Contacts of the helix formed by residues 16 - 37 (chain D) in PDB entry 3ZO7
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 ASP 16 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASN 3.4 5.2 + - - -
15D LEU* 1.3 75.9 - - - +
17D PRO* 1.3 69.3 - - - +
18D ARG* 2.6 37.3 + - - +
19D GLU* 3.3 20.2 + - + -
20D GLU* 2.8 29.3 + - - +
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Residues in contact with PRO 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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15D LEU 3.3 6.5 - - - +
16D ASP* 1.3 91.6 - - - +
18D ARG* 1.3 56.8 + - + +
20D GLU* 3.6 7.9 - - + +
21D GLU* 3.0 31.8 + - - +
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Residues in contact with ARG 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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16D ASP* 2.6 16.2 + - - +
17D PRO* 1.3 72.3 - - + +
19D GLU* 1.3 66.1 + - - +
21D GLU* 3.2 37.0 + - - +
22D ARG* 2.9 56.8 + - - +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 3.6 21.3 - - + +
16D ASP* 3.3 26.7 + - + +
18D ARG* 1.3 78.6 - - - +
20D GLU* 1.3 60.4 + - - +
22D ARG* 2.9 38.7 + - - +
23D LEU* 2.9 36.9 + - - +
76D TYR* 5.0 2.5 + - - -
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Residues in contact with GLU 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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11D LEU* 3.7 13.5 - - + +
12D PRO 5.4 0.3 - - - +
15D LEU* 3.4 41.4 - - + +
16D ASP 2.8 16.2 + - - +
17D PRO* 3.6 7.2 - - - +
19D GLU* 1.3 74.9 + - - +
21D GLU* 1.3 68.1 + - - +
23D LEU* 2.8 17.5 + - + +
24D LYS* 3.0 49.3 + - + +
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Residues in contact with GLU 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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17D PRO 3.0 15.9 + - - +
18D ARG* 3.4 35.1 + - - +
20D GLU* 1.3 81.6 - - - +
22D ARG* 1.3 60.5 + - - +
24D LYS* 3.4 10.8 + - - +
25D ALA* 3.4 18.4 + - - +
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Residues in contact with ARG 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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18D ARG* 2.9 37.2 + - - +
19D GLU* 2.9 31.9 + - - +
21D GLU* 1.3 75.8 - - - +
23D LEU* 1.3 78.9 + - - +
25D ALA* 3.1 9.1 + - + +
26D SER* 3.0 51.0 + - - +
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Residues in contact with LEU 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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11D LEU* 4.4 4.9 - - + -
15D LEU* 4.6 7.0 - - + -
19D GLU* 2.9 25.8 + - - +
20D GLU* 2.8 17.4 + - + +
22D ARG* 1.3 89.3 - - - +
24D LYS* 1.3 54.6 + - + +
26D SER* 3.4 7.2 + - - -
27D ALA* 3.1 27.2 + - - +
72D PRO* 3.6 28.2 - - + +
73D PHE* 3.6 27.1 - - + -
76D TYR* 3.5 31.2 - - + -
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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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69B TRP* 6.0 2.6 - - - -
11D LEU* 4.1 11.4 - - - +
20D GLU* 3.0 50.1 + - + +
21D GLU* 3.7 9.9 - - - +
22D ARG 3.1 0.4 - - - -
23D LEU* 1.3 75.6 - - - +
25D ALA* 1.3 64.5 + - - +
27D ALA* 3.3 3.5 + - - +
28D LYS* 3.0 23.4 + - - +
50D TYR* 4.1 21.0 + - - +
73D PHE* 4.2 17.9 - - + -
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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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21D GLU 3.4 9.6 + - - +
22D ARG* 3.1 10.6 + - + +
24D LYS* 1.3 77.8 - - - +
26D SER* 1.3 63.2 + - - +
28D LYS* 3.3 7.6 + - - +
29D ALA* 3.0 24.9 + - - +
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Residues in contact with SER 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 ARG* 3.0 38.3 + - - +
23D LEU* 3.5 10.1 - - - -
25D ALA* 1.3 78.0 - - - +
27D ALA* 1.3 62.2 + - - +
29D ALA* 3.2 6.5 + - - +
30D ARG* 2.9 25.8 + - - +
72D PRO* 3.8 18.1 - - - +
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Residues in contact with ALA 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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23D LEU 3.1 9.6 + - - +
24D LYS 3.3 6.5 + - - +
26D SER* 1.3 76.6 - - - +
28D LYS* 1.3 57.8 + - - +
30D ARG* 3.4 1.0 + - - +
31D SER* 3.0 31.6 + - - -
72D PRO* 3.7 18.5 - - + +
73D PHE* 3.5 39.7 - - + -
