Contacts of the helix formed by residues 42 - 50 (chain C) in PDB entry 3EBL
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 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 5.2 1.6 + - - -
42B GLU* 5.6 0.3 - - - +
33C ILE 3.8 15.7 - - - +
34C LEU* 2.9 37.4 + - + +
36C ARG* 2.7 42.2 + - + +
41C PHE* 1.3 73.2 - - - +
43C ARG* 1.3 57.8 + - - +
44C ASP 3.4 1.8 - - - -
45C LEU* 3.5 19.4 + - + +
46C GLY* 2.9 26.3 + - - -
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 5.4 0.2 - - - +
41C PHE* 2.8 38.8 + - + +
42C GLU* 1.3 71.2 - - - +
44C ASP* 1.3 63.9 + - - +
46C GLY* 3.3 1.5 + - - -
47C GLU* 2.9 47.1 + - + +
125C VAL 2.9 24.6 + - - -
126C HIS* 4.8 1.0 - - - +
156C ARG* 3.4 41.6 - - - +
157C ALA 2.8 29.3 + - - -
159C GLU* 2.9 36.6 + - + +
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 5.9 2.9 - - - +
42C GLU 3.4 0.2 - - - -
43C ARG* 1.3 86.7 - - - +
45C LEU* 1.3 58.0 + - - +
47C GLU* 3.5 7.1 + - - +
48C TYR* 3.0 28.5 + - - +
60D LEU* 3.8 28.4 - - + +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 3.8 21.8 - - + -
34C LEU* 3.6 19.5 - - + -
42C GLU* 3.5 28.4 + - + +
43C ARG 3.3 0.2 - - - -
44C ASP* 1.3 76.4 - - - +
46C GLY* 1.3 53.8 + - - +
48C TYR* 3.1 14.4 + - + +
49C LEU* 2.8 58.9 + - + +
60D LEU* 5.0 4.6 - - + +
61D GLU* 5.0 13.9 - - - +
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Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.7 24.7 - - - +
41C PHE* 4.8 6.5 - - - -
42C GLU 2.9 17.2 + - - -
43C ARG* 3.7 2.5 - - - -
45C LEU* 1.3 76.9 - - - +
47C GLU* 1.3 60.4 + - - +
49C LEU* 3.3 3.2 + - - +
50C ASP* 3.1 26.2 + - - +
52C ARG* 5.5 0.2 - - - -
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ARG* 2.9 36.6 + - + +
44C ASP* 3.7 8.7 - - - +
46C GLY* 1.3 74.3 - - - +
48C TYR* 1.3 64.5 + - - +
49C LEU 3.3 0.5 + - - -
50C ASP* 3.4 13.3 + - - +
52C ARG* 2.9 46.8 + - - +
156C ARG* 2.6 34.2 + - - -
53D VAL* 5.3 1.2 - - - +
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Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C ASP 3.0 15.0 + - - +
45C LEU* 3.3 17.7 - - + +
47C GLU* 1.3 78.9 - - - +
49C LEU* 1.3 76.6 + - + +
50C ASP 3.7 1.7 + - - +
53D VAL* 3.2 37.1 - - + +
60D LEU* 3.6 24.9 - - + -
132D THR* 3.7 24.9 + - + +
135D ASP* 2.7 31.1 + - - +
136D SER* 3.1 33.7 + - - -
139D ARG* 3.7 18.0 - - - -
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C SER* 5.3 5.8 - - - -
33C ILE* 5.2 7.0 - - + -
34C LEU* 4.5 12.8 - - + -
45C LEU* 2.8 48.5 + - + +
46C GLY* 3.3 4.2 + - - +
47C GLU 3.2 0.2 - - - -
48C TYR* 1.3 89.7 - - + +
50C ASP* 1.3 64.8 + - - +
501C MPD 2.8 22.9 + - + -
604C NO3 4.0 13.7 - - - +
51D ARG* 2.8 33.0 + - - +
132D THR* 4.6 1.6 - - + -
603D NO3 4.0 21.5 - - - +
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Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 4.8 9.7 - - - -
31C TYR* 4.8 3.1 + - - -
46C GLY 3.1 16.2 + - - +
47C GLU 3.4 6.5 + - - +
48C TYR 3.4 5.5 - - - +
49C LEU* 1.3 80.7 - - - +
51C ARG* 1.3 71.6 + - - +
52C ARG* 2.8 41.3 + - - +
127C SER* 4.1 14.0 + - - -
131C SER* 2.7 29.9 + - - -
501C MPD 3.7 9.1 + - - +
51D ARG* 4.2 6.3 - - - +
52D ARG 4.7 6.2 - - - +
53D VAL* 5.3 0.7 - - - +
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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