Contacts of the helix formed by residues 21 - 32 (chain E) in PDB entry 3SWD
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E GLY* 1.3 69.1 - - - -
22E LYS* 1.3 59.5 + - - +
23E ASN 4.4 1.8 - - - +
24E ALA* 3.1 11.0 + - + +
25E ALA* 2.9 30.7 + - - +
45E PRO* 4.4 0.7 - - - -
190E GLU* 4.6 9.6 - - + +
228E VAL* 3.6 3.4 - - - +
229E LEU* 2.7 40.3 + - + +
230E PRO 3.8 8.5 - - - +
231E ASP* 3.5 15.8 - - + +
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Residues in contact with LYS 22 (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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20E GLY 3.2 3.4 + - - -
21E ALA* 1.3 70.8 - - - +
23E ASN* 1.3 81.2 + - - +
24E ALA 3.2 0.2 + - - -
25E ALA* 3.4 2.0 + - - +
26E LEU* 3.1 42.8 + - + +
45E PRO* 4.1 8.7 - - - -
47E LEU* 4.1 25.8 - - + -
49E ASP* 3.1 25.7 + - - -
231E ASP* 3.2 10.6 + - - +
370E LEU* 3.5 18.2 - - - -
371E ARG* 3.7 20.2 - - - +
397E ARG 3.9 4.9 - - - +
398E GLY* 3.7 21.1 - - - -
501E EPZ 2.7 27.6 + - - +
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Residues in contact with ASN 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 ALA* 3.2 2.4 - - - +
22E LYS* 1.3 103.6 + - - +
24E ALA* 1.3 55.7 + - - +
26E LEU* 4.7 2.8 - - - +
27E PRO* 3.1 23.1 - - - +
95E TRP* 4.9 0.2 - - - -
163E VAL* 6.2 0.2 - - - +
190E GLU* 3.3 27.9 - - + +
233E ILE* 6.0 1.0 - - - +
305E ASP* 4.1 7.3 + - - -
371E ARG* 4.3 10.6 - - - +
501E EPZ 3.0 65.2 + - - +
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Residues in contact with ALA 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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21E ALA* 3.1 14.4 + - + +
23E ASN* 1.3 75.2 - - - +
25E ALA* 1.3 69.0 + - - +
26E LEU 3.2 1.3 - - - -
27E PRO* 2.9 12.6 - - - +
28E ILE* 3.2 23.3 + - + +
190E GLU* 3.9 13.0 - - + +
193E ASP* 4.0 11.9 - - + +
194E THR* 4.5 0.4 + - - -
228E VAL* 3.6 21.1 - - + -
229E LEU* 3.7 14.1 - - + -
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Residues in contact with ALA 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 ALA 2.9 16.1 + - - +
22E LYS 3.7 4.5 - - - +
24E ALA* 1.3 76.9 - - - +
26E LEU* 1.3 57.3 + - - +
28E ILE* 3.7 1.0 - - - +
29E LEU* 2.9 41.3 + - + +
44E VAL* 4.1 31.0 - - + -
45E PRO* 4.3 8.7 - - + -
50E VAL* 4.4 9.4 - - + -
228E VAL* 4.1 13.3 - - + +
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Residues in contact with LEU 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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22E LYS* 3.1 30.6 + - + +
23E ASN* 4.7 3.6 - - - +
25E ALA* 1.3 79.3 - - - +
27E PRO* 1.4 65.9 - - + +
29E LEU* 3.4 5.0 + - + +
30E PHE* 3.0 32.4 + - + -
49E ASP* 4.0 31.6 - - + +
50E VAL* 4.1 16.4 - - + -
53E SER* 3.5 19.3 - - - +
90E MET* 3.8 25.4 - - - -
92E ALA* 4.1 16.2 - - + -
95E TRP* 4.2 9.4 - - + -
501E EPZ 4.7 2.5 - - + -
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Residues in contact with PRO 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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23E ASN 3.1 25.4 - - - +
