Contacts of the helix formed by residues 30 - 46 (chain A) in PDB entry 1EJI
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 ASP 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.0 27.3 + - + +
29A SER* 1.3 80.2 - - - +
31A ALA* 1.3 56.7 + - - +
32A GLU* 3.2 6.1 + - - +
33A VAL* 3.0 28.2 + - + +
34A TYR* 3.0 26.3 + - - +
99B ARG* 2.5 39.3 + - - -
314B VAL* 3.7 16.0 - - + -
317B LYS* 3.6 18.7 + - + +
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Residues in contact with ALA 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 LYS 4.1 13.0 - - - +
28A ASP 4.0 7.3 + - - +
30A ASP* 1.3 72.6 + - - +
32A GLU* 1.3 55.8 + - - +
34A TYR* 3.5 9.2 - - + +
35A SER* 2.8 34.7 + - - -
317B LYS* 4.3 4.8 - - - +
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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
----------------------------------------------------------
30A ASP* 3.2 8.2 + - - +
31A ALA* 1.3 75.4 - - - +
33A VAL* 1.3 66.6 + - - +
35A SER* 3.1 7.8 + - - -
36A ILE* 3.1 29.5 + - + +
95B LEU* 3.5 28.2 - - + +
98B LYS* 4.8 5.7 + - - -
99B ARG* 2.8 21.8 + - - +
317B LYS* 5.3 2.1 + - - +
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Residues in contact with VAL 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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26A LEU* 4.3 5.2 - - + -
30A ASP* 3.0 29.9 + - - +
32A GLU* 1.3 79.2 - - - +
34A TYR* 1.3 63.0 + - - +
36A ILE* 3.3 9.4 + - - +
37A ILE* 3.1 40.0 + - + +
64B ALA* 5.0 0.4 - - + -
92B LEU* 4.7 7.2 - - + -
95B LEU* 4.1 9.9 - - + -
99B ARG* 3.7 11.9 - - - +
310B ALA* 4.5 11.7 - - + +
313B ALA* 4.0 18.4 - - + -
314B VAL* 3.9 19.5 - - + -
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.1 15.9 - - + +
27A LYS* 3.2 63.7 + - + -
30A ASP 3.0 19.5 + - - +
31A ALA* 3.5 10.1 - - + +
32A GLU 3.2 0.2 - - - -
33A VAL* 1.3 79.0 - - - +
35A SER* 1.3 65.2 + - - +
37A ILE* 3.4 4.6 + - - +
38A LYS* 2.7 60.1 + - + +
484A PHE* 3.7 29.8 - + - -
63B GLU* 5.3 2.5 - - - -
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Residues in contact with SER 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA 2.8 21.5 + - - -
32A GLU* 3.1 7.8 + - - -
34A TYR* 1.3 77.3 - - - +
36A ILE* 1.3 64.4 + - - +
38A LYS* 3.1 8.2 + - - +
39A LYS* 2.9 42.2 + - - +
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Residues in contact with ILE 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 GLU* 3.1 16.6 + - + +
33A VAL* 3.7 8.3 - - - +
35A SER* 1.3 76.2 - - - +
37A ILE* 1.3 64.9 + - + +
39A LYS* 3.2 12.5 + - - +
40A GLU* 2.9 23.1 + - + +
69B LEU* 5.8 2.2 - - + -
88B PHE* 3.7 30.9 - - + +
91B GLU* 4.0 24.5 - - + +
92B LEU* 4.0 33.0 - - + +
95B LEU* 3.8 29.8 - - + -
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Residues in contact with ILE 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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26A LEU* 4.0 15.9 - - + -
33A VAL* 3.1 25.8 + - + +
34A TYR 3.8 4.7 - - - +
35A SER 3.2 0.2 - - - -
36A ILE* 1.3 76.1 - - + +
38A LYS* 1.3 58.7 + - - +
40A GLU* 3.4 6.4 + - - +
41A SER* 2.9 24.8 + - - -
484A PHE* 3.1 47.1 - - + +
64B ALA* 4.2 11.7 - - + -
67B SER* 3.8 30.3 - - - +
68B SER* 3.9 2.5 + - - +
69B LEU* 3.7 24.0 - - + -
92B LEU* 5.9 0.9 - - + -
310B ALA* 4.7 0.2 - - + -
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 2.7 54.1 + - + +
35A SER* 3.1 9.2 + - - +
37A ILE* 1.3 75.5 - - - +
39A LYS* 1.3 61.6 + - - +
40A GLU 3.1 0.2 - - - -
41A SER* 3.5 5.2 - - - -
42A ASN* 2.9 30.3 + - - +
483A ASP* 3.4 35.6 + - - +
484A PHE* 3.8 16.7 - - + +
