Contacts of the helix formed by residues 30 - 46 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG* 2.5 41.2 + - - -
314A VAL* 3.9 14.9 - - + -
317A LYS* 3.6 14.0 + - + +
26B LEU* 3.0 27.3 + - + +
29B SER* 1.3 78.1 - - - +
31B ALA* 1.3 57.2 + - - +
32B GLU* 3.1 5.9 + - - +
33B VAL* 2.9 30.3 + - - +
34B TYR* 3.0 27.4 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A LYS* 4.4 3.8 - - - +
27B LYS 4.1 12.8 - - - +
28B ASP 4.0 7.5 + - - +
30B ASP* 1.3 71.7 + - - +
32B GLU* 1.3 59.6 + - - +
34B TYR* 3.5 8.5 - - + +
35B SER* 2.8 31.2 + - - -
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 3.5 27.9 - - + +
98A LYS* 5.0 5.0 + - - -
99A ARG* 2.8 22.5 + - - +
317A LYS* 5.6 1.5 - - - +
30B ASP* 3.1 7.1 + - - +
31B ALA* 1.3 75.3 - - - +
33B VAL* 1.3 66.3 + - - +
35B SER* 3.2 8.3 + - - -
36B ILE* 3.1 29.9 + - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 5.0 0.2 - - + -
92A LEU* 4.8 7.2 - - + -
95A LEU* 4.1 13.2 - - + -
99A ARG* 3.8 11.2 - - - +
310A ALA* 4.5 12.8 - - + +
313A ALA* 4.1 13.9 - - + -
314A VAL* 4.0 18.4 - - + -
26B LEU* 4.2 5.4 - - + -
30B ASP* 2.9 34.6 + - + +
32B GLU* 1.3 76.6 - - - +
34B TYR* 1.3 63.2 + - - +
36B ILE* 3.3 10.0 + - - +
37B ILE* 3.0 40.5 + - + +
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Residues in contact with TYR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 5.5 2.0 - - - -
26B LEU* 4.0 24.0 - - + +
27B LYS* 3.3 62.7 + - + -
30B ASP 3.0 19.3 + - - +
31B ALA* 3.5 9.6 - - - +
32B GLU 3.2 0.2 - - - -
33B VAL* 1.3 78.1 - - - +
35B SER* 1.3 64.1 + - - +
37B ILE* 3.4 5.8 + - + +
38B LYS* 2.6 67.6 + - + +
484B PHE* 3.8 23.3 + + + +
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 2.8 17.6 + - - -
32B GLU* 3.3 8.3 - - - -
34B TYR* 1.3 81.1 - - - +
36B ILE* 1.3 64.0 + - - +
38B LYS* 3.0 7.5 + - - +
39B LYS* 2.9 44.5 + - - +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 5.7 3.1 - - + -
88A PHE* 3.6 32.0 - - + +
91A GLU* 4.0 24.9 - - + +
92A LEU* 4.0 36.6 - - + +
95A LEU* 4.0 21.8 - - + -
32B GLU* 3.1 18.8 + - + +
33B VAL* 3.3 9.2 + - - +
35B SER* 1.3 76.3 + - - +
37B ILE* 1.3 63.7 + - + +
39B LYS* 3.2 12.0 + - - +
40B GLU* 2.9 23.1 + - + +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ALA* 4.1 12.1 - - + -
67A SER* 3.7 35.4 - - - +
68A SER* 3.7 7.1 + - - +
69A LEU* 3.7 24.2 - - + -
92A LEU* 6.3 0.7 - - + -
26B LEU* 3.9 27.6 - - + -
33B VAL* 3.0 23.2 + - + +
34B TYR* 3.8 8.7 - - + +
35B SER 3.3 0.2 - - - -
36B ILE* 1.3 76.1 - - + +
38B LYS* 1.3 59.4 + - + +
40B GLU* 3.3 6.6 + - - +
41B SER* 2.8 25.8 + - - -
484B PHE* 3.8 23.3 - - + -
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B TYR* 2.6 54.5 + - + +
35B SER* 3.0 10.3 + - - +
37B ILE* 1.3 76.9 - - + +
39B LYS* 1.3 60.9 + - + +
