Contacts of the helix formed by residues 22 - 31 (chain E) in PDB entry 2W3S
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 SER 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E THR 3.7 2.2 + - - -
21E GLN* 1.3 79.2 - - - +
23E LEU* 1.3 56.9 + - - +
24E LEU* 3.8 4.5 + - - +
25E GLU* 2.9 37.7 + - - +
26E TRP* 2.8 35.5 + - - +
40E ASN* 4.9 3.0 + - - -
62E ALA 3.9 2.2 - - - -
63E CYS* 3.4 26.3 + - - -
65E MET 3.6 6.7 - - - -
66E MET* 4.4 2.0 - - - +
67E LEU* 5.0 1.3 - - - -
209E SER* 6.3 0.7 - - - -
213E THR* 5.6 5.4 - - - +
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLN 4.2 0.4 + - - -
22E SER* 1.3 69.0 - - - +
24E LEU* 1.3 53.1 + - - +
26E TRP* 3.1 17.1 + - + +
27E LEU* 2.8 53.7 + - + +
49E VAL* 4.0 16.6 - - + -
51E ILE* 5.3 0.2 - - + -
62E ALA* 3.5 16.4 - - + +
65E MET* 3.1 25.3 + - + +
66E MET* 4.5 4.2 - - - +
67E LEU* 4.3 18.2 - - + +
70E ILE* 3.9 18.4 - - + -
75E LEU* 3.8 45.3 - - + -
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E SER* 3.1 5.8 - - - +
23E LEU* 1.3 72.1 - - - +
25E GLU* 1.3 70.4 + - - +
27E LEU* 4.1 3.2 - - - +
28E ARG* 3.2 46.1 + - + +
35E THR* 4.0 16.2 - - + +
36E LYS 4.1 7.6 - - - +
37E GLU* 3.8 24.7 - - + +
40E ASN* 3.7 25.1 - - - +
47E CYS* 3.8 20.9 - - + -
62E ALA* 2.8 31.2 + - - +
63E CYS* 3.8 11.0 - - + -
1464E FES 4.8 0.7 - - - -
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Residues in contact with GLU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLN* 3.7 22.2 - - + +
22E SER* 2.9 33.4 + - - +
24E LEU* 1.3 88.8 - - - +
26E TRP* 1.3 53.9 + - - +
28E ARG* 3.7 4.0 - - - +
29E ALA* 2.8 36.7 + - - +
37E GLU* 4.7 6.9 - - - +
40E ASN* 4.2 15.9 + - - +
213E THR* 5.9 1.6 - - - +
107F ARG* 4.8 15.2 - - - +
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Residues in contact with TRP 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.7 26.2 - + - -
7E LEU* 4.5 8.3 - - + -
12E ARG* 3.3 31.4 - - + -
14E VAL* 3.6 25.6 - - + +
21E GLN* 3.8 20.5 - - - +
22E SER 2.8 12.0 + - - +
23E LEU* 3.4 20.0 - - + +
25E GLU* 1.3 77.1 - - - +
27E LEU* 1.3 90.4 + - + +
29E ALA* 3.2 8.4 + - + +
30E GLU* 2.9 48.5 + - + +
67E LEU* 3.6 29.7 - - + +
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Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 3.7 29.8 - - + -
23E LEU* 2.8 45.6 + - + +
24E LEU* 4.1 2.9 - - - +
26E TRP* 1.3 87.1 - - + +
28E ARG* 1.3 60.6 + - + +
30E GLU* 2.8 20.4 + - - +
31E GLY 3.0 10.0 + - - -
32E LEU* 3.1 34.6 + - + +
35E THR* 3.9 18.6 - - + +
49E VAL* 4.2 7.9 - - + -
62E ALA* 4.5 1.1 - - + -
77E THR* 3.9 22.0 - - + -
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Residues in contact with ARG 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E LEU* 3.2 30.9 + - + +
25E GLU* 4.0 4.0 - - - +
27E LEU* 1.3 78.3 - - + +
29E ALA* 1.3 66.9 + - - +
31E GLY* 3.0 14.6 + - - +
32E LEU 4.6 9.4 - - - +
33E THR* 2.7 30.5 + - - +
35E THR* 2.7 39.9 + - - +
36E LYS* 4.1 7.5 - - - +
37E GLU* 4.9 11.1 - - - +
24F ASP* 3.0 44.3 + - - +
25F ASP* 2.8 21.4 + - - -
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Residues in contact with ALA 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E GLN* 5.3 5.6 - - - +
25E GLU 2.8 20.2 + - - +
26E TRP* 3.4 9.9 - - + +
28E ARG* 1.3 76.5 - - - +
30E GLU* 1.3 66.2 + - - +
31E GLY* 3.0 2.1 + - - -
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 6.3 0.2 - - + -
12E ARG* 3.0 31.9 + - - +
26E TRP* 2.9 55.8 + - + +
27E LEU* 2.8 15.4 + - - +
29E ALA* 1.3 73.9 - - - +
31E GLY* 1.3 59.6 + - - +
32E LEU* 3.3 12.3 + - + +
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Residues in contact with GLY 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU 3.0 0.2 + - - -
28E ARG 3.0 16.4 + - - -
29E ALA 3.0 2.3 - - - -
30E GLU* 1.3 78.3 - - - +
32E LEU* 1.3 57.2 + - - +
33E THR* 2.9 21.3 + - - +
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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