Contacts of the helix formed by residues 17 - 29 (chain A) in PDB entry 4CCZ
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A LEU* 1.3 65.3 + - - +
19A ARG* 3.2 14.1 - - - -
20A ASP* 3.3 25.8 + - - +
21A GLU* 3.6 6.2 + - - +
219A PRO 5.9 2.9 - - - -
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Residues in contact with LEU 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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17A THR* 1.3 70.8 - - - +
19A ARG* 1.3 54.4 + - - +
20A ASP 3.3 0.2 - - - -
21A GLU* 3.5 7.5 + - - +
22A ILE* 2.8 36.8 + - - +
141A PHE* 5.5 6.8 - - + -
189A ASP* 4.4 29.6 - - + +
220A ARG* 6.0 1.8 - - + -
221A PRO* 4.4 8.5 - - + -
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Residues in contact with ARG 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 THR* 3.2 9.3 - - - -
18A LEU* 1.3 76.3 - - - +
20A ASP* 1.3 57.3 + - - +
22A ILE* 3.6 5.9 - - - +
23A ASN* 2.8 38.2 + - - +
221A PRO* 4.6 14.6 - - + +
254A LEU* 4.6 15.1 - - + +
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Residues in contact with ASP 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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17A THR* 3.3 20.5 + - - +
18A LEU 3.3 0.6 - - - -
19A ARG* 1.3 78.4 - - - +
21A GLU* 1.3 58.2 + - - +
23A ASN* 3.8 3.7 - - - +
24A ALA* 2.8 32.3 + - - +
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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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17A THR 3.6 7.0 + - - +
18A LEU* 3.5 10.4 + - - +
19A ARG 3.4 0.2 - - - -
20A ASP* 1.3 79.0 - - - +
22A ILE* 1.3 64.6 + - - +
24A ALA* 3.6 7.2 - - - +
25A ILE* 3.3 20.6 + - - +
31A MET* 4.8 0.2 - - - +
139A LYS* 5.7 5.8 - - + +
141A PHE* 5.0 16.5 - - + -
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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 LEU 2.8 23.2 + - - +
19A ARG* 3.6 4.7 - - - +
21A GLU* 1.3 69.9 - - - +
23A ASN* 1.3 64.8 + - - +
24A ALA 3.2 0.3 + - - -
25A ILE 3.3 2.4 + - - -
26A LEU* 3.1 25.4 + - + +
31A MET* 3.3 19.8 - - + +
141A PHE* 5.3 8.5 - - + -
221A PRO* 5.1 4.9 - - + -
223A PHE* 5.9 4.3 - - + -
254A LEU* 3.9 19.7 - - + -
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Residues in contact with ASN 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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19A ARG 2.8 20.4 + - - +
20A ASP* 4.0 3.6 - - - +
22A ILE* 1.3 73.6 - - - +
24A ALA* 1.3 56.6 + - - +
26A LEU* 3.3 4.1 + - - -
27A GLN* 2.9 29.5 + - - +
254A LEU* 4.6 8.9 - - + +
281A TYR* 3.4 30.1 + - + +
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Residues in contact with ALA 24 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASP 2.8 19.1 + - - +
21A GLU* 3.6 10.8 - - - +
22A ILE 3.2 0.2 - - - -
23A ASN* 1.3 78.5 - - - +
25A ILE* 1.3 64.1 + - - +
27A GLN* 3.3 12.7 + - - +
28A LYS* 3.5 11.1 + - - +
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Residues in contact with ILE 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 3.3 9.4 + - - +
22A ILE 3.3 2.2 + - - -
24A ALA* 1.3 77.9 - - - +
26A LEU* 1.3 52.6 + - - +
28A LYS* 3.2 5.7 + - - +
29A ARG* 2.7 39.9 + - + +
31A MET* 3.3 26.0 - - + -
141A PHE* 5.7 3.6 - - + -
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Residues in contact with LEU 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* 3.1 25.4 + - + +
23A ASN* 3.7 3.1 - - - +
25A ILE* 1.3 74.3 - - - +
27A GLN* 1.3 64.6 + - - +
28A LYS 3.3 0.5 + - - -
29A ARG 3.4 10.7 - - - +
30A ILE* 5.2 0.2 - - - -
31A MET* 3.6 33.4 - - + +
223A PHE* 5.3 4.7 - - + -
254A LEU* 4.8 8.5 - - + -
255A CYS* 5.8 0.9 - - + -
281A TYR* 3.7 51.1 - - + -
318A ASN* 4.0 13.1 - - + +
319A ILE* 3.7 29.6 - - + -
343A PRO* 3.6 17.2 - - - +
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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 ASN 2.9 17.0 + - - +
24A ALA* 3.3 7.6 + - - +
26A LEU* 1.3 75.5 - - - +
28A LYS* 1.3 58.2 + - - +
281A TYR* 4.3 10.7 + - - +
343A PRO* 4.3 8.7 - - - +
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Residues in contact with LYS 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 ALA 3.5 8.2 + - - +
25A ILE* 3.2 8.8 + - - +
26A LEU 3.1 0.4 - - - -
27A GLN* 1.3 80.5 - - - +
29A ARG* 1.3 62.1 + - + +
341A CYS 5.1 0.7 - - - +
343A PRO* 3.5 16.1 - - - +
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Residues in contact with ARG 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 ILE* 2.7 25.6 + - + +
26A LEU* 3.4 12.5 + - - +
28A LYS* 1.3 77.4 - - + +
30A ILE* 1.3 64.9 + - - +
31A MET* 3.4 5.8 + - + +
339A LYS 5.5 7.0 - - - +
341A CYS 5.3 1.8 - - - -
343A PRO* 3.8 7.4 - - - -
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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