24E ALA 2.9 20.2 - - - +
26E LEU* 1.4 82.5 - - + +
28E ILE* 1.3 58.7 + - - +
30E PHE* 3.2 4.6 + - + +
31E ALA* 2.8 28.5 + - - +
95E TRP* 3.4 32.3 - - + -
163E VAL* 6.5 0.2 - - + -
167E VAL* 4.1 22.4 - - + +
190E GLU* 5.2 1.8 - - + +
194E THR* 3.4 22.1 - - + +
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Residues in contact with ILE 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 ALA* 3.2 21.8 + - + +
25E ALA* 3.7 3.1 - - - +
27E PRO* 1.3 76.3 - - - +
29E LEU* 1.3 63.5 + - - +
31E ALA* 3.0 17.6 + - - +
32E ALA* 3.0 11.4 + - - +
41E ILE* 3.5 33.4 - - + -
193E ASP* 4.1 26.5 - - - +
194E THR* 4.1 13.7 - - - +
197E PHE* 3.7 30.1 - - + -
226E TYR* 4.2 10.3 - - + -
228E VAL* 3.9 22.0 - - + -
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Residues in contact with LEU 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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25E ALA* 2.9 35.1 + - + +
26E LEU* 3.9 5.4 - - - +
27E PRO 3.3 0.2 - - - -
28E ILE* 1.3 74.2 - - + +
30E PHE* 1.3 63.1 + - + +
32E ALA* 3.3 16.6 - - - +
33E LEU 4.2 0.2 + - - -
41E ILE* 4.4 25.4 - - + -
44E VAL* 5.0 2.0 - - + -
50E VAL* 4.1 26.2 - - + +
53E SER* 3.9 25.4 - - - -
54E MET* 4.6 9.2 - - + -
57E LEU* 3.6 26.5 - - + +
70E VAL* 4.6 10.5 - - + -
72E ILE* 4.0 23.1 - - + -
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Residues in contact with PHE 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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26E LEU* 3.0 27.4 + - + -
27E PRO 3.2 6.1 + - - +
28E ILE 3.1 0.4 - - - -
29E LEU* 1.3 73.9 - - - +
31E ALA* 1.3 63.8 + - - +
32E ALA 3.1 2.0 - - - -
33E LEU* 3.2 18.4 + - + +
53E SER* 3.7 31.6 - - - -
56E LEU* 3.5 35.4 - - + -
57E LEU* 4.3 17.7 - - + -
90E MET* 4.2 9.9 - - + -
92E ALA* 4.2 10.1 - - + -
93E SER* 4.1 14.4 - - - -
95E TRP* 3.8 35.2 - + + +
96E ALA* 4.0 17.0 - - + -
99E PRO* 3.4 16.1 - - + +
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Residues in contact with ALA 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 PRO 2.8 17.0 + - - +
28E ILE* 3.0 5.8 + - - +
30E PHE* 1.3 71.8 - - - +
32E ALA* 1.3 59.3 + - - +
33E LEU 3.0 2.9 - - - -
34E LEU* 2.9 32.3 + - - +
35E ALA 4.1 0.7 + - - -
99E PRO* 4.4 8.3 - - - -
171E CYS* 4.1 14.8 - - - -
194E THR* 4.6 2.2 - - + -
197E PHE* 3.9 13.7 - - + -
198E LEU* 3.8 25.7 - - + +
201E LEU* 5.1 1.0 - - - +
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Residues in contact with ALA 32 (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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28E ILE 3.0 9.9 + - - +
29E LEU 3.3 16.2 - - - +
30E PHE 3.1 0.4 - - - -
31E ALA* 1.3 71.1 - - - +
33E LEU* 1.3 57.4 + - + +
34E LEU 2.9 11.2 + - - -
35E ALA* 2.9 22.5 + - - +
39E VAL* 4.1 13.0 - - + +
41E ILE* 5.4 0.4 - - + -
57E LEU* 5.8 0.2 - - + -
72E ILE* 3.7 33.7 - - + -
74E ALA* 3.6 10.4 - - - +
197E PHE* 4.1 11.2 - - + -
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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