Contacts of the helix formed by residues 19 - 29 (chain A) in PDB entry 3DC5
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 SER 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR 4.4 0.9 - - - -
15A GLU* 3.8 10.3 - - - -
18A ILE* 1.3 79.7 - - - +
20A HIS* 1.3 64.5 - - - +
21A GLU* 3.7 6.8 + - - +
22A ILE* 3.1 31.4 + - - +
23A MET* 3.0 22.2 + - - +
163A LEU* 5.1 1.9 - - - +
164A GLN* 2.9 23.2 - - - +
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Residues in contact with HIS 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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11A TYR* 3.4 43.7 - + + +
12A ALA* 3.9 18.3 + - + +
15A GLU* 2.9 22.6 + - - +
19A SER* 1.3 71.5 - - - +
21A GLU* 1.3 67.8 + - + +
23A MET* 3.3 2.4 + - - +
24A GLN* 2.9 50.4 + - - +
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Residues in contact with GLU 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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19A SER* 3.3 7.3 + - - +
20A HIS* 1.3 85.4 - - + +
22A ILE* 1.3 57.8 + - - +
24A GLN* 3.4 6.9 + - - +
25A LEU* 2.9 48.9 + - + +
163A LEU* 3.8 25.0 - - + +
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Residues in contact with ILE 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 ILE* 3.5 24.2 - - + -
19A SER* 3.1 24.3 + - - +
21A GLU* 1.3 72.6 - - - +
23A MET* 1.3 57.4 + - - +
24A GLN 3.2 0.2 + - - -
25A LEU* 3.3 2.2 + - - +
26A HIS* 2.7 46.9 + - + +
159A HIS 4.0 13.9 - - - +
160A ALA 3.5 14.4 - - - +
161A TYR* 3.9 20.9 - - - +
163A LEU* 3.9 23.3 - - + +
164A GLN* 3.8 31.2 - - + +
165A TYR* 5.3 1.3 - - + -
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Residues in contact with MET 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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7A LEU* 4.1 6.3 - - + -
9A PHE* 3.7 26.9 - - + -
11A TYR* 3.3 39.4 - - + +
14A LEU* 3.9 18.6 - - + -
18A ILE* 3.7 30.5 - - + +
19A SER 3.0 15.3 + - - +
20A HIS 3.8 0.9 - - - +
22A ILE* 1.3 76.2 - - - +
24A GLN* 1.3 58.5 + - - +
26A HIS* 3.8 4.1 - - - +
27A HIS* 2.9 34.3 + - - +
77A PHE* 6.2 0.7 - - - -
78A TRP* 3.6 35.2 - - + -
81A LEU* 4.8 1.8 - - + -
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Residues in contact with GLN 24 (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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11A TYR* 3.6 19.2 - - + -
20A HIS* 2.9 44.1 + - - +
21A GLU* 3.7 8.2 - - - +
23A MET* 1.3 77.2 - - - +
25A LEU* 1.3 61.3 + - + +
28A GLN* 2.9 65.6 + - - +
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Residues in contact with LEU 25 (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 GLU* 2.9 32.5 + - + +
22A ILE* 3.9 2.5 - - - +
24A GLN* 1.3 78.0 - - + +
26A HIS* 1.3 68.2 + - - +
29A LYS* 2.9 46.5 + - + +
30A HIS* 3.1 20.1 + - + +
163A LEU* 3.4 32.5 - - + -
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Residues in contact with HIS 26 (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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22A ILE* 2.7 30.1 + - + +
23A MET* 3.8 6.4 - - - +
25A LEU* 1.3 74.1 - - - +
27A HIS* 1.3 57.8 + - - +
30A HIS* 3.4 12.1 - - + +
31A HIS* 2.9 27.7 + - - +
74A HIS* 3.3 10.0 - + - -
77A PHE* 4.0 14.8 - + - -
78A TRP* 3.4 23.5 - + + -
155A ASP* 2.9 16.8 - - - -
159A HIS* 3.2 17.8 + + - +
160A ALA* 3.9 21.3 + - + -
195A MN 2.2 30.8 + - - -
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Residues in contact with HIS 27 (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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4A LEU* 3.6 29.5 - - + +
5A PRO 2.6 30.9 + - - -
6A ASP* 4.3 5.1 + - - -
7A LEU* 3.4 36.7 + - + +
11A TYR* 2.8 35.0 + + + -
23A MET 2.9 18.4 + - - +
26A HIS* 1.3 77.2 - - - +
28A GLN* 1.3 61.0 + - + +
31A HIS* 3.5 5.4 - - - +
32A ALA 3.3 23.7 + - - -
78A TRP* 3.8 18.5 + - + -
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Residues in contact with GLN 28 (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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4A LEU* 4.5 4.5 - - + -
11A TYR* 3.1 36.9 + - - +
24A GLN* 2.9 50.7 + - - +
27A HIS* 1.3 76.0 - - + +
29A LYS* 1.3 71.6 + - + +
32A ALA* 3.1 18.4 - - - +
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Residues in contact with LYS 29 (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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25A LEU* 2.9 39.2 + - + +
28A GLN* 1.3 91.1 - - + +
30A HIS* 1.3 65.5 + - + +
31A HIS 3.5 0.4 - - - -
32A ALA* 3.7 1.3 - - - +
33A THR* 2.8 38.1 + - - +
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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