Contacts of the helix formed by residues 21 - 37 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H MSE 1.3 77.4 - - - +
22H SER* 1.3 65.4 + - - +
23H ALA* 4.1 5.6 - - + +
24H VAL* 2.9 29.5 + - + +
25H ALA* 3.3 8.8 + - - +
108H ARG* 3.6 14.3 - - - +
132H ARG* 4.1 10.5 - - - +
231H GLU* 4.6 3.4 - - - +
233H PHE* 4.5 13.7 - - + -
234H LYS* 5.7 1.6 - - - -
508H SO4 4.0 18.2 - - - +
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Residues in contact with SER 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.5 8.4 - - - -
14H MSE 3.7 22.7 - - - -
20H MSE 3.5 2.2 + - - -
21H ALA* 1.3 71.6 - - - +
23H ALA* 1.3 62.9 + - - +
25H ALA 3.5 0.7 + - - -
26H ALA* 3.2 20.6 + - - +
60H ASP* 3.6 20.6 + - - -
62H SER* 3.4 12.1 + - - -
64H ALA* 4.7 3.1 - - - +
65H VAL* 3.3 17.3 - - - +
132H ARG* 4.0 14.1 - - - +
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Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA* 2.9 3.4 + - + +
22H SER* 1.3 81.4 + - - +
24H VAL* 1.3 59.6 + - - +
26H ALA* 3.9 2.0 - - - +
27H ILE* 3.3 30.6 + - - +
64H ALA* 3.8 27.1 - - + +
65H VAL* 4.1 10.5 - - - +
68H GLY* 5.2 1.9 - - - -
233H PHE* 3.1 38.8 - - + -
234H LYS* 5.6 0.2 - - - -
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Residues in contact with VAL 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H MSE 3.9 21.3 - - + -
21H ALA* 2.9 22.0 + - + +
23H ALA* 1.3 75.0 - - - +
25H ALA* 1.3 66.6 + - - +
26H ALA 3.2 0.4 - - - -
27H ILE* 2.9 16.9 - - + +
28H ARG* 2.9 47.1 + - - +
101H LEU* 4.4 3.4 - - + -
104H ILE* 4.5 18.8 - - + +
105H SER* 5.9 2.5 - - - +
233H PHE* 4.5 14.1 - - + -
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Residues in contact with ALA 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.5 14.1 - - + -
13H GLN* 3.9 9.5 - - + +
14H MSE 3.4 22.4 - - + -
20H MSE 3.2 32.5 - - + -
21H ALA 3.3 4.3 + - - +
22H SER 3.8 2.7 - - - +
24H VAL* 1.3 79.0 - - - +
26H ALA* 1.3 62.1 + - - +
28H ARG* 3.1 4.2 + - - +
29H THR* 2.9 29.3 + - - +
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.2 19.5 - - + -
22H SER 3.2 14.0 + - - +
23H ALA 3.9 5.6 - - - +
24H VAL 3.2 0.6 - - - -
25H ALA* 1.3 79.9 - - - +
27H ILE* 1.3 62.9 + - + +
29H THR* 2.9 22.6 + - - -
30H LEU* 3.1 13.2 + - + +
57H CYS* 4.7 8.0 - - - -
65H VAL* 3.7 29.8 - - + +
69H GLY* 6.3 0.4 - - - -
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Residues in contact with ILE 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H ALA 3.3 17.7 + - - +
24H VAL* 2.9 23.6 - - + +
26H ALA* 1.3 76.9 - - + +
28H ARG* 1.3 60.2 + - - +
29H THR 3.3 0.2 - - - -
30H LEU* 3.4 10.3 + - + +
31H LEU* 3.1 21.8 + - - +
68H GLY* 4.0 28.9 - - - +
69H GLY* 4.2 6.1 - - - +
72H PHE* 4.1 26.1 - - + -
100H PHE* 5.0 4.3 - - + -
101H LEU* 3.3 20.6 - - + +
104H ILE* 3.1 36.1 - - + -
233H PHE* 6.1 1.8 - - + -
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Residues in contact with ARG 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TYR* 4.2 3.8 + - + +
13H GLN* 4.0 21.8 - - + +
20H MSE 4.0 21.3 - - - -
24H VAL* 2.9 29.8 + - - +
25H ALA* 3.4 6.5 - - - +
26H ALA 3.1 0.2 - - - -
27H ILE* 1.3 76.4 - - - +
29H THR* 1.3 60.0 + - - +
31H LEU* 3.3 7.7 + - - +
32H GLU* 2.9 27.2 + - - +
101H LEU* 3.1 45.1 + - + +
105H SER* 5.3 6.3 + - - -
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Residues in contact with THR 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MSE 4.4 1.0 - - - +
6H LEU* 4.2 13.6 - - - +
9H TYR* 3.3 35.2 - - + +
10H PHE* 3.5 30.7 - - + +
13H GLN* 4.5 2.2 - - + -
