Contacts of the helix formed by residues 20 - 35 (chain A) in PDB entry 3E2I
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 GLY 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE 3.3 1.4 + - - -
19A SER* 1.3 68.4 - - - +
21A LYS* 1.3 63.4 + - - +
22A SER 3.3 3.1 - - - -
23A GLU* 3.2 23.5 + - - +
24A GLU* 3.0 22.7 + - - +
141A LEU* 4.0 2.8 - - - +
201A GOL 2.4 33.2 - - - -
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.9 15.8 - - + +
14A THR* 3.6 14.1 - - - +
15A GLY 3.2 14.6 + - - +
16A SER 2.9 15.8 + - - -
17A MSE 4.0 1.2 - - - +
19A SER* 3.3 13.4 - - - +
20A GLY* 1.3 75.3 - - - +
22A SER* 1.3 57.8 + - - +
24A GLU* 3.3 3.1 + - - +
25A LEU* 2.9 27.5 + - - +
88A ASP* 5.6 0.9 - - - +
89A GLU* 5.4 4.9 - - - -
91A GLN* 5.3 0.2 - - - -
114A ALA* 4.2 8.6 - - + +
115A GLY* 3.1 41.5 - - - +
116A LEU* 3.2 21.1 - - - +
141A LEU* 3.9 9.9 - - + -
201A GOL 2.7 32.4 + - - +
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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
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21A LYS* 1.3 75.5 - - - +
23A GLU* 1.3 67.0 + - - +
25A LEU* 3.4 5.4 + - - +
26A ILE* 3.1 30.4 + - - +
88A ASP* 2.8 37.5 + - - +
89A GLU* 3.2 7.1 + - - -
201A GOL 2.8 26.1 + - - -
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Residues in contact with GLU 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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20A GLY* 3.2 26.4 + - - +
22A SER* 1.3 79.9 - - - +
24A GLU* 1.3 57.4 + - - +
26A ILE* 3.4 7.0 + - - +
27A ARG* 3.0 28.1 + - - +
201A GOL 4.2 10.0 + - - -
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Residues in contact with GLU 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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13A ILE* 3.9 12.8 - - + -
20A GLY 3.0 13.3 + - - +
21A LYS 3.3 7.8 + - - +
23A GLU* 1.3 73.3 - - - +
25A LEU* 1.3 64.9 + - - +
27A ARG* 2.8 47.0 + - - +
28A ARG* 2.8 51.1 + - - +
139A THR* 6.0 0.4 - - - -
141A LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 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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13A ILE* 3.7 13.1 - - + +
21A LYS 2.9 14.1 + - - +
22A SER 3.5 8.7 - - - +
24A GLU* 1.3 75.5 - - - +
26A ILE* 1.3 65.8 + - + +
28A ARG* 3.2 4.6 + - - +
29A LEU* 3.0 41.6 + - + +
41A VAL* 4.1 12.1 - - + -
86A GLY* 4.1 2.0 - - - -
87A ILE 4.0 4.7 - - - +
88A ASP* 3.6 46.4 - - + +
112A ILE* 3.5 43.5 - - + +
114A ALA* 4.1 6.1 - - + -
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Residues in contact with ILE 26 (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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22A SER* 3.1 19.0 + - - +
23A GLU* 3.7 7.2 - - - +
25A LEU* 1.3 79.6 - - + +
27A ARG* 1.3 63.8 + - - +
29A LEU* 3.2 20.6 + - + +
30A ARG* 2.9 52.1 + - - +
41A VAL* 4.8 7.0 - - + -
43A LYS* 4.5 18.6 - - - +
63A ILE* 4.7 12.3 - - + -
88A ASP* 6.0 1.8 - - - +
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Residues in contact with ARG 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 GLU 3.0 15.0 + - - +
