Contacts of the helix formed by residues 31 - 42 (chain B) in PDB entry 4D10
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 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 1.3 79.3 + - + +
32B LEU* 1.3 63.7 + - - +
33B GLU 3.1 4.7 + - - -
34B ASN* 3.4 14.2 + - + +
35B GLN* 3.2 48.5 + - - +
64B LYS* 4.8 22.3 + - + -
67B TRP* 3.5 24.5 + - + +
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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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30B VAL* 3.2 25.3 + - - +
31B ASP* 1.3 77.2 - - - +
33B GLU* 1.3 66.2 + - + +
35B GLN* 3.6 17.7 - - - +
36B TYR* 3.8 16.5 + - - +
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Residues in contact with GLU 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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30B VAL 4.8 4.4 + - - +
31B ASP 3.2 0.6 - - - -
32B LEU* 1.3 77.9 - - + +
34B ASN* 1.3 62.8 + - - +
36B TYR* 3.0 22.9 + - - +
37B TYR* 2.8 53.6 + - + -
60B LEU* 5.6 6.0 - - + +
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Residues in contact with ASN 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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31B ASP* 3.4 14.8 + - - +
33B GLU* 1.3 79.3 - - - +
35B GLN* 1.3 57.2 + - - +
37B TYR* 3.9 6.1 - - - +
38B ASN* 2.9 32.6 + - - +
57B VAL* 3.7 15.3 - - - +
60B LEU* 3.5 44.2 + - - +
61B GLU 4.8 1.4 + - - -
67B TRP* 4.3 25.8 - - + +
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Residues in contact with GLN 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 ASP* 3.2 40.4 + - - +
32B LEU* 3.6 25.4 - - - +
33B GLU 3.2 0.4 - - - -
34B ASN* 1.3 76.5 - - - +
36B TYR* 1.3 55.3 + - - +
38B ASN* 3.7 2.1 - - - +
39B SER* 2.8 37.7 + - - +
67B TRP* 3.5 41.2 - - + -
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Residues in contact with TYR 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 3.8 10.0 + - - +
33B GLU* 3.0 10.1 + - - +
35B GLN* 1.3 77.7 - - - +
37B TYR* 1.3 70.6 + + + +
39B SER* 3.3 8.8 + - - -
40B LYS* 2.8 69.7 + - + +
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Residues in contact with TYR 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 GLU* 2.8 63.3 + - + +
34B ASN 4.1 2.5 - - - +
36B TYR* 1.3 84.5 - + + +
38B ASN* 1.3 60.4 + - - +
40B LYS* 3.8 14.1 - - + +
41B ALA* 3.0 30.0 + - - +
53B SER* 5.7 0.2 - - - -
57B VAL* 3.7 19.4 - - + +
60B LEU* 3.7 29.2 - - + -
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Residues in contact with ASN 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 ASN 2.9 20.3 + - - +
35B GLN 3.7 3.4 - - - +
37B TYR* 1.3 76.1 - - - +
39B SER* 1.3 59.6 + - - +
41B ALA* 3.6 3.6 + - - +
42B LEU* 3.1 38.3 + - - +
54B PHE* 4.1 6.8 - - - -
57B VAL* 3.8 13.1 - - + +
67B TRP* 3.6 36.7 - - + +
70B LYS* 4.1 8.7 - - - +
71B ALA* 3.6 33.0 + - - +
74B GLN* 5.9 0.9 - - - +
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Residues in contact with SER 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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35B GLN* 2.8 23.0 + - - +
36B TYR* 3.3 10.7 + - - -
38B ASN* 1.3 79.2 + - - +
40B LYS* 1.3 62.9 + - - +
42B LEU* 3.4 24.1 + - - +
43B LYS* 3.9 18.5 + - - +
67B TRP* 5.7 2.3 - - - -
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Residues in contact with LYS 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 TYR* 2.8 53.0 + - + +
37B TYR* 3.8 15.2 - - + +
38B ASN 3.3 0.2 - - - -
39B SER* 1.3 76.1 - - - +
41B ALA* 1.3 61.0 + - - +
42B LEU 3.5 0.3 + - - -
43B LYS* 3.6 22.7 + - + +
44B GLU* 4.2 11.8 - - - +
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Residues in contact with ALA 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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37B TYR 3.0 18.8 + - - +
38B ASN* 4.0 0.7 - - - +
40B LYS* 1.3 73.6 - - - +
42B LEU* 1.3 62.6 + - - +
43B LYS 3.2 8.5 + - - +
44B GLU* 4.3 4.8 - - - +
50B ALA* 4.3 9.2 - - - +
53B SER* 3.9 29.4 - - - -
54B PHE* 3.3 45.1 - - + +
57B VAL* 4.8 0.4 - - + -
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Residues in contact with LEU 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 ASN* 3.1 29.0 + - - +
39B SER* 3.4 16.4 - - - +
40B LYS 3.2 0.4 - - - -
41B ALA* 1.3 76.5 - - - +
43B LYS* 1.3 66.3 + - + +
54B PHE* 3.7 7.6 - - + -
74B GLN* 3.6 39.6 - - + +
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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