Contacts of the helix formed by residues 18 - 27 (chain A) in PDB entry 2IUI
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 1.3 77.7 - - - +
19A ARG* 1.3 65.8 + - - +
20A GLU* 3.1 11.6 + - - +
21A GLU* 3.1 35.9 + - - +
22A VAL* 3.0 26.2 + - - +
37A ARG* 4.6 0.4 - - - -
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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 ILE 4.1 0.4 + - - -
18A SER* 1.3 73.9 - - - +
20A GLU* 1.3 57.3 + - - +
22A VAL* 3.5 5.2 + - + +
23A ASN* 3.0 43.5 + - - +
37A ARG* 3.7 24.5 - - - +
40A SER* 5.2 4.9 - - - -
59A LEU* 4.4 19.0 - - + +
203C ASP* 2.9 39.4 + - - -
204C PTR 2.7 34.3 + - - -
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Residues in contact with GLU 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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18A SER* 3.0 9.2 + - - +
19A ARG* 1.3 76.8 - - - +
21A GLU* 1.3 66.3 + - - +
23A ASN* 3.1 22.1 + - + +
24A GLU* 3.2 18.5 + - + +
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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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16A ASP 5.0 0.2 - - - +
17A ILE* 3.6 27.6 - - + +
18A SER* 3.1 38.9 + - - +
20A GLU* 1.3 76.8 - - + +
22A VAL* 1.3 62.5 + - - +
24A GLU* 3.1 20.1 + - - +
25A LYS* 3.2 24.6 + - - +
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Residues in contact with VAL 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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17A ILE* 3.5 23.3 - - + -
18A SER 3.0 17.4 + - - +
19A ARG* 3.7 9.0 - - - +
21A GLU* 1.3 75.3 - - - +
23A ASN* 1.3 60.5 + - - +
25A LYS* 3.1 7.7 + - - +
26A LEU* 2.9 30.3 + - + +
35A LEU* 3.6 29.2 - - + -
37A ARG* 3.9 18.2 - - - +
50A THR* 3.7 32.1 - - + +
57A ASN* 5.5 0.2 - - - +
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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* 3.0 34.0 + - - +
20A GLU* 3.1 14.2 + - + +
22A VAL* 1.3 77.8 - - - +
24A GLU* 1.3 56.6 + - - +
26A LEU 3.8 0.7 - - - -
27A ARG* 2.9 42.0 + - - +
50A THR* 5.6 0.5 - - - +
57A ASN* 2.8 31.6 + - - +
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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 GLU* 3.2 16.2 + - + +
21A GLU* 3.1 13.8 + - - +
23A ASN* 1.3 78.5 - - - +
25A LYS* 1.3 63.8 + - + +
27A ARG* 2.6 53.6 + - - +
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Residues in contact with LYS 25 (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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14A TRP* 3.3 39.8 - - + -
17A ILE* 3.8 19.5 - - + -
21A GLU* 3.2 18.4 + - - +
22A VAL* 3.1 7.0 + - - +
24A GLU* 1.3 81.3 - - + +
26A LEU* 1.3 62.6 + - - +
27A ARG 3.5 1.4 + - - +
29A THR* 3.6 13.7 - - - +
35A LEU* 3.9 22.4 - - + -
107A VAL* 4.2 24.9 - - + +
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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 VAL* 2.9 23.3 + - + +
23A ASN 3.8 0.2 - - - -
25A LYS* 1.3 75.0 - - - +
27A ARG* 1.3 63.4 + - - +
28A ASP 3.1 2.4 + - - -
29A THR* 2.8 25.4 + - - +
33A THR* 3.9 13.0 - - + +
34A PHE* 4.5 4.5 - - - +
35A LEU* 4.3 8.1 - - + -
50A THR* 3.6 39.0 - - + +
52A ARG* 3.3 29.0 + - + +
57A ASN* 3.7 24.7 - - - +
107A VAL* 3.6 29.6 - - + -
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Residues in contact with ARG 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 23.4 + - - +
24A GLU* 2.6 62.6 + - - +
25A LYS 3.3 2.8 - - - +
26A LEU* 1.3 75.6 - - - +
28A ASP* 1.3 86.6 + - - +
29A THR* 3.2 7.5 + - - +
52A ARG* 4.7 4.7 - - - +
57A ASN* 6.1 0.2 - - - +
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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