Contacts of the helix formed by residues 21 - 35 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MSE 1.3 77.9 - - - +
22A SER* 1.3 66.4 + - - +
23A ALA 4.2 1.6 - - - +
24A VAL* 3.1 34.0 + - + +
25A ALA* 3.2 10.4 + - - +
108A ARG* 3.1 23.9 - - - +
132A ARG* 4.4 6.7 - - - +
231A GLU* 4.4 3.8 - - - +
233A PHE* 3.8 21.1 - - + -
234A LYS* 5.9 2.0 - - - -
501A SO4 5.4 2.9 - - - +
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.5 8.5 - - - -
14A MSE 3.6 27.0 - - - +
20A MSE 3.4 2.0 + - - -
21A ALA* 1.3 73.3 - - - +
23A ALA* 1.3 62.0 + - - +
25A ALA* 3.3 5.4 + - - +
26A ALA 3.3 15.4 + - - -
60A ASP* 2.4 31.4 + - - -
62A SER* 3.6 13.8 + - - -
64A ALA* 5.7 2.0 - - - -
65A VAL* 3.6 8.7 - - - +
132A ARG* 4.8 3.6 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 3.1 0.6 - - - -
22A SER* 1.3 78.3 - - - +
24A VAL* 1.3 61.3 + - - +
26A ALA* 3.2 4.0 + - - +
27A ILE* 2.9 33.7 + - + +
64A ALA* 3.8 25.2 - - + +
65A VAL* 4.1 12.7 - - - +
68A GLY* 5.0 4.9 - - - -
233A PHE* 3.5 37.0 - - + -
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MSE 3.8 15.9 - - + -
21A ALA* 3.1 27.9 + - + +
23A ALA* 1.3 72.3 - - - +
25A ALA* 1.3 55.6 + - - +
27A ILE* 3.7 5.4 - - - +
28A ARG* 2.7 59.2 + - - +
101A LEU* 4.2 13.6 - - + +
104A ILE* 4.3 15.9 - - + +
105A SER* 5.3 6.5 - - - -
233A PHE* 4.0 20.0 - - + -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 3.6 10.3 - - + -
13A GLN* 4.1 8.2 - - + +
14A MSE 3.5 20.9 - - + -
20A MSE 3.1 34.5 - - + -
21A ALA 3.2 5.0 + - - +
22A SER 3.4 10.3 - - - +
23A ALA 3.2 0.2 - - - -
24A VAL* 1.3 78.9 - - - +
26A ALA* 1.3 57.8 + - - +
28A ARG* 3.1 6.6 - - - +
29A THR* 2.9 27.9 + - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.2 26.7 - - + -
22A SER 3.3 3.5 + - - +
23A ALA* 3.2 9.5 + - - +
25A ALA* 1.3 74.6 - - - +
27A ILE* 1.3 63.2 + - + +
28A ARG 3.0 0.9 - - - -
29A THR* 2.7 20.7 + - - -
30A LEU* 2.8 20.3 + - + +
57A CYS* 4.7 10.5 - - + -
65A VAL* 4.4 21.1 - - + +
69A GLY* 6.3 1.8 - - - -
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 2.9 24.6 + - + +
24A VAL 3.8 3.1 - - - +
26A ALA* 1.3 73.5 - - + +
28A ARG* 1.3 65.3 + - - +
30A LEU* 3.2 9.9 + - + +
31A LEU* 3.0 22.9 + - + +
68A GLY* 3.9 25.1 - - - +
69A GLY* 4.7 3.6 - - - +
72A PHE* 3.7 35.0 - - + -
100A PHE* 3.4 27.8 - - + -
101A LEU* 4.2 19.5 - - + -
104A ILE* 3.5 19.7 - - + -
233A PHE* 5.3 3.1 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A TYR* 3.5 14.7 + - - +
13A GLN* 2.9 44.2 - - - +
20A MSE 4.4 8.4 - - - -
24A VAL* 2.7 25.1 + - - +
25A ALA* 3.1 14.1 - - - +
27A ILE* 1.3 78.8 - - - +