41B SER* 3.1 9.8 + - - -
42B ASN* 2.9 30.5 + - - +
483B ASP* 5.6 4.5 + - - +
484B PHE* 3.6 32.1 - - + +
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.4 40.0 - - + -
91A GLU* 3.1 33.1 + - - -
35B SER* 2.9 32.4 + - - +
36B ILE* 3.5 21.3 - - - +
38B LYS* 1.3 75.1 - - + +
40B GLU* 1.3 57.5 + - - +
42B ASN* 3.4 8.4 + - - +
43B ARG 3.1 20.1 + - - -
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Residues in contact with GLU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A SER* 4.2 2.5 - - - +
69A LEU* 4.0 25.6 - - + -
72A LYS* 4.4 5.5 - - + +
85A GLY 4.0 3.8 - - - +
88A PHE* 3.5 22.6 - - + +
89A ILE* 4.4 12.3 - - + +
36B ILE* 2.9 16.9 + - + +
37B ILE 3.6 5.4 - - - +
39B LYS* 1.3 74.5 - - - +
41B SER* 1.3 64.9 + - - +
42B ASN 3.1 1.6 - - - -
43B ARG* 2.9 44.7 + - - +
44B GLN* 3.2 44.6 + - - +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A SER* 3.5 21.6 + - - -
37B ILE* 2.8 18.0 + - - -
38B LYS* 3.5 11.4 - - - -
40B GLU* 1.3 77.8 - - - +
42B ASN* 1.3 64.8 + - - +
44B GLN* 3.4 8.0 + - - +
45B ARG* 3.3 13.7 + - - +
478B LEU* 3.8 14.8 - - - +
484B PHE* 5.3 8.4 - - - -
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS 2.9 12.4 + - - +
39B LYS* 3.4 13.9 + - - +
41B SER* 1.3 75.5 - - - +
43B ARG* 1.3 58.6 + - - +
45B ARG* 2.7 62.0 + - - +
46B VAL* 3.1 19.2 + - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 3.3 24.7 - - - +
84A GLY 5.0 0.2 + - - -
85A GLY* 3.2 34.4 + - - -
87A GLU* 6.0 1.1 - - - -
88A PHE* 4.0 18.2 - - + -
39B LYS 3.1 11.9 + - - +
40B GLU* 2.9 44.1 + - - +
42B ASN* 1.3 81.7 - - - +
44B GLN* 1.3 70.7 + - - +
45B ARG 3.2 0.5 + - - -
46B VAL* 3.5 24.0 + - - +
47B GLY* 3.7 4.9 + - - -
49B GLU* 3.0 28.9 + - - -
54B GLU* 4.7 0.8 + - - -
383B ALA* 5.1 5.1 - - - +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A SER* 3.4 37.9 + - - +
71A ASN* 3.7 16.1 - - - +
72A LYS* 5.5 2.0 - - - +
40B GLU* 3.2 38.4 + - - +
41B SER* 3.7 7.0 - - - +
42B ASN 3.2 0.6 - - - -
43B ARG* 1.3 92.6 - - - +
45B ARG* 1.3 57.8 + - - +
47B GLY* 3.8 6.5 - - - +
49B GLU* 5.0 6.5 - - - +
54B GLU* 6.1 0.7 - - - +
56B PHE* 3.4 39.0 - - + -
411B ARG* 3.0 20.1 + - - -
478B LEU* 4.1 9.8 - - + +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 3.3 5.6 + - - +
42B ASN* 2.7 47.2 + - - +
44B GLN* 1.3 73.4 - - - +
46B VAL* 1.3 89.1 + - - +
47B GLY 3.2 2.4 + - - -
411B ARG* 2.8 32.8 + - - +
473B ALA* 3.9 4.9 - - - +
474B SER* 3.5 25.2 + - - +
476B PHE 5.3 2.0 - - - +
478B LEU* 3.4 32.0 - - + +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASN* 3.4 28.9 - - - +
43B ARG* 3.6 8.6 - - - +
45B ARG* 1.3 105.8 - - - +
47B GLY* 1.3 55.8 + - - +
381B SER* 4.0 3.5 + - - -
470B GLU* 3.2 43.5 - - + +
473B ALA* 3.8 10.8 - - - -
474B 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