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Residues in contact with LYS 39 (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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35A SER* 2.9 32.7 + - - +
36A ILE* 3.2 23.2 + - - +
38A LYS* 1.3 74.9 - - - +
40A GLU* 1.3 57.5 + - - +
42A ASN* 3.5 9.6 + - - +
43A ARG 3.1 19.8 + - - -
88B PHE* 3.4 37.3 - - + -
91B GLU* 3.1 30.2 + - - +
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Residues in contact with GLU 40 (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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36A ILE* 2.9 17.3 + - + +
37A ILE 3.7 4.9 - - - +
39A LYS* 1.3 74.3 - - - +
41A SER* 1.3 65.4 + - - +
42A ASN 3.1 1.3 - - - -
43A ARG* 2.9 42.4 + - - +
44A GLN* 3.2 43.6 + - - +
68B SER* 4.1 1.6 - - - +
69B LEU* 3.9 27.4 - - + -
72B LYS* 4.4 4.0 - - - +
85B GLY 4.1 3.3 - - - +
88B PHE* 3.3 26.0 - - + +
89B ILE* 4.2 13.0 - - + +
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE 2.9 11.4 + - - -
38A LYS* 3.5 8.7 - - - -
40A GLU* 1.3 76.6 - - - +
42A ASN* 1.3 64.3 + - - +
44A GLN* 3.4 8.1 + - - +
45A ARG* 3.3 13.7 + - - +
478A LEU* 3.8 13.6 - - - +
483A ASP* 4.2 12.1 + - - -
484A PHE* 3.4 41.4 + - - -
68B SER* 3.5 12.5 + - - -
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Residues in contact with ASN 42 (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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38A LYS 2.9 16.4 + - - +
39A LYS* 3.5 9.2 + - - +
41A SER* 1.3 75.2 - - - +
43A ARG* 1.3 58.0 + - - +
45A ARG* 2.7 58.4 + - - +
46A VAL* 3.1 24.2 + - - +
483A ASP* 6.2 0.4 - - - -
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Residues in contact with ARG 43 (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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39A LYS 3.1 11.9 + - - +
40A GLU* 2.9 39.6 + - - +
42A ASN* 1.3 81.3 - - - +
44A GLN* 1.3 72.2 + - - +
45A ARG 3.2 0.3 + - - -
46A VAL* 3.5 23.5 + - - +
47A GLY* 3.7 5.2 + - - -
49A GLU* 3.0 29.3 + - - +
54A GLU* 4.7 0.6 + - - -
383A ALA* 4.7 5.5 - - - +
72B LYS* 3.3 24.4 - - - +
85B GLY* 3.0 37.3 + - - -
87B GLU* 5.5 1.8 - - - +
88B PHE* 3.7 22.7 - - + -
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Residues in contact with GLN 44 (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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40A GLU* 3.2 35.1 + - - +
41A SER* 3.6 6.7 - - - +
42A ASN 3.2 0.6 - - - -
43A ARG* 1.3 90.5 - - - +
45A ARG* 1.3 58.9 + - - +
47A GLY 3.8 6.5 - - - +
49A GLU* 5.0 7.1 - - - +
54A GLU* 6.1 0.2 - - - +
56A PHE* 3.4 40.5 - - + -
411A ARG* 3.0 19.4 + - - -
478A LEU* 4.1 7.8 - - + +
68B SER* 3.1 43.4 + - - +
71B ASN* 3.7 16.0 - - - +
72B LYS* 5.5 2.1 - - - +
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Residues in contact with ARG 45 (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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41A SER 3.3 5.1 + - - +
42A ASN* 2.7 42.9 + - - +
44A GLN* 1.3 75.1 - - - +
46A VAL* 1.3 88.3 + - - +
47A GLY 3.2 1.9 + - - -
411A ARG* 2.8 36.3 + - - +
473A ALA* 3.9 4.9 - - - +
474A SER* 3.6 26.3 + - - +
476A PHE 5.0 3.6 - - - +
478A LEU* 3.5 28.9 - - + +
483A ASP* 5.2 10.5 + - - -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 3.1 29.1 + - - +
43A ARG* 3.7 9.9 - - - +
45A ARG* 1.3 108.7 - - - +
47A GLY* 1.3 56.3 + - - +
381A SER* 4.0 3.6 + - - -
470A GLU* 3.2 43.4 - - + +
473A ALA* 3.8 10.3 - - - -
474A SER* 3.6 14.6 - - - +
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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