Contacts of the helix formed by residues 11 - 23 (chain A) in PDB entry 1IUF
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 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 1.3 76.0 - - - +
12A HIS* 1.3 73.5 + - - +
13A GLU 3.0 4.5 - - - -
14A LYS* 2.9 28.4 + - + +
15A ARG* 3.1 24.4 + - - +
61A LEU* 3.3 31.4 - - + +
64A THR 5.2 0.9 - - - +
65A VAL* 4.3 7.8 - - - +
66A GLU* 3.0 46.1 + - + +
71A VAL* 3.2 25.3 - - + +
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Residues in contact with HIS 12 (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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10A THR* 3.8 7.2 + - - +
11A GLU* 1.3 89.6 + - - +
13A GLU* 1.3 61.1 + - - +
14A LYS 3.2 0.2 - - - -
15A ARG* 3.8 32.7 + - + +
16A ALA* 3.1 30.8 + - + +
36A TRP* 4.0 1.7 - - - -
66A GLU* 5.9 0.2 + - - -
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Residues in contact with GLU 13 (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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3A LYS* 5.4 2.3 - - - +
4A ILE* 3.3 24.1 + - - +
7A ARG 3.9 4.9 - - - +
9A ILE* 3.3 40.3 + - + +
10A THR* 3.6 27.8 + - - +
11A GLU 3.0 0.4 - - - -
12A HIS* 1.3 79.8 - - - +
14A LYS* 1.3 57.2 + - - +
17A LEU* 3.1 26.4 + - + +
36A TRP* 3.2 21.2 - - + +
37A PHE* 5.0 5.9 - - + -
40A LYS* 3.2 34.7 + - - +
41A PHE* 5.4 0.3 - - - -
53A ILE* 5.0 2.9 - - + -
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Residues in contact with LYS 14 (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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10A THR 3.9 1.1 + - - +
11A GLU* 2.9 10.2 + - - +
13A GLU* 1.3 76.2 - - - +
15A ARG* 1.3 88.6 + - + +
16A ALA 3.0 1.8 - - - -
17A LEU* 2.6 26.6 + - - +
18A ARG* 2.7 20.1 + - + +
53A ILE* 4.6 10.5 - - + +
57A LYS* 4.4 3.8 - - + +
58A TYR* 3.3 52.9 - - + -
61A LEU* 3.0 63.1 + - + +
62A ASP* 4.8 1.0 - - - +
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Residues in contact with ARG 15 (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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11A GLU* 3.1 22.4 + - - +
12A HIS* 3.7 35.1 + - + +
14A LYS* 1.3 102.5 - - + +
16A ALA* 1.3 58.8 + - - +
18A ARG* 3.1 26.8 - - - +
19A HIS* 3.5 26.5 + - + +
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A HIS* 3.1 13.7 + - + +
14A LYS 3.0 0.8 - - - -
15A ARG* 1.3 76.9 - - - +
17A LEU* 1.3 61.6 + - - +
19A HIS* 3.6 5.2 + - - +
20A TYR* 2.9 29.4 + - - +
36A TRP* 3.3 35.2 - - + -
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Residues in contact with LEU 17 (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 GLU* 3.1 12.7 + - + +
14A LYS* 2.6 13.6 + - - +
16A ALA* 1.3 69.2 - - - +
18A ARG* 1.3 62.6 + - - +
20A TYR* 2.8 25.5 - - + +
21A PHE 3.4 3.8 + - - -
33A LEU* 3.4 41.9 - - + +
36A TRP* 2.9 49.4 - - + +
37A PHE* 4.0 8.1 - - + -
53A ILE* 3.0 45.8 - - + +
54A LEU* 3.9 10.6 - - + +
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Residues in contact with ARG 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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14A LYS* 2.7 18.9 + - + +
15A ARG* 3.1 28.9 - - - +
17A LEU* 1.3 72.6 - - - +
19A HIS* 1.3 111.7 + - - +
20A TYR 3.2 0.3 + - - -
21A PHE* 3.7 1.0 + - - +
22A PHE* 3.0 50.5 + - + +
54A LEU* 4.5 17.4 - - + +
58A TYR* 3.4 46.2 + - + -
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Residues in contact with HIS 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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15A ARG* 3.5 27.2 + - + +
16A ALA* 3.7 7.0 - - - +
17A LEU 3.3 0.2 - - - -
18A ARG* 1.3 102.7 + - + +
20A TYR* 1.3 59.3 + - - +
22A PHE* 4.6 1.8 - - - +
23A GLN* 2.5 70.8 + - + +
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Residues in contact with TYR 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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16A ALA 2.9 16.2 + - - +
17A LEU* 2.8 25.3 + - + +
19A HIS* 1.3 83.0 - - - +
21A PHE* 1.3 57.6 + - - +
23A GLN 3.6 0.9 + - - -
24A LEU* 3.3 18.9 - - + +
28A SER* 2.8 20.0 + - - -
32A ASP* 2.8 50.0 + - + -
33A LEU* 3.5 25.4 - - + -
35A GLU* 4.0 4.0 - - - +
36A TRP* 3.3 44.5 + + + +
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Residues in contact with PHE 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 LEU 3.4 3.8 + - - +
18A ARG 4.8 1.1 - - - +
20A TYR* 1.3 74.3 - - - +
22A PHE* 1.3 79.2 + + + +
26A ASN 5.5 1.0 - - - +
27A ARG* 4.6 19.2 - - + -
28A SER* 2.5 32.2 + - - -
29A GLY* 3.8 26.9 - - - +
30A GLN* 4.5 13.7 - - + +
33A LEU* 4.4 13.2 - - + +
54A LEU* 5.1 14.8 - - + -
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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
----------------------------------------------------------
18A ARG* 3.0 41.1 + - + +
19A HIS* 4.6 2.0 - - - +
21A PHE* 1.3 101.6 - + + +
23A GLN* 1.3 57.3 + - - +
24A LEU 3.7 3.5 + - - +
26A ASN 5.7 1.4 - - - +
54A LEU* 5.9 7.2 - - + -
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Residues in contact with GLN 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 HIS* 2.5 59.8 + - + +
22A PHE* 1.3 73.6 - - - +
24A LEU* 1.3 73.5 + - - +
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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