Contacts of the helix formed by residues 9 - 22 (chain E) in PDB entry 2IZZ
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 GLY 9 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E GLY 3.6 4.0 + - - -
8E ALA* 1.3 77.8 - - - +
10E GLN* 1.3 66.7 + - - +
11E LEU 3.3 2.0 - - - -
12E ALA* 3.4 4.4 + - - +
13E PHE* 3.0 23.7 + - - +
41E THR* 3.4 14.2 - - - -
69E ALA 5.1 0.8 + - - -
350E NAD 3.3 28.0 + - - -
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Residues in contact with GLN 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLY* 1.3 71.6 - - - +
11E LEU* 1.3 58.7 + - - +
13E PHE* 3.6 7.6 + - - +
14E ALA* 3.0 28.2 + - - +
40E ALA* 6.3 0.2 - - - +
41E THR* 3.6 24.2 - - - +
124E THR* 5.3 8.1 - - + +
350E NAD 3.0 40.7 + - - +
1273E EDO 4.4 15.1 - - - +
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Residues in contact with LEU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLN* 1.3 72.5 - - - +
12E ALA* 1.3 58.5 + - - +
14E ALA* 3.2 7.0 + - + -
15E LEU* 2.9 41.0 + - + +
69E ALA* 4.6 7.2 - - + -
95E CYS* 3.5 31.6 - - + -
122E THR* 3.8 22.4 - - + -
123E ASN 4.6 11.0 - - - +
124E THR* 5.1 1.6 - - + +
126E VAL* 5.1 0.2 - - + -
350E NAD 2.8 76.7 + - + +
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Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.8 31.9 - - + -
7E GLY 3.3 26.5 - - - +
8E ALA* 4.0 4.5 - - - -
9E GLY 3.4 12.9 + - - +
11E LEU* 1.3 77.7 - - - +
13E PHE* 1.3 63.8 + - - +
15E LEU* 4.2 0.2 - - - +
16E ALA* 3.0 28.7 + - - +
32E ALA* 5.1 0.2 - - + -
45E LEU* 4.4 7.6 - - + -
69E ALA* 4.5 5.4 - - + +
350E NAD 4.6 0.2 + - - -
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Residues in contact with PHE 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLY 3.0 17.7 + - - +
10E GLN* 3.6 8.3 - - - +
12E ALA* 1.3 77.9 - - - +
14E ALA* 1.3 61.6 + - + +
16E ALA* 3.8 0.5 - - - +
17E LYS* 2.9 58.8 + - + +
41E THR* 4.4 15.7 - - + -
44E ALA* 3.4 32.8 - - + -
45E LEU* 3.8 16.2 - - + +
48E MET* 3.9 26.9 - - + -
127E VAL* 4.1 9.6 - - + -
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Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E GLN 3.0 17.2 + - - +
11E LEU* 3.2 7.2 + - + +
13E PHE* 1.3 80.3 - - + +
15E LEU* 1.3 58.7 + - - +
17E LYS* 3.7 0.5 - - - +
18E GLY 3.0 22.9 + - - -
124E THR* 3.7 24.7 - - - +
126E VAL* 3.6 19.2 - - + +
127E VAL* 3.5 27.0 + - + -
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Residues in contact with LEU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.8 29.4 - - + -
11E LEU* 2.9 35.8 + - + +
14E ALA* 1.3 76.7 - - - +
16E ALA* 1.3 58.3 + - - +
18E GLY* 3.3 1.2 + - - -
19E PHE* 2.9 47.8 + - + -
67E PHE* 4.4 10.3 - - + -
95E CYS* 4.4 17.0 - - - -
122E THR* 4.6 6.7 - - + -
126E VAL* 3.7 28.5 - - + -
153E LEU* 3.9 26.2 - - + -
156E VAL* 4.5 3.0 - - + +
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Residues in contact with ALA 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.3 9.6 - - + -
12E ALA 3.0 20.3 + - - +
15E LEU* 1.3 72.9 - - - +
17E LYS* 1.3 56.9 + - - +
19E PHE* 3.9 3.0 - - - +
20E THR* 2.8 40.4 + - - +
30E ILE* 4.1 24.0 - - + -
45E LEU* 3.7 21.8 - - + -
48E MET* 4.1 5.8 - - + -
50E VAL* 4.3 4.0 - - + -
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Residues in contact with LYS 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E PHE* 2.9 46.0 + - + +
14E ALA 3.7 4.0 - - - +
16E ALA* 1.3 76.7 - - - +
18E GLY* 1.3 55.0 - - - +
20E THR* 2.9 17.9 + - - -
21E ALA* 3.0 24.6 + - + +
48E MET* 4.0 18.2 - - - +
127E VAL* 3.7 28.8 + - + +
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Residues in contact with GLY 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ALA 3.0 10.7 + - - -
15E LEU 3.8 1.3 - - - -
17E LYS* 1.3 75.0 - - - +
19E PHE* 1.3 58.0 + - - +
21E ALA* 3.3 2.7 + - - +
22E ALA* 2.8 31.5 + - - +
126E VAL 3.4 23.7 + - - -
127E VAL 4.6 2.7 - - - -
129E ARG* 3.9 9.6 - - - +
156E VAL* 3.3 13.1 - - - +
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Residues in contact with PHE 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.2 6.7 - + - -
15E LEU* 2.9 48.6 + - + +
16E ALA* 3.9 7.9 - - - +
18E GLY* 1.3 74.6 - - - +
20E THR* 1.3 62.8 + - - +
22E ALA* 3.3 3.3 + - - +
23E GLY 3.2 16.5 + - - -
24E VAL* 3.4 15.0 + - + +
25E LEU* 3.8 34.6 + - + -
30E ILE* 4.7 2.0 - - + -
67E PHE* 4.1 25.8 - + - -
152E LEU* 3.3 44.4 - - + -
153E LEU* 4.1 5.4 - - + -
155E SER* 3.8 7.6 - - - -
156E VAL* 3.6 25.1 - - + -
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Residues in contact with THR 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ALA 2.8 22.1 + - - +
17E LYS* 2.9 16.1 + - - +
19E PHE* 1.3 75.1 - - - +
21E ALA* 1.3 63.2 + - - +
23E GLY* 3.2 12.6 + - - -
25E LEU 3.4 21.3 - - - +
27E ALA* 3.7 32.8 - - + +
30E ILE* 3.9 11.0 - - + -
48E MET* 4.8 7.8 - - + +
50E VAL* 5.4 2.5 - - + -
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Residues in contact with ALA 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LYS* 3.0 26.2 + - + +
18E GLY* 3.7 5.4 - - - +
20E THR* 1.3 77.4 + - - +
22E ALA* 1.3 59.5 + - - +
23E GLY* 3.3 1.2 + - - -
127E VAL 5.7 2.0 - - - +
129E ARG* 4.1 20.9 + - + -
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Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLY 2.8 17.8 + - - +
19E PHE 3.4 7.0 - - - +
21E ALA* 1.3 75.8 - - - +
23E GLY* 1.3 60.7 + - - +
24E VAL* 3.2 7.4 + - + +
129E ARG* 3.6 32.6 + - - +
155E SER* 3.6 29.4 - - - +
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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