Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 1X47
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 GLU 18 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A SER* 1.3 74.2 - - - +
19A VAL* 1.3 58.1 + - - +
20A CYS 2.9 0.3 + - - -
21A ILE* 2.9 17.1 + - - +
22A LEU* 2.6 35.5 + - - +
72A ASN* 3.5 31.9 + - - +
75A ALA* 4.1 2.5 - - + -
76A ARG* 4.1 23.4 - - + +
79A LEU* 3.8 16.9 - - + +
86A PHE* 3.0 34.1 - - - -
87A VAL* 5.8 0.7 - - - +
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Residues in contact with VAL 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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17A SER* 4.1 16.8 - - - -
18A GLU* 1.3 74.9 - - - +
20A CYS* 1.3 66.6 + - + +
22A LEU* 4.0 0.2 - - - +
23A HIS* 3.2 17.0 + - - +
36A TYR* 2.7 34.0 + - + +
71A LYS* 3.5 57.4 - - + +
72A ASN* 3.8 7.6 - - + +
75A ALA* 3.6 6.2 - - + +
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Residues in contact with CYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 5.2 3.6 - - - -
16A LYS* 4.2 14.1 - - + -
17A SER 2.7 28.1 + - - +
19A VAL* 1.3 76.9 - - + +
21A ILE* 1.3 68.3 + - - +
23A HIS* 2.7 19.7 + - - +
24A GLU* 2.7 19.2 + - - +
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 4.2 28.9 - - + +
17A SER 2.7 25.7 + - - +
18A GLU* 3.5 22.4 - - - +
20A CYS* 1.3 71.5 - - - +
22A LEU* 1.3 66.3 + - - +
24A GLU* 2.7 22.2 + - + +
25A TYR* 2.9 15.8 + - + +
79A LEU* 4.2 18.6 - - + -
86A PHE* 4.6 11.9 - - + -
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Residues in contact with LEU 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 2.6 19.9 + - - +
19A VAL 4.0 0.2 - - - +
21A ILE* 1.3 73.7 - - - +
23A HIS* 1.3 65.1 + - - +
25A TYR* 3.5 1.6 + - - +
26A MET* 2.8 44.5 + - + +
34A PRO* 4.0 16.2 - - + -
36A TYR* 3.7 17.5 - - - +
52A VAL* 4.5 9.4 - - + -
75A ALA* 3.8 18.4 - - + +
78A THR* 3.3 31.0 - - + -
79A LEU* 3.8 34.5 - - + -
82A LEU* 4.1 3.8 - - + -
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Residues in contact with HIS 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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9A PHE* 4.7 13.4 - + - -
19A VAL 3.2 11.8 + - - +
20A CYS* 2.7 20.5 + - - +
22A LEU* 1.3 83.0 - - + +
24A GLU* 1.3 51.2 + - - +
26A MET* 2.9 4.0 + - - +
27A GLN* 2.5 61.9 + - + +
33A ARG* 3.9 35.2 + - + +
34A PRO* 3.4 34.5 - - + +
36A TYR* 4.8 8.3 - - - +
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Residues in contact with GLU 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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20A CYS* 2.7 19.8 + - - +
21A ILE* 2.7 15.9 + - + +
23A HIS* 1.3 71.9 - - - +
25A TYR* 1.3 53.2 + - - +
27A GLN* 3.3 6.0 - - - +
28A ARG* 2.5 58.6 + - - +
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Residues in contact with TYR 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 ILE* 2.9 12.5 + - + +
22A LEU 3.8 7.0 - - - +
24A GLU* 1.3 76.4 - - - +
26A MET* 1.3 61.2 + - - +
28A ARG* 3.8 20.6 - - - +
29A VAL* 2.5 69.2 + - + +
30A LEU* 4.9 3.8 - - + -
79A LEU* 4.8 8.7 - - + -
82A LEU* 3.5 53.4 - - + +
83A ILE* 4.1 24.9 - - + -
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Residues in contact with MET 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 LEU* 2.8 40.0 + - + +
23A HIS* 3.1 7.9 - - - +
25A TYR* 1.3 79.5 - - + +
27A GLN* 1.3 51.2 + - - +
28A ARG 3.0 4.2 + - - -
30A LEU* 2.6 36.7 + - + +
31A LYS 2.5 30.7 + - - -
32A VAL* 3.3 44.2 - - + +
34A PRO* 3.4 30.5 - - + -
54A ILE* 3.5 29.6 - - + -
78A THR* 4.7 0.4 - - - -
82A LEU* 4.7 1.3 - - + -
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Residues in contact with GLN 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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23A HIS* 2.5 44.4 + - + +
24A GLU* 4.0 4.5 - - - +
26A MET* 1.3 72.7 - - - +
28A ARG* 1.3 55.4 + - - +
31A LYS* 3.4 23.2 - - + +
32A VAL 3.7 18.8 + - - +
33A ARG* 4.2 25.8 + - - +
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Residues in contact with ARG 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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24A GLU* 2.5 40.8 + - - +
25A TYR* 3.6 15.0 - - - +
27A GLN* 1.3 77.0 - - - +
29A VAL* 1.3 77.3 + - + +
31A LYS* 4.4 8.8 - - - +
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Residues in contact with VAL 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 TYR* 2.5 58.7 + - + +
28A ARG* 1.3 95.9 - - + +
30A LEU* 1.3 70.4 + - + +
31A LYS* 3.2 5.2 + - - +
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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