Contacts of the helix formed by residues 23 - 38 (chain D) in PDB entry 5DPR
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 SER 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLN 3.6 6.1 - - - -
21C ARG 3.3 21.3 - - - -
22C ARG* 4.2 1.1 - - - -
23C SER* 3.8 22.6 - - - +
26C ASP* 5.3 2.6 + - - -
22D ARG* 1.3 76.1 - - - +
24D PHE* 1.3 64.4 + - - +
25D ALA* 3.8 6.6 + - - +
26D ASP* 3.2 33.0 + - - +
27D ARG* 2.9 22.4 + - - -
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Residues in contact with PHE 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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16C ARG* 3.2 63.7 - - - +
20C GLN 2.9 11.5 + - - +
21C ARG* 4.4 3.7 + - - +
23D SER* 1.3 73.2 - - - +
25D ALA* 1.3 60.6 + - + +
27D ARG* 3.4 26.9 + - - +
28D CYS* 3.0 53.4 + - - -
115D ASP* 5.1 0.9 - - - -
116D GLU* 3.9 21.1 - - + -
117D ASP* 4.0 16.8 - - + -
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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
----------------------------------------------------------
21C ARG 5.4 0.8 + - - +
23D SER* 3.2 7.4 + - - +
24D PHE* 1.3 82.8 - - + +
26D ASP* 1.3 67.4 + - - +
28D CYS* 3.3 7.2 + - - +
29D LYS* 3.1 40.8 + - - +
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Residues in contact with ASP 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 5.1 3.6 + - - -
26C ASP* 5.0 6.6 - - - +
22D ARG* 3.5 38.7 + - - +
23D SER* 3.2 28.2 + - - +
25D ALA* 1.3 78.9 - - - +
27D ARG* 1.3 58.0 + - - +
29D LYS* 3.3 13.1 + - - +
30D GLU* 2.9 28.9 + - - +
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Residues in contact with ARG 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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16C ARG* 5.6 1.0 - - - +
20C GLN* 3.4 13.9 + - - +
18D PHE* 3.6 33.7 - - + -
19D LYS* 3.2 49.3 + - - +
22D ARG* 3.1 34.0 + - + +
23D SER 2.9 9.0 + - - +
24D PHE* 3.4 41.1 - - - +
26D ASP* 1.3 75.8 - - - +
28D CYS* 1.3 64.0 + - - +
30D GLU* 3.4 3.7 + - - -
31D VAL* 3.1 29.3 + - - +
115D ASP* 4.4 1.8 + - - -
117D ASP* 3.1 31.4 + - + +
119D PHE* 3.7 6.6 - - + -
121D TYR* 3.6 3.2 + - - -
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Residues in contact with CYS 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 PHE* 3.0 55.7 + - - +
25D ALA* 3.6 7.0 - - - +
27D ARG* 1.3 76.4 - - - +
29D LYS* 1.3 63.8 + - + +
31D VAL* 3.6 3.3 + - - +
32D GLN* 3.2 21.3 + - - +
116D GLU 4.6 2.7 - - - -
117D ASP* 3.7 25.1 - - - +
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Residues in contact with LYS 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* 3.1 30.4 + - - +
26D ASP* 3.7 14.7 + - - +
27D ARG 3.2 0.2 - - - -
28D CYS* 1.3 75.4 - - + +
30D GLU* 1.3 65.6 - - - +
32D GLN* 2.9 17.6 + - - +
33D GLN* 3.0 25.9 + - + +
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Residues in contact with GLU 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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18D PHE* 4.3 10.7 - - - -
22D ARG* 3.8 26.7 + - - +
26D ASP 2.9 17.1 + - - +
27D ARG* 3.4 6.2 + - - +
29D LYS* 1.3 76.0 - - - +
31D VAL* 1.3 63.0 + - - +
33D GLN* 3.5 16.1 + - - +
34D ILE* 3.2 33.2 + - + +
62D LYS* 2.6 38.9 + - - -
119D PHE* 4.1 12.7 - - + -
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Residues in contact with VAL 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 ARG 3.1 10.6 + - - +
28D CYS 3.9 2.5 - - - +
30D GLU* 1.3 76.9 - - - +
32D GLN* 1.3 65.2 + - - +
34D ILE* 3.8 5.2 - - - +
35D ARG* 3.0 32.8 + - + +
43D PRO* 4.3 5.6 - - + -
110D TYR* 4.2 8.1 - - - +
117D ASP 3.6 12.3 - - - +
118D GLY* 3.8 24.0 - - - +
119D PHE* 3.3 52.0 - - + +
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Residues in contact with GLN 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 CYS 3.2 11.2 + - - +
29D LYS* 2.9 12.4 + - - +
31D VAL* 1.3 79.0 - - - +
33D GLN* 1.3 66.0 + - + +
35D ARG* 4.2 5.1 - - - +
36D ASP* 3.2 55.4 + - - +
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Residues in contact with GLN 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 LYS* 3.0 19.3 + - + +
30D GLU* 3.9 20.6 - - - +
32D GLN* 1.3 76.9 - - + +
34D ILE* 1.3 60.3 + - + +
36D ASP* 3.4 5.8 + - - +
37D GLN* 2.9 34.6 + - - +
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Residues in contact with ILE 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 GLU* 3.2 28.8 + - + +
31D VAL* 3.8 5.8 - - - +
32D GLN 3.2 0.2 - - - -
33D GLN* 1.3 80.9 - - + +
35D ARG* 1.3 59.3 + - - +
37D GLN* 4.4 10.8 - - - +
38D HIS* 2.8 46.6 + - + +
41D LYS 5.4 0.4 - - - +
43D PRO* 4.2 17.7 - - + -
64D LEU* 3.7 34.5 - - + -
119D PHE* 6.3 1.6 - - + -
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Residues in contact with ARG 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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31D VAL* 3.0 28.9 + - + +
32D GLN* 4.3 7.2 - - - +
34D ILE* 1.3 73.8 - - + +
36D ASP* 1.3 65.8 + - - +
38D HIS 4.0 5.8 - - - -
39D PRO* 3.1 47.4 + - - +
41D LYS 4.2 8.6 + - - +
42D ILE* 4.0 17.9 - - - +
43D PRO* 4.4 12.7 - - + +
67D ASP* 4.6 1.8 + - - -
110D TYR* 3.2 43.1 - - - +
111D GLU* 3.8 11.9 + - - -
114D LYS* 5.2 1.4 - - - +
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Residues in contact with ASP 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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32D GLN* 3.2 43.7 + - - +
33D GLN* 3.6 5.5 - - - +
35D ARG* 1.3 81.5 - - - +
37D GLN* 1.3 61.7 + - - +
39D PRO* 3.6 12.3 - - - +
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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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33D GLN* 2.9 19.8 + - - +
34D ILE* 3.8 10.6 - - - +
36D ASP* 1.3 78.5 - - - +
38D HIS* 1.3 93.1 + - + +
39D PRO* 3.6 5.1 - - - +
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Residues in contact with HIS 38 (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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34D ILE* 2.8 32.1 + - + +
35D ARG* 3.4 4.9 - - - +
37D GLN* 1.3 117.4 + - + +
39D PRO* 1.3 63.6 - - - +
40D SER* 2.9 18.1 + - - +
41D LYS* 3.1 37.5 + - + +
64D LEU* 3.8 26.4 - - + +
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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