29A THR* 1.3 58.0 + - - +
31A LEU* 3.7 3.2 + - - +
32A GLU* 3.1 16.8 + - - +
101A LEU* 3.3 47.8 - - + +
105A SER* 5.0 7.7 + - - -
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.3 0.6 - - + +
6A LEU* 3.5 41.1 - - + +
9A TYR* 3.5 20.9 + - + -
10A PHE* 3.2 28.3 + - + +
25A ALA 2.9 13.1 + - - -
26A ALA* 2.7 19.7 + - - -
28A ARG* 1.3 70.0 - - - +
30A LEU* 1.3 66.1 + - + +
32A GLU* 3.1 4.7 - - - +
33A PHE* 2.8 19.4 + - - +
57A CYS* 5.1 6.5 - - - -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.8 0.2 - - + -
26A ALA* 2.8 24.7 + - + +
27A ILE* 3.6 9.4 - - - +
29A THR* 1.3 75.7 - - + +
31A LEU* 1.3 57.1 + - - +
33A PHE* 2.4 34.3 + - - +
34A LEU* 2.9 12.6 + - + -
50A THR* 5.2 2.9 - - + -
53A ILE* 3.3 36.6 - - + +
54A GLU* 3.2 32.5 - - + +
57A CYS* 5.4 6.7 - - - -
69A GLY* 4.6 7.2 - - - -
72A PHE* 3.3 38.4 - - + -
73A LEU* 4.3 1.3 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE 3.0 14.3 + - - +
28A ARG* 3.7 5.2 - - - +
30A LEU* 1.3 77.2 - - - +
32A GLU* 1.3 60.6 + - - +
34A LEU* 3.5 8.4 + - + +
35A LYS* 3.2 36.0 + - - +
72A PHE* 4.1 14.4 - - + -
93A MSE 5.0 0.2 - - - +
94A ILE* 3.8 33.4 - - + +
97A GLY* 4.0 17.7 - - - +
98A GLU* 3.7 27.8 - - + -
101A LEU* 3.6 26.5 - - + -
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.9 14.8 - - + -
9A TYR* 3.2 56.1 + - + +
28A ARG 3.1 5.8 + - - +
29A THR 3.1 9.6 - - - +
30A LEU 2.6 3.8 + - - -
31A LEU* 1.3 71.7 - - - +
33A PHE* 1.3 56.9 + - - +
35A LYS* 2.7 51.8 + - - +
36A ARG* 4.0 18.6 + - - +
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.5 37.7 - - + -
2A ASP* 4.8 2.2 - - - -
6A LEU* 3.4 26.0 - - + -
29A THR 2.8 11.8 + - - +
30A LEU* 2.4 29.4 + - - +
32A GLU* 1.3 64.2 - - - +
34A LEU* 1.3 65.4 + - + -
35A LYS 2.9 4.9 - - - -
36A ARG* 2.9 25.7 - - + +
49A LEU* 3.4 42.6 - - + -
50A THR* 4.4 8.7 - - - -
53A ILE* 3.4 27.6 - - + -
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Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 2.9 11.7 + - + +
31A LEU* 3.7 11.7 - - + +
32A GLU 3.2 0.2 - - - -
33A PHE* 1.3 82.0 - - + +
35A LYS* 1.3 55.9 + - - +
36A ARG 2.9 13.8 + - - +
50A THR* 3.7 20.4 - - + +
72A PHE* 4.7 8.3 - - + -
76A ILE* 3.7 30.1 - - + -
90A LYS* 3.5 36.5 - - + +
93A MSE 3.8 26.5 - - + +
94A ILE* 3.1 27.2 - - + +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.2 27.2 - - - +
32A GLU* 2.7 32.8 + - - +
34A LEU* 1.3 76.1 - - - +
36A ARG* 1.3 70.5 + - - +
94A ILE* 3.5 29.8 - - + -
98A GLU* 2.8 30.3 + - - -
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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