Contacts of the helix formed by residues 23 - 35 (chain A) in PDB entry 1C06
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 ASN 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.3 14.0 - - - +
21A GLY 3.5 5.3 + - - -
22A VAL* 1.3 77.8 - - - +
24A GLU* 1.3 57.9 + - - +
25A ARG* 3.2 27.5 + - - +
26A GLN* 3.0 17.3 + - + +
27A PHE* 2.7 32.4 + - - +
52A ARG* 5.1 2.0 - - - +
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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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13A LYS* 5.7 8.5 + - - +
17A ARG* 3.0 26.5 - - - +
23A ASN* 1.3 75.3 - - - +
25A ARG* 1.3 71.0 + - - +
27A PHE* 2.7 18.8 + - + -
28A ARG* 2.8 26.5 + - + +
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Residues in contact with ARG 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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23A ASN* 3.2 15.8 + - + +
24A GLU* 1.3 82.2 + - - +
26A GLN* 1.3 63.7 + - + +
28A ARG* 4.6 28.2 - - - +
29A LYS* 2.9 61.3 + - - +
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Residues in contact with GLN 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 VAL* 3.6 18.4 - - + +
23A ASN* 3.0 21.2 + - + +
25A ARG* 1.3 85.2 + - + +
27A PHE* 1.3 61.4 + - - +
29A LYS* 4.6 5.8 - - - +
30A THR* 2.4 44.7 + - - +
52A ARG* 4.7 13.1 + - - +
89A SER* 2.6 51.1 + - - +
91A ARG* 4.5 13.5 + - - +
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Residues in contact with PHE 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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13A LYS* 4.2 32.3 - - + -
16A LEU* 4.1 14.6 - - + -
17A ARG* 3.8 46.2 - - + +
22A VAL* 4.3 14.6 - - + -
23A ASN 2.7 15.5 + - - +
24A GLU* 2.7 18.0 + - + +
26A GLN* 1.3 73.2 - - - +
28A ARG* 1.3 62.7 + - - +
31A PHE* 3.2 18.7 + + - +
45A PHE* 3.0 48.0 - + - -
49A LEU* 5.2 1.1 - - + -
153A ILE* 4.5 11.7 - - + -
157A TYR* 4.1 15.7 - - - -
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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* 2.8 27.2 + - + +
25A ARG* 4.6 23.3 - - - +
27A PHE* 1.3 74.4 - - - +
29A LYS* 1.3 66.4 + - - +
31A PHE* 3.1 15.2 + - - +
32A GLU* 3.2 16.6 + - + +
157A TYR* 4.0 30.2 - - + +
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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 ARG* 2.9 53.7 + - - +
26A GLN* 4.5 6.7 - - - +
28A ARG* 1.3 82.3 - - - +
30A THR* 1.3 65.0 + - - +
31A PHE 2.8 1.2 + - - -
32A GLU* 3.1 6.6 + - + +
33A GLU* 2.8 36.9 + - + +
91A ARG* 4.6 6.7 - - - +
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Residues in contact with THR 30 (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 VAL* 5.2 1.6 - - - +
26A GLN* 2.4 33.7 + - - +
27A PHE 4.0 1.6 - - - -
29A LYS* 1.3 78.3 - - - +
31A PHE* 1.3 62.1 + - - +
33A GLU* 3.3 1.5 + - - +
34A ALA* 2.9 17.8 + - - +
45A PHE* 4.1 16.4 - - + -
48A LEU* 3.2 41.1 - - + +
49A LEU* 4.5 9.3 - - + +
91A ARG* 3.1 27.0 + - - +
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Residues in contact with PHE 31 (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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27A PHE* 3.2 14.6 + + - +
28A ARG 3.1 11.4 + - - +
29A LYS 2.8 1.6 + - - -
30A THR* 1.3 72.4 - - - +
32A GLU* 1.3 71.1 + - + +
33A GLU 2.8 3.1 - - - -
34A ALA 2.5 21.8 + - - -
41A HIS* 2.5 69.9 + + + -
42A GLY* 5.2 1.6 - - - -
45A PHE* 3.9 29.8 - + + -
150A GLU* 5.7 0.9 - - + -
153A ILE* 4.9 7.9 - - + -
154A VAL* 4.4 22.0 - - + -
157A TYR* 3.6 49.6 - + + +
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Residues in contact with GLU 32 (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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28A ARG* 3.2 18.6 + - + +
29A LYS* 3.1 8.8 + - + +
31A PHE* 1.3 97.1 - - + +
33A GLU* 1.3 61.5 + - + +
34A ALA 3.4 0.2 + - - -
35A GLY* 3.5 7.5 + - - -
36A LYS* 3.3 16.4 - - - +
41A HIS* 4.1 5.6 - - - -
157A TYR* 5.0 11.2 - - + +
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Residues in contact with GLU 33 (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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29A LYS* 2.8 30.2 + - + +
30A THR* 3.5 6.1 - - - +
32A GLU* 1.3 79.5 - - + +
34A ALA* 1.3 59.0 + - - +
35A GLY 3.4 0.2 - - - -
36A LYS* 3.3 31.8 - - - +
37A MET* 4.6 2.3 - - - +
48A LEU* 4.2 3.6 - - - +
91A ARG* 3.8 25.6 + - - +
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Residues in contact with ALA 34 (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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30A THR 2.9 5.1 + - - +
31A PHE 2.5 17.0 + - - +
33A GLU* 1.3 71.5 - - - +
35A GLY* 1.3 51.6 + - - -
36A LYS 2.6 16.7 + - - -
37A MET* 3.3 12.1 + - - +
41A HIS* 3.7 7.9 - - + +
44A ASN* 3.3 46.2 + - + -
45A PHE* 3.9 3.4 - - - +
48A LEU* 3.3 25.6 - - + -
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Residues in contact with GLY 35 (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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31A PHE 3.2 0.6 + - - -
32A GLU 3.5 6.0 + - - -
33A GLU 3.4 1.0 - - - -
34A ALA* 1.3 75.6 - - - +
36A LYS* 1.3 66.4 + - - +
37A MET 4.1 5.0 - - - +
41A HIS* 2.9 36.8 - - - -
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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