Contacts of the helix formed by residues 21 - 37 (chain C) in PDB entry 3ECS
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 ALA 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C MSE 1.3 79.5 - - - +
22C SER* 1.3 66.0 + - - +
23C ALA 4.4 0.7 - - - +
24C VAL* 3.1 16.7 + - + +
25C ALA 3.0 15.9 + - - -
108C ARG* 3.6 23.8 - - - +
132C ARG* 4.1 7.6 - - - +
231C GLU* 4.2 4.0 - - - +
233C PHE* 3.9 28.3 - - + -
234C LYS* 5.9 1.1 - - - -
503C SO4 5.6 4.3 - - - +
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Residues in contact with SER 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.6 5.3 - - - -
14C MSE 4.1 26.5 - - - -
20C MSE 3.3 3.0 + - - -
21C ALA* 1.3 71.8 - - - +
23C ALA* 1.3 56.1 + - - +
25C ALA* 2.8 4.9 + - - +
26C ALA* 2.7 35.4 + - - +
60C ASP* 4.2 13.7 - - - -
62C SER* 3.2 22.4 + - - -
64C ALA* 4.6 3.5 - - - +
65C VAL* 4.0 2.2 - - - +
132C ARG* 4.3 12.2 - - - +
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.2 0.8 - - - +
22C SER* 1.3 82.3 + - - +
24C VAL* 1.3 57.4 + - + +
26C ALA* 2.9 11.5 + - - +
27C ILE* 2.8 34.8 + - + +
64C ALA* 3.9 23.1 - - + +
65C VAL* 4.6 4.5 - - - +
68C GLY* 4.9 5.4 - - - -
104C ILE* 5.4 1.3 - - + -
233C PHE* 3.3 37.7 - - + -
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MSE 3.8 22.2 - - + -
21C ALA* 3.1 23.0 + - + +
23C ALA* 1.3 77.2 - - - +
25C ALA* 1.3 63.5 + - - +
27C ILE* 3.5 6.5 + - - +
28C ARG* 3.1 43.7 + - + +
101C LEU* 4.5 7.0 - - + -
104C ILE* 3.3 39.3 - - + +
105C SER* 5.5 3.8 - - - +
233C PHE* 4.6 4.7 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.4 13.9 - - + -
13C GLN* 3.8 10.1 - - + +
14C MSE 3.5 26.2 - - + -
20C MSE 3.6 21.1 - - - -
21C ALA 3.0 8.6 + - - +
22C SER 2.8 8.9 + - - +
24C VAL* 1.3 76.7 - - - +
26C ALA* 1.3 60.7 + - - +
28C ARG* 3.4 3.9 + - - +
29C THR* 2.9 30.3 + - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.2 18.1 - - + -
22C SER 2.7 12.2 + - - +
23C ALA* 2.9 17.5 + - - +
25C ALA* 1.3 77.7 - - - +
27C ILE* 1.3 58.8 + - + +
29C THR* 3.1 11.9 + - - -
30C LEU* 2.9 25.5 - - + +
57C CYS* 4.7 5.4 - - + -
65C VAL* 4.1 26.9 - - + +
69C GLY* 6.3 0.9 - - - +
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Residues in contact with ILE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ALA* 2.8 24.2 + - + +
24C VAL* 3.8 8.3 - - - +
26C ALA* 1.3 72.3 - - + +
28C ARG* 1.3 66.4 + - - +
29C THR 3.2 0.2 - - - -
30C LEU* 3.6 11.2 - - + +
31C LEU* 3.1 24.9 + - - +
68C GLY* 4.4 15.0 - - - +
69C GLY* 4.9 3.8 - - - +
72C PHE* 4.0 32.3 - - + -
100C PHE* 3.6 32.8 - - + -
101C LEU* 3.5 36.8 - - + +
104C ILE* 4.0 8.3 - - + -
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 3.7 11.9 + - + +
13C GLN* 3.2 29.8 - - - +
20C MSE 3.0 31.3 - - - +
24C VAL* 3.1 26.4 + - - +
25C ALA 3.7 5.8 - - - +
26C ALA 3.2 0.4 - - - -
27C ILE* 1.3 76.7 - - - +
29C THR* 1.3 59.8 + - - +
31C LEU* 3.6 5.9 + - - +
32C GLU* 3.2 15.9 + - - +
101C LEU* 2.9 46.4 - - + +
105C SER* 4.8 4.0 + - - -
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 4.3 2.0 - - - +
6C LEU* 4.9 8.2 + - - +
9C TYR* 3.3 34.5 - - + -
10C PHE* 3.6 27.8 - - + -
13C GLN* 4.2 2.0 - - + -
