Contacts of the helix formed by residues 15 - 29 (chain E) in PDB entry 1ZMD
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 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E GLY 3.5 1.8 - - - -
14E SER* 1.3 78.5 - - - +
16E PRO* 1.4 77.5 - - - +
17E GLY 3.1 3.7 + - - -
18E GLY 3.1 0.9 + - - +
19E TYR* 2.7 24.0 + - - -
42E GLY 3.7 0.7 - - - -
43E GLY 3.6 8.5 - - - -
480E FAD 3.2 29.5 + - - -
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Residues in contact with PRO 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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15E GLY* 1.4 82.5 - - - +
17E GLY* 1.3 61.0 + - - +
19E TYR* 3.8 11.8 - - + -
20E VAL* 3.1 29.6 + - - +
42E GLY 3.9 4.3 - - - +
45E CYS* 3.4 35.0 - - + -
46E LEU* 4.8 4.5 - - + -
328E ALA* 3.6 13.7 - - + +
331E ALA* 4.3 0.2 - - + -
332E GLU* 3.4 27.9 - - + +
480E FAD 3.2 31.6 - - - +
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Residues in contact with GLY 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E PRO* 1.3 80.8 - - - +
18E GLY* 1.3 56.7 + - - +
20E VAL* 4.2 0.7 - - - +
21E ALA* 2.9 31.0 + - - +
147E ALA* 4.9 0.4 - - - -
318E ILE* 3.5 15.6 - - - +
331E ALA* 3.5 29.4 - - - +
332E GLU* 4.3 0.2 - - - -
335E GLY* 4.1 2.1 - - - -
480E FAD 3.0 12.7 + - - -
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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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11E VAL* 3.5 17.1 - - - +
13E GLY 3.2 22.9 - - - -
15E GLY 3.1 4.2 + - - +
17E GLY* 1.3 71.9 - - - +
19E TYR* 1.3 60.0 + - - +
21E ALA* 3.1 3.4 + - - +
22E ALA* 2.7 31.6 + - - +
34E CYS* 4.9 0.2 - - - -
147E ALA* 3.6 14.5 - - - +
480E FAD 4.0 1.0 + - - -
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Residues in contact with TYR 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER* 3.4 22.6 - - - +
15E GLY 2.7 28.7 + - - -
16E PRO* 3.8 15.3 - - + -
18E GLY* 1.3 71.5 - - - -
20E VAL* 1.3 76.1 + - + +
22E ALA* 3.5 2.1 - - - +
23E ILE* 3.2 41.9 + - + +
42E GLY* 4.9 1.8 - - - -
46E LEU* 4.5 11.2 - - + -
103E ILE* 3.4 44.3 - - + +
106E LEU* 4.5 0.7 - - + -
107E PHE* 3.5 24.1 - + + -
332E GLU* 4.7 6.9 + - - -
452F HIS* 6.0 1.9 - - - -
472F ILE* 4.8 0.2 - - + -
473F ASN* 2.7 33.2 + - - -
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Residues in contact with VAL 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 PRO 3.1 23.6 + - - +
17E GLY 4.2 0.9 - - - +
18E GLY 3.2 0.4 - - - -
19E TYR* 1.3 99.0 - - + +
21E ALA* 1.3 65.9 + - - +
22E ALA 3.2 0.2 - - - -
23E ILE* 4.0 1.4 - - - +
24E LYS* 3.0 23.0 + - - +
332E GLU* 3.7 32.1 - - + +
336E ILE* 3.5 36.3 - - + -
472F ILE* 4.0 23.1 - - + +
473F ASN* 5.3 0.9 - - - +
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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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11E VAL* 4.6 3.1 - - + -
17E GLY 2.9 22.6 + - - +
18E GLY* 3.1 6.7 + - - +
20E VAL* 1.3 76.4 - - - +
22E ALA* 1.3 56.3 + - - +
24E LYS* 4.0 0.2 - - - +
25E ALA* 3.0 30.7 + - - +
145E LEU* 3.6 30.1 - - + -
318E ILE* 4.1 0.7 - - + -
335E GLY* 3.7 24.4 - - - +
339E VAL* 3.5 7.6 - - + +
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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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11E VAL* 4.2 6.2 - - + +
18E GLY 2.7 16.3 + - - +
19E TYR 3.5 7.0 - - - +
21E ALA* 1.3 74.5 - - - +
