Contacts of the helix formed by residues 25 - 37 (chain R) in PDB entry 2DYS
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 25 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23R ASP 3.4 6.0 + - - +
24R ILE* 1.3 75.9 - - - +
26R ALA* 1.3 65.3 + - - +
27R TRP* 3.0 12.4 + - - +
28R GLU* 2.8 51.9 + - - +
29R LEU* 3.0 20.6 + - - +
58R LEU* 3.9 8.0 - - - +
43S LYS* 5.2 7.3 + - - -
81S ARG* 4.7 4.3 + - - -
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Residues in contact with ALA 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25R ASP* 1.3 71.8 - - - +
27R TRP* 1.3 66.5 + - - +
29R LEU* 3.1 7.0 + - + +
30R ARG* 2.9 40.5 + - + +
58R LEU* 3.9 21.1 - - + +
60R ASP* 5.8 4.3 - - - +
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Residues in contact with TRP 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R TYR* 5.3 0.9 - - - -
25R ASP* 3.0 10.8 + - - +
26R ALA* 1.3 76.9 - - - +
28R GLU* 1.3 60.9 + - + +
30R ARG* 3.1 31.1 + - - +
31R LYS* 2.8 72.6 + - + +
81S ARG* 3.5 59.8 + - + +
82S CYS 3.6 20.0 - - - -
83S PRO* 4.3 5.3 - - + +
86S GLY* 3.5 22.7 - - - -
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Residues in contact with GLU 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R TYR* 2.4 38.9 + - + +
21R LYS* 2.8 33.4 + - - -
23R ASP 4.5 0.3 - - - +
24R ILE* 3.6 18.2 - - + +
25R ASP* 2.8 42.1 + - - +
27R TRP* 1.3 78.8 - - + +
29R LEU* 1.3 61.7 + - - +
31R LYS* 4.3 0.2 - - - -
32R GLY 3.0 8.7 + - - -
81S ARG* 3.4 29.8 + - - +
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Residues in contact with LEU 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q LEU* 4.5 8.7 - - + -
19R PHE* 4.0 15.7 - - + -
24R ILE* 4.3 6.5 - - + +
25R ASP 3.0 13.1 + - - +
26R ALA* 3.1 10.5 + - + +
28R GLU* 1.3 78.3 - - - +
30R ARG* 1.3 64.9 + - + +
32R GLY* 3.3 0.9 + - - -
33R MET* 3.1 23.9 + - + +
51R ALA 4.0 11.0 - - - +
54R ALA* 4.0 25.8 - - + -
55R CYS* 4.1 21.5 - - - -
58R LEU* 3.9 20.2 - - + -
60R ASP* 4.4 8.7 - - - +
63R SER* 4.3 15.3 - - - +
67R ILE* 4.9 6.1 - - + -
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Residues in contact with ARG 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q LEU* 3.4 30.5 + - + -
25Q PRO 2.9 29.3 + - - -
26Q ASP* 4.0 26.4 + - - +
26R ALA* 2.9 38.8 + - + +
27R TRP* 3.5 30.9 - - - +
29R LEU* 1.3 75.6 - - + +
31R LYS* 1.3 59.0 + - - +
33R MET 3.3 0.5 + - - -
34R ASN* 2.8 47.5 + - - +
63R SER* 5.8 1.8 - - - +
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Residues in contact with LYS 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18R TYR* 3.9 5.8 - - - +
27R TRP* 2.8 55.6 + - + +
28R GLU 3.9 4.0 - - - +
30R ARG* 1.3 71.3 - - - +
32R GLY* 1.3 56.0 + - - +
34R ASN* 3.8 3.8 - - + +
35R THR* 2.7 57.8 + - - +
83S PRO 3.1 28.3 - - - +
84S SER* 2.8 25.9 + - - +
85S CYS* 4.4 7.9 - - - +
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Residues in contact with GLY 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R TRP* 3.3 24.5 - - - -
18R TYR* 3.5 17.2 + - - -
19R PHE* 3.7 8.1 - - - -
28R GLU 3.0 11.6 + - - -
29R LEU 3.7 0.9 - - - -
31R LYS* 1.3 77.5 - - - +
33R MET* 1.3 56.8 + - - +
36R LEU* 2.8 32.1 + - - +
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Residues in contact with MET 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q PRO* 4.6 4.3 - - + -
24Q LEU* 3.7 24.2 - - + -
19R PHE* 3.6 29.8 - - + -
29R LEU* 3.1 13.1 + - + +
32R GLY* 1.3 72.2 - - - +
34R ASN* 1.3 67.4 + - - +
36R LEU* 3.2 14.4 + - + -
37R VAL* 3.1 36.9 + - + +
43R PRO* 5.5 1.8 - - + -
48R ILE* 4.9 9.2 - - + -
51R ALA* 4.1 12.1 - - - -
67R ILE* 4.0 33.2 - - + -
70R VAL* 4.0 26.5 - - + -
71R VAL* 5.5 0.7 - - + -
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Residues in contact with ASN 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q ASP 4.1 5.1 - - - +
22Q TYR* 3.4 36.7 + - + -
23Q PRO* 2.9 27.8 - - - +
24Q LEU* 2.9 35.5 + - - +
30R ARG* 2.8 32.5 + - - +
31R LYS* 4.1 4.2 - - + +
33R MET* 1.3 71.6 - - - +
35R THR* 1.3 60.4 + - - +
37R VAL* 3.5 18.0 - - - +
38R GLY* 4.1 3.5 + - - -
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Residues in contact with THR 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O SER* 5.8 0.9 - - - -
15R TRP* 3.9 22.2 - - + -
31R LYS* 2.7 48.9 + - - +
32R GLY 3.7 3.1 - - - -
34R ASN* 1.3 76.6 - - - +
36R LEU* 1.3 65.0 + - - +
38R GLY* 3.1 15.9 + - - -
39R TYR* 3.8 17.6 - - + +
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Residues in contact with LEU 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R PHE* 3.9 30.7 - - + -
15R TRP* 3.9 19.7 - - + -
19R PHE* 4.0 15.5 - - + -
32R GLY 2.8 17.1 + - - +
33R MET* 3.2 16.1 + - + +
35R THR* 1.3 78.4 - - - +
37R VAL* 1.3 58.5 + - + +
38R GLY 3.0 4.2 + - - -
39R TYR* 3.2 27.5 + - + +
41R LEU* 4.7 4.9 - - + +
43R PRO* 3.8 28.5 - - + +
47R ILE* 3.8 28.3 - - + -
48R ILE* 5.3 0.2 - - + -
74R LYS* 5.0 1.2 - - - -
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Residues in contact with VAL 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O THR* 4.0 6.1 + - - -
53O THR* 4.7 1.4 + - - -
20Q ARG 5.2 0.2 - - - +
21Q ASP* 3.7 27.7 - - + +
23Q PRO* 3.9 13.0 - - + -
33R MET* 3.1 20.6 + - + +
34R ASN 3.5 16.4 - - - +
35R THR 3.3 0.2 - - - -
36R LEU* 1.3 76.1 - - + +
38R GLY* 1.3 56.9 + - - +
39R TYR 3.3 0.7 - - - -
43R PRO* 5.6 4.7 - - + -
70R VAL* 3.7 35.4 - - + -
74R LYS* 3.1 41.9 + - + +
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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