Contacts of the helix formed by residues 32 - 39 (chain A) in PDB entry 1E0C
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 SER 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A THR* 1.3 85.0 + - - +
33A ALA* 1.3 67.0 + - - +
34A ALA* 3.7 7.0 + - - +
35A ARG* 3.1 23.6 + - - +
36A TYR* 2.8 24.1 + - - +
46A PHE* 3.5 12.1 - - - -
48A ASP* 5.5 0.7 - - - -
49A PRO* 5.0 2.2 - - - -
89A ASP* 4.9 1.9 + - - -
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Residues in contact with ALA 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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32A SER* 1.3 72.4 - - - +
34A ALA* 1.3 57.4 + - - +
36A TYR* 3.8 4.8 - - - +
37A ALA* 3.0 30.5 + - - +
46A PHE* 3.3 23.7 - - + -
48A ASP* 4.8 6.7 + - - +
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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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32A SER* 3.1 7.0 + - - +
33A ALA* 1.3 76.9 - - - +
35A ARG* 1.3 60.7 + - - +
37A ALA* 3.4 4.6 + - - +
38A GLU* 2.9 30.5 + - - +
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Residues in contact with ARG 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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29A ASP* 5.7 0.2 - - - +
31A THR* 3.4 15.3 - - + +
32A SER* 3.1 19.8 + - - +
34A ALA* 1.3 74.6 - - - +
36A TYR* 1.3 66.0 + - - +
38A GLU* 3.3 47.3 + - - +
39A GLY* 3.0 40.6 + - - +
89A ASP* 3.5 17.5 - - - +
117A LEU* 3.5 29.7 - - + +
121A LEU* 3.8 20.5 - - - +
127A LEU* 3.9 16.2 - - - +
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Residues in contact with TYR 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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29A ASP* 3.4 22.4 - - - -
31A THR* 3.6 5.5 + - - +
32A SER 2.8 17.3 + - - +
33A ALA* 3.8 4.7 - - - +
35A ARG* 1.3 77.8 - - - +
37A ALA* 1.3 62.8 + - + +
39A GLY* 3.5 6.1 + - - -
40A HIS* 2.7 62.7 + + + -
44A ALA 2.6 29.5 + - - -
45A ARG* 3.9 0.6 - - - -
46A PHE* 3.6 47.3 + + + -
131A LEU* 3.9 21.7 - - + +
132A PRO* 3.3 18.2 - - - +
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Residues in contact with ALA 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 ALA 3.0 18.4 + - - +
34A ALA* 3.8 4.9 - - - +
36A TYR* 1.3 79.7 - - + +
38A GLU* 1.3 66.5 + - - +
39A GLY 3.3 0.5 + - - -
40A HIS* 5.6 0.9 - - - -
129A ARG* 2.9 37.6 + - - +
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Residues in contact with GLU 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 2.9 18.0 + - - +
35A ARG* 3.3 44.4 + - - +
37A ALA* 1.3 77.5 - - - +
39A GLY* 1.3 57.9 + - - +
127A LEU* 5.3 1.6 - - - +
129A ARG* 3.6 20.7 + - - +
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Residues in contact with GLY 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 ARG* 3.0 34.7 + - - +
36A TYR 3.8 1.3 - - - -
37A ALA 3.2 2.4 - - - -
38A GLU* 1.3 80.7 - - - +
40A HIS* 1.3 60.7 + - - -
117A LEU* 4.5 4.2 - - - +
127A LEU* 4.0 20.6 - - - +
128A SER 3.4 11.0 - - - -
129A ARG* 4.2 3.8 - - - -
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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