23E ILE* 1.3 65.5 + - - +
25E ALA* 3.3 4.5 + - - +
26E ALA 3.1 18.5 + - - -
32E THR* 3.6 18.4 - - + +
34E CYS* 4.2 8.7 - - + -
107E PHE* 3.9 20.4 - - + -
112E VAL* 3.7 19.4 - - + +
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Residues in contact with ILE 23 (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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19E TYR* 3.2 33.3 + - + +
20E VAL 3.5 4.0 + - - +
22E ALA* 1.3 75.0 - - - +
24E LYS* 1.3 63.9 - - - +
26E ALA* 3.3 3.1 + - - +
27E GLN* 2.9 48.4 + - - +
106E LEU* 3.6 32.3 - - + +
107E PHE* 3.9 15.5 - - + -
110E ASN* 3.4 18.8 - - - +
112E VAL* 4.2 6.3 - - + -
472F ILE* 3.7 25.6 - - + +
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Residues in contact with LYS 24 (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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20E VAL 3.0 18.4 + - - +
21E ALA 4.0 0.2 - - - +
23E ILE* 1.3 76.2 - - - +
25E ALA* 1.3 58.2 + - - +
27E GLN* 3.3 10.2 + - + +
28E LEU* 2.9 55.2 + - + +
336E ILE* 4.1 20.4 - - + +
339E VAL* 3.8 22.9 - - + -
340E GLU* 3.8 21.2 + - + -
464F LEU* 4.2 17.8 - - - +
468F PHE* 3.4 39.4 - - - -
472F ILE* 3.9 21.0 - - + +
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Residues in contact with ALA 25 (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 VAL* 4.2 14.4 - - + -
21E ALA 3.0 19.5 + - - +
22E ALA 3.4 5.2 - - - +
24E LYS* 1.3 73.6 - - - +
26E ALA* 1.3 64.2 - - - +
28E LEU* 3.1 13.7 + - - +
29E GLY 3.2 0.3 + - - -
30E PHE* 3.1 31.6 + - + +
32E THR* 3.5 15.3 - - + +
339E VAL* 3.9 18.5 - - + +
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Residues in contact with ALA 26 (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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22E ALA 3.1 13.1 + - - +
23E ILE 3.8 6.3 - - - +
25E ALA* 1.3 75.1 - - - +
27E GLN* 1.3 62.7 + - - +
29E GLY* 3.1 16.1 + - - -
30E PHE 3.4 14.4 - - - +
32E THR* 3.4 7.0 + - - +
110E ASN* 3.2 28.5 - - + +
111E LYS* 4.9 2.9 - - + +
112E VAL* 4.0 12.6 - - + -
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Residues in contact with GLN 27 (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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23E ILE* 2.9 30.4 + - - +
24E LYS* 3.6 16.9 + - + +
26E ALA* 1.3 77.7 - - - +
28E LEU* 1.3 59.7 + - - +
109E GLN* 5.8 1.4 - - - +
110E ASN* 3.0 29.7 + - - +
464F LEU* 5.8 0.2 - - - +
468F PHE* 3.8 33.3 - - + -
470F LYS* 3.8 42.4 + - + +
471F SER 3.2 26.2 + - - +
472F ILE* 4.2 5.2 + - - +
474F PHE* 5.3 0.6 + - - -
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Residues in contact with LEU 28 (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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24E LYS* 2.9 39.4 + - + +
25E ALA* 3.1 7.1 + - - +
27E GLN* 1.3 76.7 - - - +
29E GLY* 1.3 57.0 + - - +
30E PHE* 3.8 11.2 - - + -
339E VAL* 3.7 28.0 - - + +
340E GLU* 3.8 25.1 - - + +
343E ALA* 4.4 14.1 - - + +
468F PHE* 4.1 24.5 - - + -
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Residues in contact with GLY 29 (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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8E ASP* 4.7 1.9 - - - +
26E ALA 3.1 11.8 + - - -
27E GLN 3.3 0.8 + - - -
28E LEU* 1.3 81.4 - - - +
30E PHE* 1.3 65.2 + - - +
31E LYS* 3.8 1.0 + - - -
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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