.2 19.0 + - - +
124A ALA 3.2 0.2 - - - -
125A GLN* 1.3 83.3 + - - +
127A ALA* 1.3 67.1 + - - +
129A ASN* 3.2 16.4 - - - +
130A THR* 3.5 6.4 + - - -
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Residues in contact with ALA 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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73A LEU* 5.0 2.5 - - + -
91A PHE* 4.8 2.2 - - + -
94A PHE* 3.6 29.4 - - + +
118A PHE* 3.8 19.1 - - + -
123A GLU 3.4 1.2 + - - -
124A ALA 3.3 9.7 + - - +
125A GLN 3.2 0.4 - - - -
126A ALA* 1.3 77.7 - - - +
128A ILE* 1.3 58.9 + - + +
130A THR* 2.7 5.0 + - - -
131A LEU* 2.6 52.5 + - + -
146A VAL* 5.3 0.9 - - + -
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Residues in contact with ILE 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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73A LEU* 3.5 31.9 - - + -
124A ALA 3.5 7.8 + - - +
125A GLN* 3.1 12.9 + - - +
127A ALA* 1.3 77.7 - - - +
129A ASN* 1.3 67.7 + - - +
130A THR 2.6 2.6 + - - -
132A HIS* 2.6 40.2 + - + +
146A VAL* 3.3 41.1 - - + +
147A LYS* 4.1 2.0 - - - -
148A PHE* 3.6 40.2 - - + +
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Residues in contact with ASN 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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63A SER* 2.9 30.9 + - - -
125A GLN* 2.8 33.8 + - - +
126A ALA* 3.2 13.5 - - - +
128A ILE* 1.3 73.7 - - - +
130A THR* 1.3 69.3 + - - +
132A HIS* 4.7 3.4 - - - +
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Residues in contact with THR 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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94A PHE* 4.3 23.8 - - + -
126A ALA 3.5 4.5 + - - -
127A ALA 2.7 8.8 + - - -
128A ILE 2.6 2.4 + - - -
129A ASN* 1.3 86.6 + - - +
131A LEU* 1.3 71.8 + - + +
132A HIS 2.6 16.8 + - - +
134A SER* 3.2 19.1 - - - +
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Residues in contact with LEU 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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90A MET* 4.0 13.2 - - + +
91A PHE* 3.6 45.1 - - + -
94A PHE* 3.3 42.2 - - + -
127A ALA* 2.6 23.4 + - + +
130A THR* 1.3 75.4 - - + +
132A HIS* 1.3 62.1 + - - +
133A SER 3.0 1.7 + - - -
134A SER* 2.9 24.9 + - - +
135A ARG* 5.3 6.3 - - - +
144A LEU* 3.2 25.3 - - + +
146A VAL* 3.8 12.3 - - + -
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 2.6 30.9 + - + +
129A ASN* 4.7 3.4 - - - +
130A THR 2.6 15.8 + - - +
131A LEU* 1.3 70.9 - - - +
133A SER* 1.3 79.5 + - - +
134A SER* 3.9 0.2 - - - -
144A LEU 3.7 3.1 - - - -
145A VAL* 4.8 11.2 - - + -
146A VAL* 2.7 40.4 + - - +
147A LYS* 4.9 6.3 - - + -
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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