Contacts of the helix formed by residues 17 - 27 (chain A) in PDB entry 1ICZ
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A HIS* 2.7 49.5 + - - +
15A TYR 4.9 0.4 - - - -
16A VAL* 1.3 65.6 - - + +
18A SER* 1.3 62.5 + - - +
19A PHE 3.0 3.7 + - - -
20A ARG* 3.1 22.6 + - + +
21A ARG* 2.8 40.2 + - + +
71A LEU* 3.6 18.9 - - - +
249A ASN* 3.0 43.8 + - - +
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Residues in contact with SER 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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9A PHE* 4.2 4.3 - - - -
12A HIS 4.1 1.4 + - - -
13A GLY* 3.5 5.5 - - - -
14A LYS 2.9 21.3 + - - -
15A TYR 3.7 4.7 + - - -
16A VAL 2.7 9.6 + - - -
17A GLU* 1.3 68.4 - - - +
19A PHE* 1.3 55.7 + - - -
21A ARG* 2.9 8.3 + - - +
22A PHE* 2.8 45.2 + - - -
65A GLU* 2.5 46.2 + - - -
70A ILE* 5.7 0.2 - - - -
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Residues in contact with PHE 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 GLU 3.0 3.4 + - - -
18A SER* 1.3 74.8 - - - +
20A ARG* 1.3 87.4 + - + +
23A LEU* 2.9 56.9 + - + +
32A MET* 3.8 19.3 - - + -
37A ASP* 4.3 4.9 - - + -
65A GLU 3.1 15.5 + - - +
66A ILE 3.4 12.0 - - - +
67A ASP 3.2 22.4 - - - -
68A LEU 3.9 14.8 - - - +
69A GLN* 3.2 44.4 - - + -
70A ILE* 4.6 4.1 - - + +
71A LEU* 3.8 26.9 - - + +
72A SER* 4.7 0.2 - - - -
141A MET* 5.1 1.1 - - + -
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Residues in contact with ARG 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 GLU* 3.1 9.7 + - + +
19A PHE* 1.3 94.9 - - + +
21A ARG* 1.3 56.9 + - - +
23A LEU* 3.8 3.1 - - - +
24A ASN* 2.9 28.5 + - - +
32A MET 3.8 14.3 - - - +
33A GLN* 3.1 34.9 + - + +
34A GLU* 5.4 1.3 - - - +
37A ASP* 2.8 27.5 + - - +
38A LYS* 5.6 0.6 - - - +
41A PRO* 3.8 13.1 - - - +
71A LEU* 3.4 17.1 - - - +
72A SER* 3.0 16.3 + - - +
246A GLU 4.7 4.2 + - - -
248A CYS 2.8 28.1 + - - -
249A ASN* 2.9 39.5 + - - +
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Residues in contact with ARG 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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8A LEU 5.9 0.2 - - - -
11A ASP* 2.7 49.3 + - - -
12A HIS* 3.1 38.9 + - - +
13A GLY* 5.3 0.2 - - - -
17A GLU* 2.8 37.0 + - + +
18A SER* 2.9 12.8 + - - +
20A ARG* 1.3 76.5 - - - +
22A PHE* 1.3 58.5 + - + +
24A ASN* 3.3 8.5 - - + +
25A HIS* 2.9 54.0 + - + +
33A GLN* 6.0 1.1 - - - -
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Residues in contact with PHE 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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5A MET* 4.1 23.3 - - + -
8A LEU* 4.2 23.1 - - + -
9A PHE* 3.6 52.3 - + - -
13A GLY* 6.1 1.1 - - - -
18A SER* 2.8 31.4 + - - +
21A ARG* 1.3 69.3 - - + +
23A LEU* 1.3 57.1 + - - +
25A HIS* 3.0 14.8 + + + +
26A SER* 2.9 36.7 + - - +
65A GLU 4.5 0.7 - - - -
66A ILE* 3.1 44.9 - - + +
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Residues in contact with LEU 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 PHE* 2.9 51.6 + - + +
20A ARG 3.8 3.8 - - - +
22A PHE* 1.3 71.0 - - - +
24A ASN* 1.3 51.9 + - - +
26A SER* 3.7 2.9 - - - -
27A THR* 2.8 41.4 + - - +
31A CYS* 4.9 1.1 - - - -
32A MET* 3.9 30.7 - - + +
66A ILE 4.3 4.3 - - - +
67A ASP* 4.0 22.9 - - + +
142A ILE* 6.2 0.7 - - - -
143A GLN* 4.0 36.8 - - + +
144A MET* 4.6 17.9 - - + -
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Residues in contact with ASN 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 ARG 2.9 21.4 + - - +
21A ARG* 3.3 10.1 - - - +
22A PHE 3.3 0.2 - - - -
23A LEU* 1.3 74.0 - - - +
25A HIS* 1.3 89.3 + - - +
27A THR 3.6 13.2 + - - +
28A GLU* 4.0 2.6 + - - -
31A CYS* 3.5 26.7 - - - -
33A GLN* 2.9 26.7 + - - +
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Residues in contact with HIS 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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1A MET* 4.8 23.0 - - + +
8A LEU* 5.0 14.1 + - + +
11A ASP* 2.7 28.6 + - - -
21A ARG* 2.9 45.8 + - + +
22A PHE* 3.0 15.5 + + + +
24A ASN* 1.3 99.7 + - - +
26A SER* 1.3 60.4 + - - +
28A GLU 5.5 0.2 + - - -
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Residues in contact with SER 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 PHE* 2.9 24.9 + - - +
23A LEU* 3.8 3.6 - - - -
25A HIS* 1.3 75.2 - - - +
27A THR* 1.3 66.9 + - - +
28A GLU 4.1 1.9 + - - -
66A ILE* 6.0 1.7 - - - +
144A MET* 3.9 24.5 - - - +
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Residues in contact with THR 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 LEU* 2.8 19.7 + - - +
24A ASN 3.6 6.3 - - - +
25A HIS 3.5 0.8 - - - -
26A SER* 1.3 80.4 - - - +
28A GLU* 1.3 62.9 + - - +
29A HIS* 3.5 22.2 - - + +
31A CYS* 3.3 19.8 - - - +
143A GLN* 3.0 38.8 + - - +
144A MET* 4.8 8.8 - - - +
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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