25H ALA 2.9 17.2 + - - +
26H ALA 2.9 12.6 + - - -
28H ARG* 1.3 76.1 - - - +
30H LEU* 1.3 54.8 + - - +
32H GLU* 3.5 1.4 - - - +
33H PHE* 2.6 36.3 + - - +
57H CYS* 4.1 15.8 - - - -
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Residues in contact with LEU 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA* 3.1 13.1 + - + +
27H ILE* 3.5 12.6 - - - +
28H ARG 3.2 0.2 - - - -
29H THR* 1.3 82.8 + - - +
31H LEU* 1.3 59.5 + - - +
33H PHE* 3.3 5.7 + - - +
34H LEU* 2.8 28.1 + - - +
50H THR* 4.1 16.5 + - - +
53H ILE* 3.2 39.3 - - + +
54H GLU* 3.3 34.5 - - - +
57H CYS* 5.1 4.5 - - - -
69H GLY* 4.6 8.3 - - - -
72H PHE* 3.7 30.3 - - + -
73H LEU* 5.7 2.2 - - + -
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H ILE 3.1 12.8 + - - +
28H ARG* 3.5 9.2 - - - +
29H THR 3.2 0.2 - - - -
30H LEU* 1.3 73.0 - - - +
32H GLU* 1.3 61.9 + - - +
34H LEU* 2.9 22.2 + - + +
35H LYS* 2.9 46.2 + - + +
72H PHE* 4.2 11.4 - - + -
94H ILE* 3.8 20.2 - - + +
97H GLY* 3.9 12.6 - - - +
98H GLU* 3.6 24.9 - - + +
101H LEU* 3.3 28.7 - - + -
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Residues in contact with GLU 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MSE 3.3 16.1 - - + +
9H TYR* 3.4 37.8 + - + +
28H ARG 2.9 16.6 + - - +
29H THR 3.5 4.7 - - - +
31H LEU* 1.3 78.0 - - - +
33H PHE* 1.3 56.9 + - - +
35H LYS* 3.6 27.0 + - - +
36H ARG* 2.8 47.2 + - - +
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Residues in contact with PHE 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MSE 3.4 48.9 - - + +
2H ASP* 5.5 0.2 - - - -
6H LEU* 4.1 5.2 - - + -
29H THR 2.6 21.1 + - - +
30H LEU 3.6 4.0 - - - +
31H LEU 3.1 0.2 - - - -
32H GLU* 1.3 72.4 - - - +
34H LEU* 1.3 57.8 + - - +
36H ARG* 4.4 0.4 - - - -
37H ASP* 2.7 65.1 + - + +
46H ARG* 5.4 3.8 - - - -
49H LEU* 4.3 16.6 - - + -
50H THR* 4.0 26.5 - - - -
53H ILE* 3.5 40.8 - - + -
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H LEU 2.8 13.3 + - - +
31H LEU* 2.9 12.1 + - + +
33H PHE* 1.3 80.2 - - - +
35H LYS* 1.3 66.1 + - - +
37H ASP* 3.3 15.0 - - - +
46H ARG* 3.4 38.1 + - - +
50H THR* 5.7 4.7 - - - +
72H PHE* 4.7 9.2 - - + -
76H ILE* 3.7 29.6 - - + -
91H LYS* 4.2 10.5 + - + -
93H MSE 4.0 2.9 - - + +
94H ILE* 3.5 41.6 - - + +
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Residues in contact with LYS 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 2.9 40.4 + - + +
32H GLU* 3.6 27.8 + - - +
34H LEU* 1.3 71.5 - - - +
36H ARG* 1.3 66.9 + - - +
37H ASP 3.0 13.4 + - - +
38H LYS* 3.9 14.2 - - - +
91H LYS* 5.5 0.2 + - - -
94H ILE* 3.6 26.2 - - + -
98H GLU* 3.6 20.4 + - - -
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Residues in contact with ARG 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MSE 3.3 48.7 + - + +
5H GLU* 2.9 38.6 + - - -
32H GLU* 2.8 28.6 + - - +
33H PHE* 4.4 0.9 - - - -
35H LYS* 1.3 78.1 - - - +
37H ASP* 1.3 60.0 + - - +
38H LYS* 3.7 7.8 + - - +
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Residues in contact with ASP 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MSE 5.3 3.8 - - - +
33H PHE* 2.7 52.8 + - + +
34H LEU* 3.3 10.7 - - - +
35H LYS 3.0 7.3 + - - +
36H ARG* 1.3 76.4 - - - +
38H LYS* 1.3 84.1 + - - +
40H GLU* 4.9 0.2 - - - +
42H ILE* 3.6 17.3 - - - +
46H ARG* 4.2 17.0 + - - +
49H LEU* 5.1 6.1 - - - +
91H LYS* 3.9 7.4 + - - -
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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
------------------------------------------------------------
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