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Residues in contact with LYS 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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88A PRO* 4.5 13.2 + - + +
89A ALA* 4.3 29.7 - - + +
24D LYS 3.0 13.0 + - - +
25D ALA* 3.6 11.2 - - - +
26D SER 3.2 0.2 - - - -
27D ALA* 1.3 77.0 - - - +
29D ALA* 1.3 58.2 + - - +
31D SER* 3.0 8.2 + - - -
32D ARG* 3.0 32.0 + - + +
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Residues in contact with ALA 29 (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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25D ALA 3.0 16.6 + - - +
26D SER* 3.8 5.8 - - - +
28D LYS* 1.3 74.4 - - - +
30D ARG* 1.3 65.3 + - - +
32D ARG* 3.4 11.9 + - - +
33D THR* 3.1 26.6 + - - -
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Residues in contact with ARG 30 (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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26D SER 2.9 17.5 + - - +
27D ALA 3.8 3.4 - - - +
29D ALA* 1.3 75.1 - - - +
31D SER* 1.3 65.7 + - - +
33D THR* 3.1 20.4 + - - +
34D LEU* 3.0 64.9 + - + +
37D GLN* 5.4 1.4 + - - +
67D ILE* 4.6 10.1 - - - +
70D SER* 3.4 30.3 + - - -
71D LEU* 4.2 7.8 - - + +
72D PRO* 4.1 24.2 - - + -
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Residues in contact with SER 31 (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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89A ALA* 3.7 16.8 - - - +
27D ALA 3.0 14.0 + - - -
28D LYS* 3.0 17.7 + - - -
30D ARG* 1.3 77.7 - - - +
32D ARG* 1.3 56.6 + - - +
34D LEU* 3.9 0.3 - - - +
35D GLN* 2.9 46.1 + - - +
40D TRP* 3.6 36.8 - - - -
43D LEU* 5.1 2.0 - - - -
71D LEU* 5.8 0.2 - - - +
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Residues in contact with ARG 32 (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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89A ALA 5.3 0.9 - - - +
91A VAL* 4.2 34.2 - - + +
28D LYS* 3.0 22.6 + - + +
29D ALA* 3.4 11.7 - - - +
30D ARG 3.1 0.2 - - - -
31D SER* 1.3 78.6 + - - +
33D THR* 1.3 58.4 + - - +
35D GLN* 3.4 1.9 + - - +
36D GLU* 2.6 75.1 + - + +
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Residues in contact with THR 33 (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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29D ALA 3.1 13.0 + - - -
30D ARG* 3.1 22.5 + - - +
32D ARG* 1.3 79.4 - - - +
34D LEU* 1.3 58.1 + - - +
36D GLU* 3.4 13.9 + - + +
37D GLN* 3.0 61.7 + - + +
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Residues in contact with LEU 34 (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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30D ARG* 3.0 66.0 + - + +
31D SER 4.0 2.9 - - - +
33D THR* 1.3 76.1 - - - +
35D GLN* 1.3 57.8 + - - +
37D GLN* 3.6 8.7 + - - +
38D GLY 3.1 4.9 + - - -
39D GLN* 3.1 38.1 + - + +
40D TRP* 3.0 50.0 + - + +
67D ILE* 3.9 27.4 - - + -
71D LEU* 4.2 4.3 - - + -
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Residues in contact with GLN 35 (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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89A ALA 2.9 23.8 + - - -
90A ARG* 3.1 24.8 + - - +
91A VAL* 2.9 39.0 + - + +
31D SER* 2.9 40.4 + - - +
32D ARG 3.8 3.7 - - - +
34D LEU* 1.3 74.9 - - - +
36D GLU* 1.3 64.2 + - - +
37D GLN 3.1 0.2 - - - -
38D GLY* 3.2 12.8 + - - -
40D TRP* 3.4 33.1 - - + +
43D LEU* 3.8 13.1 - - - +
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Residues in contact with GLU 36 (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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91A VAL* 4.6 13.7 - - + -
32D ARG* 2.6 66.0 + - + +
33D THR* 3.7 13.4 + - - +
35D GLN* 1.3 75.8 - - - +
37D GLN* 1.3 61.1 + - + +
38D GLY* 4.8 0.2 - - - -
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Residues in contact with GLN 37 (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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30D ARG* 5.4 1.1 + - - +
33D THR* 3.0 43.2 + - + +
34D LEU* 3.6 8.4 + - - +
35D GLN 3.1 0.2 - - - -
36D GLU* 1.3 77.7 - - + +
38D GLY* 1.3 59.1 + - - +
39D GLN* 2.6 38.8 + - - +
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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
------------------------------------------------------------
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