24A GLU* 2.8 46.9 + - - +
26A ILE* 1.3 78.6 - - - +
28A ARG* 1.3 77.1 + - - +
30A ARG* 4.7 2.7 - - - +
31A ARG* 2.7 63.9 + - - +
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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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11A GLU* 3.1 40.9 + - - +
12A CYS 4.9 1.6 + - - -
13A ILE* 3.8 26.8 - - - +
24A GLU* 2.8 39.0 + - - +
25A LEU* 3.7 7.4 - - - +
27A ARG* 1.3 86.3 - - - +
29A LEU* 1.3 64.4 + - - +
31A ARG* 3.2 22.6 + - - +
32A GLY 3.6 2.6 + - - -
110A ARG* 4.0 17.3 + - - +
112A ILE* 3.8 16.4 - - + -
137A GLN* 4.4 8.1 + - - +
139A THR* 2.9 39.2 + - - +
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Residues in contact with LEU 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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25A LEU* 3.0 30.4 + - + +
26A ILE* 3.2 17.0 + - + +
28A ARG* 1.3 76.8 - - - +
30A ARG* 1.3 56.4 + - - +
32A GLY* 2.9 23.2 + - - -
33A ILE* 3.4 5.0 + - - +
39A VAL* 3.6 22.7 - - + +
41A VAL* 3.6 36.3 - - + -
63A ILE* 3.8 15.0 - - + -
84A VAL* 3.6 29.4 - - + -
86A GLY* 4.0 15.3 - - - +
112A ILE* 4.0 10.8 - - + -
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Residues in contact with ARG 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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26A ILE* 2.9 40.3 + - - +
27A ARG* 5.3 1.6 - - - +
28A ARG 3.3 0.2 - - - -
29A LEU* 1.3 73.8 - - - +
31A ARG* 1.3 87.6 + - - +
33A ILE* 3.1 24.5 + - + +
34A TYR* 3.2 42.6 + - + -
57A SER 4.7 16.0 + - - +
63A ILE* 4.1 10.1 - - + +
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Residues in contact with ARG 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 ARG* 2.7 68.4 + - - +
28A ARG* 3.2 12.8 + - - +
30A ARG* 1.3 96.3 - - - +
32A GLY* 1.3 61.6 + - - +
34A TYR* 3.3 35.7 + - - +
35A ALA* 3.1 22.3 + - - +
110A ARG* 5.2 5.8 - - - +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ARG 3.6 4.0 + - - -
29A LEU 2.9 10.3 + - - -
31A ARG* 1.3 76.2 - - - +
33A ILE* 1.3 61.6 + - - +
35A ALA* 3.0 8.2 + - - +
37A GLN* 2.9 45.0 + - - +
39A VAL* 3.9 14.8 - - - -
84A VAL* 4.8 3.8 - - - -
110A ARG* 5.1 3.8 - - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU 3.4 6.8 + - - +
30A ARG* 3.1 17.4 + - + +
32A GLY* 1.3 75.3 - - - +
34A TYR* 1.3 58.6 + - + +
36A LYS* 2.9 18.7 + - - +
37A GLN 4.3 0.2 - - - +
39A VAL* 3.9 16.6 - - + +
57A SER* 4.6 4.0 - - - +
58A HIS* 3.7 27.8 - - + +
61A ASN* 3.2 49.1 + - + +
62A ALA 3.5 8.5 - - - +
63A ILE* 3.5 46.2 - - + +
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG* 3.2 39.2 + - + -
31A ARG* 3.3 37.0 + - - +
33A ILE* 1.3 76.2 - - + +
35A ALA* 1.3 56.5 + - - +
36A LYS* 3.2 7.1 + - - +
57A SER 5.6 0.7 + - - -
58A HIS* 3.3 54.2 + + + +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ARG 3.1 10.8 + - - +
32A GLY 3.0 10.1 + - - +
34A TYR* 1.3 75.9 - - - +
36A LYS* 1.3 75.8 + - - +
37A GLN* 3.4 19.5 + - + +
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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