Contacts of the helix formed by residues 38 - 49 (chain A) in PDB entry 5EJC
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.4 3.2 + - + +
34A ASP* 4.7 10.5 + - - +
36A ARG* 3.5 7.8 + - - +
37A LEU* 1.3 68.8 - - - +
39A THR* 1.3 65.1 + - - +
40A GLU* 3.2 13.9 - - - +
41A LYS* 3.1 54.3 + - + +
42A LEU* 3.2 16.2 + - - +
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Residues in contact with THR 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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37A LEU 3.2 10.4 + - - +
38A ASP* 1.3 71.4 + - - +
40A GLU* 1.3 67.1 + - - +
42A LEU* 3.3 11.3 + - - +
43A CYS* 3.1 29.1 + - - -
62A VAL* 4.2 25.8 - - + +
63A LEU* 3.8 8.9 - - - +
69A PRO* 4.3 16.4 - - + -
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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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38A ASP* 3.2 14.6 - - - +
39A THR* 1.3 86.3 + - - +
41A LYS* 1.3 61.4 + - + +
43A CYS* 3.4 8.1 + - - +
44A THR* 3.2 28.7 + - - +
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Residues in contact with LYS 41 (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 LEU* 3.7 32.6 - - + +
34A ASP* 6.1 0.2 - - - +
38A ASP* 3.1 33.5 + - + +
40A GLU* 1.3 77.0 - - + +
42A LEU* 1.3 61.4 + - - +
44A THR* 3.0 20.6 + - - +
45A PHE* 3.0 19.9 + - - +
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Residues in contact with LEU 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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28A LEU* 3.9 28.3 - - + -
31A LEU* 4.4 13.9 - - + -
32A LEU* 4.4 14.6 - - + -
37A LEU* 4.2 22.2 - - + -
38A ASP 3.2 15.5 + - - +
39A THR* 3.3 10.1 + - - +
41A LYS* 1.3 72.7 - - - +
43A CYS* 1.3 56.8 + - - +
45A PHE* 3.8 4.1 - - + +
46A SER* 2.7 35.7 + - - -
59A VAL* 4.5 14.1 - - + -
62A VAL* 3.9 30.1 - - + -
63A LEU* 3.9 12.8 - - + -
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Residues in contact with CYS 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 THR* 3.1 20.2 + - - -
40A GLU* 3.5 9.6 - - - +
41A LYS 3.2 0.2 - - - -
42A LEU* 1.3 74.0 - - - +
44A THR* 1.3 57.7 + - + +
46A SER* 2.8 6.1 + - - -
47A GLN* 2.7 38.9 + - + +
63A LEU* 3.6 17.3 - - - -
228A VAL 5.6 0.4 - - - -
229A SER* 3.8 31.2 - - - +
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Residues in contact with THR 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 15.6 + - - +
41A LYS* 3.0 23.0 + - - +
43A CYS* 1.3 79.0 - - + +
45A PHE* 1.3 59.2 + - - +
47A GLN* 3.6 10.2 + - + +
48A ARG* 3.2 26.7 + - - +
288A THR* 5.7 1.5 - - + +
289A PRO* 5.1 18.0 - - + +
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Residues in contact with PHE 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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24A GLU* 3.8 24.0 - - + -
27A SER* 3.8 11.7 - - - -
28A LEU* 3.7 40.8 - - + -
31A LEU* 4.4 19.7 - - + -
41A LYS 3.0 17.9 + - - +
42A LEU* 3.8 5.4 - - + +
44A THR* 1.3 74.7 + - - +
46A SER* 1.3 59.2 + - - +
48A ARG* 3.1 1.4 + - - -
49A PHE* 2.7 74.6 + + + +
50A PRO 4.3 7.9 - - - -
51A LEU* 4.0 19.3 - - + -
52A PRO* 5.1 2.2 - - + -
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Residues in contact with SER 46 (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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42A LEU 2.7 20.1 + - - -
43A CYS 2.8 7.9 + - - -
45A PHE* 1.3 77.4 - - - +
47A GLN* 1.3 57.2 + - - +
49A PHE 3.2 6.6 - - - +
51A LEU* 3.6 24.9 - - - +
59A VAL* 3.9 12.8 - - - +
63A LEU* 4.1 2.6 - - - +
225A ASP* 4.1 9.0 - - - +
226A LYS* 2.9 32.7 + - - +
229A SER* 3.6 20.5 + - - -
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Residues in contact with GLN 47 (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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43A CYS* 2.7 28.6 + - + +
44A THR* 3.7 9.4 - - + +
46A SER* 1.3 73.1 - - - +
48A ARG* 1.3 61.6 + - - +
226A LYS* 3.3 32.9 + - - +
229A SER* 2.5 38.2 + - - +
230A GLY 3.8 1.0 - - - +
231A SER* 3.9 12.0 - - - +
282A TRP* 3.2 29.5 - - + -
283A HIS* 3.4 16.0 + - - -
288A THR* 4.1 22.0 - - + +
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Residues in contact with ARG 48 (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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44A THR 3.2 15.3 + - - +
45A PHE* 3.1 3.8 + - - +
47A GLN* 1.3 82.0 - - - +
49A PHE* 1.3 89.3 + - + +
50A PRO* 4.5 1.9 - - - +
226A LYS* 4.5 1.9 + - - -
279A ILE* 5.3 1.2 - - - +
283A HIS* 3.8 50.8 + - - +
287A GLY* 4.7 1.0 - - - -
288A THR* 2.9 37.5 + - + +
289A PRO 4.1 17.5 + - - +
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Residues in contact with PHE 49 (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 GLU* 3.1 37.0 - - + +
27A SER* 5.5 3.4 - - - -
45A PHE* 2.7 61.3 + + + +
46A SER* 3.2 12.1 - - - +
48A ARG* 1.3 99.7 - - + +
50A PRO* 1.3 71.1 - - + +
51A LEU* 3.8 1.2 + - - +
226A LYS* 3.1 14.8 + - - -
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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