Contacts of the helix formed by residues 26 - 38 (chain A) in PDB entry 4EWS
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 GLU 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL 4.7 2.3 - - - +
23A LEU* 3.1 18.9 + - + +
25A HIS* 1.3 85.0 - - - +
27A THR* 1.3 62.6 + - - +
28A ALA 3.2 3.1 - - - -
29A LYS* 2.8 60.3 + - + +
30A VAL* 3.4 10.0 + - - +
463A PHE* 3.3 38.6 - - + +
465A GLU* 3.4 29.7 + - - +
468A LEU* 3.5 20.9 - - + -
505A PGE 4.7 4.3 - - - -
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Residues in contact with THR 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 LEU 3.8 1.4 + - - -
24A ASN* 3.2 27.8 + - - +
26A GLU* 1.3 75.9 - - - +
28A ALA* 1.3 56.6 + - - +
30A VAL* 3.1 8.0 + - - +
31A ILE* 2.9 41.4 + - + +
72A SER* 3.4 28.3 - - - +
84A VAL* 4.3 21.3 - - + +
86A ILE* 4.3 1.8 - - + -
501A 2OB 4.5 10.1 - - + -
505A PGE 3.5 19.2 - - - -
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Residues in contact with ALA 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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24A ASN 4.8 1.0 + - - -
25A HIS 5.1 5.1 + - - +
26A GLU 3.2 1.0 - - - -
27A THR* 1.3 76.7 - - - +
29A LYS* 1.4 53.8 + - + +
31A ILE* 3.4 2.9 + - - -
32A GLN* 2.8 39.9 + - - +
69A ILE* 3.7 42.1 - - + +
72A SER* 4.8 3.3 + - - +
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Residues in contact with LYS 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 HIS 3.7 10.5 + - - +
26A GLU* 2.8 46.3 + - + +
28A ALA* 1.4 76.7 - - + +
30A VAL* 1.3 52.9 + - + +
32A GLN* 3.6 11.2 - - - +
33A THR* 2.7 36.2 + - - -
465A GLU* 3.3 21.6 + - - +
468A LEU* 4.8 6.3 - - + -
469A VAL* 4.2 26.7 - - + -
472A LEU* 3.4 15.9 - - + +
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Residues in contact with VAL 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 GLU 3.5 14.6 - - - +
27A THR* 3.1 7.2 + - - +
29A LYS* 1.3 75.8 - - - +
31A ILE* 1.4 62.3 + - + +
33A THR* 3.2 5.4 + - - -
34A ALA* 2.9 28.0 + - + +
187A ILE* 5.9 2.9 - - + +
190A ILE* 3.8 26.1 - - + +
191A SER* 5.5 2.9 - - - +
194A MET* 3.7 29.2 - - + -
468A LEU* 4.8 2.7 - - + -
472A LEU* 4.3 10.8 - - + -
501A 2OB 3.7 25.4 - - + -
505A PGE 4.2 14.1 - - - -
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Residues in contact with ILE 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 THR* 2.9 21.0 + - + +
28A ALA* 3.9 4.3 - - - +
30A VAL* 1.4 75.5 - - + +
32A GLN* 1.3 60.9 + - - +
34A ALA* 3.2 5.7 + - + +
35A PHE* 3.1 49.8 + - + -
69A ILE* 3.8 22.2 - - + -
86A ILE* 3.8 24.5 - - + -
89A VAL* 5.1 0.7 - - + -
123A LEU* 4.7 8.5 - - + -
125A ILE* 4.0 15.3 - - + -
187A ILE* 3.9 31.2 - - + -
501A 2OB 4.1 16.6 - - + -
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Residues in contact with GLN 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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28A ALA* 2.8 24.5 + - - +
29A LYS* 3.6 12.4 - - - +
31A ILE* 1.3 73.4 - - - +
33A THR* 1.3 57.2 + - - +
35A PHE* 3.3 3.8 + - - +
36A GLN* 3.0 50.4 + - - +
67A LEU* 3.8 38.9 + - + +
68A SER* 6.0 1.4 - - - +
69A ILE* 4.1 8.0 - - + +
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Residues in contact with THR 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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29A LYS 2.7 22.1 + - - -
30A VAL* 3.5 6.1 - - - -
32A GLN* 1.3 75.7 - - - +
34A ALA* 1.3 57.7 + - - +
36A GLN* 3.1 13.0 + - + +
37A ARG* 2.9 32.1 + - + +
190A ILE* 4.0 10.8 - - + -
472A LEU* 3.4 30.6 - - + +
475A LEU* 3.8 28.7 - - + -
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Residues in contact with ALA 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 VAL* 2.9 14.8 + - + +
31A ILE 3.2 10.3 + - - +
33A THR* 1.3 74.6 - - - +
35A PHE* 1.3 61.4 + - - +
37A ARG 3.2 8.8 + - - -
38A ALA* 3.3 12.1 + - - +
183A ILE* 4.5 7.3 - - + +
186A GLU* 3.5 12.6 - - + +
187A ILE* 3.8 35.0 - - + +
190A ILE* 3.4 21.2 - - + +
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Residues in contact with PHE 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 ILE* 3.1 45.6 + - + -
32A GLN 3.3 0.9 + - - +
34A ALA* 1.3 73.8 - - - +
36A GLN* 1.3 61.9 + - - +
37A ARG 3.2 1.0 + - - -
38A ALA 3.4 6.9 + - - +
40A TYR* 2.7 27.8 + - - -
64A ILE* 3.3 8.5 - - + +
67A LEU* 3.5 26.7 - - + -
89A VAL* 4.2 19.5 - - + -
91A VAL* 3.8 31.6 - - + -
93A PHE* 5.0 5.6 - + - -
121A ILE* 4.2 16.8 - - + -
123A LEU* 4.5 9.2 - - + -
145A LEU* 5.8 1.1 - - + -
179A LEU* 5.6 1.1 - - + -
183A ILE* 3.6 46.7 - - + -
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Residues in contact with GLN 36 (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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32A GLN* 3.0 44.3 + - - +
33A THR* 3.1 10.5 + - - +
35A PHE* 1.3 76.0 - - - +
37A ARG* 1.3 58.7 + - - +
38A ALA 3.6 2.8 - - - +
64A ILE* 4.3 10.8 - - + +
67A LEU* 4.4 12.2 - - + +
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Residues in contact with ARG 37 (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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33A THR* 2.9 16.0 + - + +
34A ALA 3.7 4.5 - - - +
35A PHE 3.2 0.6 - - - -
36A GLN* 1.3 76.2 - - - +
38A ALA* 1.3 65.0 + - - +
39A SER* 3.8 6.9 + - - -
186A GLU* 2.8 34.9 + - + +
189A VAL* 3.6 20.0 - - - +
190A ILE* 3.6 24.2 - - - +
193A ILE* 4.4 10.1 - - - +
475A LEU* 3.4 45.8 + - + +
476A SER* 4.3 16.5 + - - +
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Residues in contact with ALA 38 (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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34A ALA 3.3 7.8 + - - +
35A PHE 3.4 4.8 + - - +
36A GLN 4.6 2.6 - - - +
37A ARG* 1.3 78.7 - - - +
39A SER* 1.3 60.7 + - - +
40A TYR* 3.5 44.8 - - + +
182A GLN* 3.8 20.9 - - + -
183A ILE* 3.8 10.3 - - + -
186A GLU* 3.8 10.5 - - + +
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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