Contacts of the helix formed by residues 16 - 23 (chain A) in PDB entry 2DB9
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 LEU 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.5 12.1 - - - +
15A SER* 1.3 88.3 - - - +
17A PRO* 1.4 75.9 - - + +
18A GLU* 3.0 22.5 + - + +
19A GLU* 3.4 42.0 + - + +
20A LEU 3.9 0.3 + - - -
113A PHE* 3.2 17.7 - - - -
114A MET* 6.0 0.2 - - - -
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Residues in contact with PRO 17 (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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16A LEU* 1.4 91.0 - - + +
18A GLU* 1.3 64.6 + - + +
20A LEU* 3.7 4.3 + - - +
21A ASN* 3.1 32.0 + - - +
108A PHE* 3.7 16.7 - - + +
109A THR 4.6 0.2 - - - +
110A GLU* 4.2 22.0 - - + -
113A PHE* 3.2 45.3 - - + -
114A MET* 5.3 3.8 - - + -
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Residues in contact with GLU 18 (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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16A LEU* 3.0 25.9 - - + +
17A PRO* 1.3 80.9 - - + +
19A GLU* 1.3 60.9 + - + +
20A LEU 3.0 1.8 - - - -
21A ASN* 2.5 36.7 + - - +
22A ARG* 2.8 17.5 + - + +
107A GLU* 5.0 7.3 - - - +
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Residues in contact with GLU 19 (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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14A VAL* 3.8 10.1 - - + -
16A LEU* 3.4 26.4 + - + +
18A GLU* 1.3 76.7 - - + +
20A LEU* 1.3 62.4 + - - +
22A ARG* 3.1 43.2 + - - +
23A VAL 3.5 0.9 + - - -
130A LEU* 3.2 39.8 - - + +
133A ILE* 2.8 44.0 - - + +
134A ASN* 5.1 1.6 + - - +
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Residues in contact with LEU 20 (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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14A VAL* 3.6 10.4 - - + +
17A PRO 3.7 9.7 + - - +
18A GLU 3.0 0.4 - - - -
19A GLU* 1.3 78.4 - - - +
21A ASN* 1.3 62.4 + - - +
23A VAL* 3.3 6.4 + - - +
24A ARG* 3.2 19.1 + - - +
47A PHE* 3.3 32.8 - - + -
63A VAL* 3.8 14.6 - - + -
108A PHE* 3.4 15.1 - - + -
113A PHE* 3.6 17.3 - - + -
116A TRP* 3.1 39.5 - - + -
128A PRO* 3.4 25.8 - - + -
133A ILE* 3.8 3.1 - - + -
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Residues in contact with ASN 21 (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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17A PRO* 3.1 18.6 + - - +
18A GLU* 2.5 25.5 + - - +
20A LEU* 1.3 70.9 - - - +
22A ARG* 1.3 62.5 + - - +
24A ARG* 3.1 27.5 + - - +
107A GLU* 3.1 38.6 + - - +
108A PHE* 2.6 47.2 + - - +
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Residues in contact with ARG 22 (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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18A GLU* 2.8 20.3 + - + +
19A GLU* 3.1 51.1 + - - +
21A ASN* 1.3 80.8 - - - +
23A VAL* 1.3 50.8 + - + +
24A ARG 3.2 2.1 + - - +
29A LYS* 5.6 3.6 + - - -
133A ILE* 4.1 6.3 - - + -
134A ASN* 4.8 16.4 - - - +
137A GLU* 2.4 38.4 - - + +
141A LYS* 5.7 4.9 - - - +
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Residues in contact with VAL 23 (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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20A LEU 3.4 9.6 - - - +
21A ASN 3.2 0.2 - - - -
22A ARG* 1.3 74.3 - - - +
24A ARG* 1.3 58.1 + - - +
25A LEU 3.3 2.8 + - - -
46A CYS* 3.6 5.4 - - - +
47A PHE* 3.0 40.9 + - + +
133A ILE* 2.8 68.2 - - + +
136A LYS* 3.9 15.3 - - + -
137A GLU* 3.2 25.8 - - + +
140A ILE* 4.6 4.3 - - + -
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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