Contacts of the helix formed by residues 15 - 28 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D GLY 3.6 1.0 - - - -
14D SER* 1.3 77.7 - - - +
16D PRO* 1.3 79.0 - - - +
17D GLY 3.0 3.6 + - - -
18D GLY 3.1 1.3 + - - +
19D TYR* 2.8 23.8 + - - -
42D GLY 3.6 10.5 - - - -
480D FAD 3.2 30.0 + - - -
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Residues in contact with PRO 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY* 1.3 82.3 - - - +
17D GLY* 1.3 60.6 + - - +
19D TYR* 3.9 15.3 - - + -
20D VAL* 3.1 28.4 + - - +
42D GLY 3.7 9.0 - - - +
45D CYS* 3.3 28.7 - - + -
328D ALA* 3.9 15.9 - - + +
331D ALA* 4.5 0.2 - - + -
332D GLU* 3.5 29.1 - - + +
480D FAD 3.3 31.4 - - - +
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Residues in contact with GLY 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PRO* 1.3 79.7 - - - +
18D GLY* 1.3 56.8 + - - +
20D VAL* 4.1 1.0 - - - +
21D ALA* 3.0 31.2 + - - +
318D ILE* 3.4 27.8 - - - +
331D ALA* 3.4 18.8 - - - +
335D GLY* 4.1 2.1 - - - -
480D FAD 2.9 12.6 + - - -
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Residues in contact with GLY 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 3.4 16.9 - - - +
13D GLY 3.3 23.8 - - - -
15D GLY 3.1 5.0 + - - +
17D GLY* 1.3 74.7 - - - +
19D TYR* 1.3 59.4 + - - +
21D ALA* 3.7 1.3 - - - +
22D ALA* 2.8 31.1 + - - +
34D CYS* 4.8 0.7 - - - -
147D ALA* 3.7 14.9 - - - +
480D FAD 4.1 0.8 + - - -
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Residues in contact with TYR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C HIS* 5.9 1.9 - - - -
472C ILE* 4.7 0.2 - - + -
473C ASN* 2.6 33.9 + - - -
14D SER* 3.5 19.1 - - - +
15D GLY 2.8 27.0 + - - -
16D PRO* 3.9 11.4 - - + -
18D GLY* 1.3 72.9 - - - +
20D VAL* 1.3 81.9 + - + +
23D ILE* 3.1 43.7 + - + +
34D CYS* 4.9 0.2 - - - -
42D GLY* 5.0 1.3 - - - -
46D LEU* 5.6 1.3 - - + -
103D ILE* 3.8 44.6 - - + +
106D LEU* 4.7 2.2 - - + -
107D PHE* 3.5 26.5 - + + -
332D GLU* 4.7 6.7 + - - -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C ILE* 4.1 23.4 - - + +
473C ASN* 5.3 0.9 - - - +
16D PRO 3.1 21.8 + - - +
17D GLY 4.1 0.9 - - - +
18D GLY 3.2 0.6 - - - -
19D TYR* 1.3 105.2 - - + +
21D ALA* 1.3 64.7 + - - +
23D ILE* 3.2 3.1 + - - +
24D LYS* 2.9 22.3 + - - +
332D GLU* 3.9 30.5 - - + +
336D ILE* 3.6 33.2 - - + -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.7 1.1 - - + -
17D GLY 3.0 20.5 + - - +
18D GLY 3.7 2.9 - - - +
20D VAL* 1.3 76.8 - - - +
22D ALA* 1.3 57.4 + - - +
24D LYS* 3.5 3.1 + - - +
25D ALA* 2.8 32.6 + - - +
145D LEU* 3.4 31.9 - - + -
335D GLY* 3.7 26.9 - - - +
339D VAL* 3.8 5.9 - - + +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D VAL* 4.1 6.9 - - + +
18D GLY 2.8 19.2 + - - +
19D TYR 3.6 5.2 - - - +
20D VAL 3.2 0.2 - - - -
21D ALA* 1.3 78.2 - - - +
23D ILE* 1.3 61.7 + - - +
25D ALA 3.4 0.2 + - - -
26D ALA* 3.1 24.1 + - - +
32D THR* 3.6 23.2 - - + +
34D CYS* 4.1 23.1 - - + -
107D PHE* 4.1 4.3 - - + -
112D VAL* 3.6 13.6 - - + +
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Residues in contact with ILE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C ILE* 3.8 28.0 - - + +
19D TYR* 3.1 45.3 + - + +
20D VAL 3.7 6.1 - - - +
22D ALA* 1.3 74.8 - - - +
24D LYS* 1.3 58.7 + - - +
26D ALA* 3.3 3.2 + - - +
27D GLN* 2.8 57.5 + - - +
106D LEU* 3.8 24.0 - - + +
107D PHE* 3.9 16.8 - - + -
110D ASN* 3.8 17.0 - - - +
112D VAL* 4.3 5.8 - - + -
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Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C LEU* 4.3 17.6 - - - +
468C PHE* 3.6 47.8 - - - -
472C ILE* 4.0 18.8 - - + +
20D VAL 2.9 16.7 + - - +
21D ALA* 4.4 0.7 - - - -
23D ILE* 1.3 79.0 - - - +
25D ALA* 1.3 57.2 + - - +
27D GLN* 3.2 8.4 + - - +
28D LEU* 2.9 49.1 + - + +
336D ILE* 4.2 24.7 - - + +
339D VAL* 3.6 23.3 - - + -
340D GLU* 4.0 20.6 + - - -
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.3 12.3 - - + -
21D ALA 2.8 22.4 + - - +
22D ALA 3.8 2.0 - - - +
24D LYS* 1.3 73.7 - - - +
26D ALA* 1.3 63.0 + - - +
28D LEU* 3.1 9.4 + - - +
29D GLY 3.2 0.2 + - - -
30D PHE* 2.9 41.5 + - + +
32D THR* 3.6 16.2 - - + +
339D VAL* 3.8 19.0 - - + +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ALA 3.1 17.2 + - - +
23D ILE 3.7 3.1 - - - +
25D ALA* 1.3 76.9 - - - +
27D GLN* 1.3 58.5 + - - +
29D GLY* 2.9 20.6 + - - -
30D PHE 3.5 14.2 + - - +
32D THR* 3.4 7.3 + - - +
110D ASN* 3.1 29.4 - - + +
111D LYS* 4.9 1.8 - - + -
112D VAL* 3.8 14.4 - - + +
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Residues in contact with GLN 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C LEU* 5.8 0.2 - - - +
468C PHE* 3.8 30.9 - - + -
470C LYS* 3.9 34.6 + - + +
471C SER 2.9 27.0 + - - +
472C ILE* 3.9 14.7 + - - +
474C PHE 5.2 1.4 + - - -
23D ILE* 2.8 36.7 + - - +
24D LYS* 3.2 10.3 + - + +
26D ALA* 1.3 77.8 - - - +
28D LEU* 1.3 59.7 + - - +
29D GLY 3.1 1.1 + - - -
109D GLN* 5.9 1.2 - - - +
110D ASN* 3.3 26.8 + - - +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468C PHE* 4.1 25.4 - - + -
24D LYS* 2.9 33.4 + - + +
25D ALA* 3.1 8.0 + - - +
27D GLN* 1.3 75.4 - - - +
29D GLY* 1.3 58.9 + - - +
30D PHE* 3.6 12.2 - - + -
339D VAL* 3.7 39.0 - - + +
340D GLU* 4.0 13.5 - - + +
343D ALA* 4.3 13.5 - - + -
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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