Contacts of the helix formed by residues 31 - 40 (chain B) in PDB entry 3EUP
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 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY 3.5 3.1 + - - -
30B THR* 1.3 73.3 - - - +
32B LEU* 1.3 63.8 + - - +
33B THR* 3.4 10.5 + - - -
34B ASP* 2.8 46.3 + - - +
35B LEU* 3.0 19.0 + - - +
53B LYS* 4.4 2.7 - - - +
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Residues in contact with LEU 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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31B SER* 1.3 71.8 - - - +
33B THR* 1.3 59.2 + - - +
35B LEU* 3.0 16.6 + - + +
36B THR* 2.9 39.7 + - + -
43B LYS* 3.7 50.3 - - + +
46B ILE* 5.2 1.3 - - + -
47B TYR* 4.2 17.0 - - + +
53B LYS* 5.2 3.6 - - - +
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Residues in contact with THR 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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31B SER* 3.2 9.5 + - - -
32B LEU* 1.3 79.6 - - - +
34B ASP* 1.3 57.2 + - - +
36B THR* 3.6 8.7 - - - +
37B GLU* 2.9 63.8 + - + +
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Residues in contact with ASP 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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21B VAL* 4.1 12.8 - - + +
25B LYS* 3.1 33.2 + - - +
29B GLY 3.5 6.9 - - - +
30B THR* 3.5 12.3 - - + -
31B SER* 2.8 38.7 + - - +
33B THR* 1.3 77.3 - - - +
35B LEU* 1.3 59.6 + - - +
37B GLU* 4.0 8.9 - - - +
38B ALA* 3.0 31.7 + - - +
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Residues in contact with LEU 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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14B ILE* 6.1 0.2 - - + -
18B THR* 3.5 27.1 - - + +
21B VAL* 6.1 0.4 - - + -
22B PHE* 3.8 15.9 - - + -
30B THR* 3.7 20.2 - - + -
31B SER 3.0 15.2 + - - +
32B LEU* 3.0 16.6 + - + +
34B ASP* 1.3 77.0 - - - +
36B THR* 1.3 60.8 + - - +
38B ALA* 3.4 1.6 + - - +
39B THR* 2.8 32.8 + - - +
46B ILE* 4.1 20.9 - - + -
47B TYR* 3.6 27.4 - - + +
53B LYS* 4.3 17.9 - - + -
56B VAL* 4.7 5.8 - - + -
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Residues in contact with THR 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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32B LEU* 2.9 32.1 + - + +
33B THR* 3.4 14.2 + - - +
35B LEU* 1.3 72.1 - - - +
37B GLU* 1.3 64.4 + - - +
39B THR* 3.7 1.3 - - - -
40B ASN* 2.7 33.6 + - - -
41B LEU 3.4 23.1 - - - +
42B THR* 4.2 1.3 - - - -
43B LYS* 3.9 19.1 - - + +
46B ILE* 4.1 8.3 - - + -
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Residues in contact with GLU 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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33B THR* 2.9 44.7 + - + +
34B ASP* 4.1 9.0 - - - +
36B THR* 1.3 79.6 + - - +
38B ALA* 1.3 60.8 + - - +
39B THR 3.4 0.3 + - - -
40B ASN* 4.1 14.9 + - - +
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Residues in contact with ALA 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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13B PHE* 4.8 2.4 - - - -
17B SER* 3.6 34.7 + - - +
18B THR* 4.3 10.3 - - + -
21B VAL* 4.9 9.4 - - + -
34B ASP 3.0 21.1 + - - +
35B LEU 3.4 4.0 + - - +
37B GLU* 1.3 78.4 - - - +
39B THR* 1.3 60.1 + - - +
40B ASN* 5.1 1.9 - - - +
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Residues in contact with THR 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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13B PHE* 3.4 25.1 - - + -
14B ILE* 4.1 22.2 - - + -
17B SER* 3.8 18.8 - - - +
18B THR* 3.9 13.0 - - + -
35B LEU 2.8 22.0 + - - +
36B THR* 3.6 3.8 + - - -
38B ALA* 1.3 82.5 - - - +
40B ASN* 1.3 69.3 + - - +
41B LEU* 3.1 33.4 + - - +
46B ILE* 3.9 4.6 - - + +
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Residues in contact with ASN 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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36B THR 2.7 20.5 + - - -
37B GLU* 4.1 13.0 + - - +
38B ALA 3.8 1.8 - - - +
39B THR* 1.3 75.5 - - - +
41B LEU* 1.3 61.2 + - - +
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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