Contacts of the helix formed by residues 21 - 34 (chain D) in PDB entry 5DDP
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 LYS 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A A 4.9 0.2 - - - +
30A G 3.2 41.7 - - - +
31A G 3.2 30.3 - - - +
19D LYS 4.4 4.0 - - - +
20D ILE* 1.3 75.7 - - - +
22D LYS* 1.3 67.9 + - - +
23D ASP* 3.2 5.7 + - + +
24D GLU* 3.2 23.4 + - + +
25D LEU* 2.9 20.3 + - - +
46D ARG* 3.7 6.5 - - - +
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Residues in contact with LYS 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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29A A 5.5 10.5 - - - +
30A G 3.9 4.2 + - - +
20D ILE 3.5 2.4 + - - -
21D LYS* 1.3 72.4 - - - +
23D ASP* 1.3 60.2 + - + +
25D LEU* 3.3 6.8 + - - +
26D LYS* 2.9 52.1 + - - +
44D VAL* 3.1 38.1 + - + +
45D SER* 5.0 4.3 - - - +
46D ARG* 3.7 30.1 - - + +
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Residues in contact with ASP 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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21D LYS* 3.2 4.3 - - + +
22D LYS* 1.3 81.2 - - - +
24D GLU* 1.3 64.0 + - - +
26D LYS* 3.3 8.9 + - - +
27D LYS* 3.0 59.2 + - - +
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Residues in contact with GLU 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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20D ILE* 4.3 8.4 - - + +
21D LYS* 3.2 28.2 + - + +
23D ASP* 1.3 80.5 + - - +
25D LEU* 1.3 59.5 + - - +
27D LYS* 3.4 6.8 + - + +
28D SER* 2.8 30.7 + - - +
77D TYR* 2.8 35.2 + - + +
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Residues in contact with LEU 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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16D LEU* 4.1 26.7 - - + -
17D ASN 5.1 5.6 - - - +
20D ILE* 3.5 24.8 - - + +
21D LYS 2.9 13.6 + - - +
22D LYS* 3.4 10.3 - - - +
24D GLU* 1.3 72.1 - - - +
26D LYS* 1.3 67.4 + - - +
28D SER* 3.3 3.2 + - - -
29D LEU* 2.9 35.3 + - + +
44D VAL* 3.6 31.4 - - + -
46D ARG* 6.1 1.6 - - + -
52D GLY 6.3 0.9 - - - +
53D GLN 4.9 2.5 - - - +
76D PHE* 3.9 23.1 - - + -
77D TYR* 4.9 2.5 - - + -
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Residues in contact with LYS 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 LYS* 2.9 47.5 + - - +
23D ASP* 3.6 8.1 - - - +
25D LEU* 1.3 75.3 - - - +
27D LYS* 1.3 60.0 + - + +
29D LEU* 3.3 6.0 + - - +
30D HIS* 3.0 28.3 + - - +
41D ASP* 6.0 0.2 - - - +
42D ILE* 3.1 45.0 + - + +
43D LEU* 4.4 2.4 - - - +
44D VAL* 3.7 27.4 + - + +
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Residues in contact with LYS 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 ASP* 3.0 48.8 + - - +
24D GLU* 3.8 6.7 - - + +
26D LYS* 1.3 76.1 - - + +
28D SER* 1.3 65.3 + - - +
30D HIS* 3.4 6.7 + - - +
31D ALA* 3.0 23.6 + - - +
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Residues in contact with SER 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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24D GLU* 2.8 18.5 + - - +
25D LEU 3.9 2.0 - - - -
27D LYS* 1.3 78.3 - - - +
29D LEU* 1.3 61.7 + - - +
31D ALA* 3.3 7.1 + - - +
32D ILE* 3.0 29.6 + - - +
76D PHE* 3.5 25.4 - - - -
77D TYR* 2.7 27.2 + - - -
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Residues in contact with LEU 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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13D ILE* 3.9 8.1 - - + -
16D LEU* 4.5 4.3 - - + -
25D LEU* 2.9 36.9 + - + +
26D LYS 3.5 4.7 - - - +
28D SER* 1.3 75.0 - - - +
30D HIS* 1.3 63.1 + - - +
32D ILE* 3.4 3.2 + - - -
33D PHE* 3.1 55.8 + - + +
42D ILE* 3.9 18.1 - - + +
44D VAL* 4.0 11.7 - - + -
54D ALA* 3.5 29.8 - - + -
56D VAL* 5.1 1.6 - - + -
76D PHE* 4.2 11.0 - - + -
81D MET* 3.8 16.6 - - + -
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Residues in contact with HIS 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 LYS 3.0 16.1 + - - +
27D LYS* 3.7 8.1 - - - +
29D LEU* 1.3 75.5 - - - +
31D ALA* 1.3 67.4 + - - +
34D SER* 3.0 51.1 + - - -
39D ILE* 4.2 26.7 + - + +
42D ILE* 3.5 20.6 - - + +
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Residues in contact with ALA 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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27D LYS 3.0 16.6 + - - +
28D SER* 3.3 8.0 + - - +
30D HIS* 1.3 78.6 + - - +
32D ILE* 1.3 66.7 + - + +
33D PHE 3.4 0.5 + - - -
34D SER* 3.9 10.1 + - - -
35D ARG* 4.9 4.2 + - - +
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Residues in contact with ILE 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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28D SER* 3.0 21.1 + - - +
29D LEU* 3.7 5.2 - - - +
30D HIS 3.2 0.2 - - - -
31D ALA* 1.3 83.0 - - + +
33D PHE* 1.3 84.2 + - + +
35D ARG* 4.7 5.0 - - - +
36D PHE* 3.5 16.3 - - - -
71D MET* 4.3 18.7 - - - +
74D PHE* 5.3 11.4 - - + -
76D PHE* 3.6 26.5 - - + -
81D MET* 4.9 7.9 - - - -
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Residues in contact with PHE 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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11D ILE* 4.0 7.0 - - + -
13D ILE* 3.7 14.1 - - + -
29D LEU* 3.1 33.6 + - + +
32D ILE* 1.3 89.0 - - + +
34D SER* 1.3 64.7 + - - +
35D ARG 3.2 2.9 - - - -
36D PHE* 3.1 22.7 + + - -
39D ILE* 3.7 13.5 - - + -
56D VAL* 4.4 9.6 - - + -
58D PHE* 3.5 20.4 - + + -
67D ALA* 3.6 31.4 - - + -
71D MET* 3.5 27.8 - - + -
81D MET* 3.7 31.6 - - + -
83D ILE* 3.9 13.0 - - + -
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Residues in contact with SER 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 HIS* 3.0 41.6 + - - -
31D ALA* 3.9 7.4 + - - -
32D ILE 3.8 0.4 - - - -
33D PHE* 1.3 76.2 - - - +
35D ARG* 1.3 63.7 + - - +
37D GLY* 3.0 22.5 + - - +
39D ILE* 3.6 10.1 - - - +
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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