25C ALA 2.9 19.7 - - - +
26C ALA 3.1 8.0 + - - -
27C ILE 3.2 0.2 - - - -
28C ARG* 1.3 76.7 - - - +
30C LEU* 1.3 62.1 + - - +
31C LEU 3.2 0.4 - - - -
32C GLU* 3.1 1.7 + - - +
33C PHE* 2.7 36.9 + - - +
53C ILE* 4.7 4.5 - - - +
57C CYS* 3.9 11.6 - - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 2.9 30.0 + - + +
27C ILE* 3.6 11.2 - - + +
28C ARG 3.4 0.2 - - - -
29C THR* 1.3 87.6 + - - +
31C LEU* 1.3 51.7 + - - +
33C PHE* 3.1 7.2 + - + +
34C LEU* 2.5 37.6 + - - +
50C THR* 3.4 16.0 + - - +
53C ILE* 3.4 34.5 - - + +
54C GLU* 3.0 31.9 - - - +
57C CYS* 4.6 10.3 - - + -
69C GLY* 6.0 1.1 - - - -
72C PHE* 3.6 24.9 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ILE 3.1 12.7 + - - +
28C ARG* 3.7 9.9 - - - +
29C THR 3.2 0.2 - - - -
30C LEU* 1.3 77.6 - - - +
32C GLU* 1.3 62.5 + - - +
34C LEU* 3.2 8.2 + - + +
35C LYS* 3.0 37.6 + - - +
72C PHE* 4.2 13.2 - - + -
94C ILE* 3.9 35.0 - - + +
97C GLY* 4.0 19.5 - - - +
98C GLU* 3.8 23.6 - - + +
101C LEU* 4.0 25.4 - - + -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 4.4 9.0 - - - -
9C TYR* 3.1 47.1 - - + +
28C ARG 3.2 4.5 + - - +
29C THR 3.1 7.4 + - - +
31C LEU* 1.3 77.7 - - - +
33C PHE* 1.3 54.6 + - - +
35C LYS* 2.9 26.7 + - - +
36C ARG* 2.6 69.2 + - - +
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Residues in contact with PHE 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 3.5 41.2 - - + -
6C LEU* 3.4 23.6 - - + -
29C THR 2.7 21.4 + - - +
30C LEU* 3.4 5.2 - - + +
32C GLU* 1.3 72.6 - - - +
34C LEU* 1.3 54.7 + - - +
37C ASP* 2.6 66.4 + - + +
46C ARG* 4.7 3.8 - - - -
49C LEU* 3.4 36.1 - - + -
50C THR* 4.0 28.7 - - - -
53C ILE* 3.4 24.5 - - + -
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU 2.5 19.5 + - - +
31C LEU* 3.4 13.5 - - + +
32C GLU 3.1 0.2 - - - -
33C PHE* 1.3 81.5 - - + +
35C LYS* 1.3 63.2 + - - +
37C ASP* 3.7 4.9 + - - +
46C ARG* 3.4 26.9 - - - +
50C THR* 5.6 6.1 - - - +
72C PHE* 5.1 1.1 - - + -
76C ILE* 3.5 31.9 - - + -
91C LYS* 3.5 25.5 + - + -
93C MSE 4.0 9.9 - - + -
94C ILE* 3.4 40.1 - - + +
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 3.0 22.6 + - - +
32C GLU* 2.9 29.6 + - - +
34C LEU* 1.3 75.3 - - - +
36C ARG* 1.3 54.2 + - + +
37C ASP 2.7 14.6 + - - -
38C LYS* 2.8 26.0 + - - +
91C LYS* 4.1 0.7 + - - +
94C ILE* 3.7 33.4 - - + -
98C GLU* 3.3 24.9 + - - +
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 3.5 60.2 + - + +
5C GLU* 5.2 9.7 + - - +
9C TYR* 4.4 16.6 - - - -
32C GLU* 2.6 44.7 + - - +
35C LYS* 1.3 72.6 - - + +
37C ASP* 1.3 54.5 + - - +
38C LYS* 3.0 7.3 + - - +
39C GLY 4.6 2.3 + - - -
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MSE 4.0 10.6 + - - +
33C PHE* 2.6 53.0 + - + +
34C LEU 3.9 4.4 - - - +
35C LYS 2.7 6.5 + - - -
36C ARG* 1.3 72.8 - - - +
38C LYS* 1.3 61.5 + - - +
39C GLY 3.3 2.5 - - - -
40C GLU* 3.2 39.7 - - - +
46C ARG* 3.6 11.5 + - - +
49C LEU* 3.5 12.5 - - - +
91C LYS* 3.5 9.4 + - - -
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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
------------------------------------------------------------
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