Contacts of the helix formed by residues 42 - 56 (chain B) in PDB entry 4DHV
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP* 2.8 22.7 + - - +
44A GLU 4.5 6.8 - - - +
45A LEU* 6.2 0.2 - - + -
48A CYS* 4.0 18.6 - - + +
2B TRP* 4.2 0.9 - - - -
40B ILE* 3.5 6.4 - - - +
41B GLU* 1.3 78.5 + - - +
43B GLU* 1.3 63.6 + - - +
44B GLU* 3.0 27.5 + - - +
45B LEU* 3.1 15.5 + - + +
46B TYR* 2.9 24.4 + - - +
102B NCO 3.1 36.0 + - - +
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Residues in contact with GLU 43 (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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2B TRP* 4.1 18.1 - - + -
41B GLU 4.6 3.8 - - - -
42B ASP* 1.3 73.0 - - - +
44B GLU* 1.3 72.2 + - + +
46B TYR* 2.9 13.7 + - + +
47B ASN* 2.9 28.8 + - - +
102B NCO 3.0 36.2 + - - -
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Residues in contact with GLU 44 (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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44A GLU* 3.3 30.0 - - + +
47A ASN* 6.2 3.6 - - - +
42B ASP* 3.0 10.5 + - - +
43B GLU* 1.3 87.8 - - + +
45B LEU* 1.3 56.7 + - - +
47B ASN* 3.0 29.6 + - + +
48B CYS 3.0 20.4 + - - -
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Residues in contact with LEU 45 (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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23A ASP* 3.6 34.8 - - + +
44A GLU* 4.0 4.4 - - + +
45A LEU* 4.3 23.8 - - + +
23B ASP* 3.9 26.5 - - + +
24B VAL* 3.8 22.7 - - + -
37B VAL* 6.3 2.2 - - + -
40B ILE* 4.0 15.9 - - + +
42B ASP* 3.1 21.2 + - + +
43B GLU 3.1 0.4 - - - -
44B GLU* 1.3 75.3 - - - +
46B TYR* 1.3 65.8 + - - +
48B CYS* 3.2 13.5 + - + +
49B ALA* 3.0 23.4 + - - +
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Residues in contact with TYR 46 (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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2B TRP* 3.5 66.5 + + + -
40B ILE* 3.5 10.6 - - + +
42B ASP 2.9 14.1 + - - +
43B GLU* 3.1 11.2 - - + +
45B LEU* 1.3 77.2 - - - +
47B ASN* 1.3 70.7 + - - +
49B ALA* 3.3 1.7 + - - +
50B LYS* 2.9 59.2 + - + +
53B MET* 5.9 1.6 - - + +
63B ILE* 3.8 23.1 - - + -
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Residues in contact with ASN 47 (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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44A GLU* 5.8 0.7 - - + +
43B GLU* 2.9 11.2 + - - +
44B GLU* 3.0 45.0 + - - +
45B LEU 3.3 0.2 - - - -
46B TYR* 1.3 88.8 - - - +
48B CYS* 1.3 62.6 + - - +
50B LYS* 3.3 10.6 + - - +
51B GLU* 3.2 23.7 + - - +
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Residues in contact with CYS 48 (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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42A ASP* 4.7 1.8 - - - -
44A GLU* 3.3 24.1 + - - +
101A NCO 3.2 28.3 - - - -
20B LEU 4.6 1.7 - - - +
21B CYS* 2.1 60.3 - - - +
23B ASP* 5.1 3.4 - - - -
44B GLU 3.0 10.5 + - - +
45B LEU* 3.3 16.2 - - + +
47B ASN* 1.3 77.6 - - - +
49B ALA* 1.3 58.6 + - - +
51B GLU* 3.6 7.0 + - - +
52B ALA 3.4 12.6 + - - -
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Residues in contact with ALA 49 (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 CYS* 3.5 2.2 - - - -
24B VAL* 4.0 7.9 - - + -
25B PHE* 3.9 23.6 - - + -
40B ILE* 3.4 33.0 - - + -
45B LEU 3.0 8.0 + - - +
46B TYR 4.0 1.1 - - - +
48B CYS* 1.3 74.3 - - - +
50B LYS* 1.3 61.2 + - - +
52B ALA* 3.1 2.8 + - - +
53B MET* 2.8 28.4 + - - +
63B ILE* 3.5 13.8 - - + +
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Residues in contact with LYS 50 (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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46B TYR* 2.9 53.8 + - + +
47B ASN* 3.3 11.6 + - - +
49B ALA* 1.3 77.2 - - - +
51B GLU* 1.3 58.0 + - - +
53B MET* 3.3 14.0 + - + +
54B GLU* 2.5 64.9 + - - +
63B ILE* 3.7 9.8 - - + +
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Residues in contact with GLU 51 (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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101A NCO 2.9 41.5 + - - -
20B LEU* 3.8 23.3 - - + +
47B ASN 3.2 12.1 + - - +
48B CYS* 3.7 10.5 - - - +
50B LYS* 1.3 76.9 - - - +
52B ALA* 1.3 62.9 + - - +
54B GLU* 3.4 9.3 + - - +
55B ALA* 3.2 23.1 + - + +
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Residues in contact with ALA 52 (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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17B CYS* 3.7 30.1 - - - +
20B LEU* 4.0 13.9 - - + +
21B CYS* 4.1 2.5 - - + -
25B PHE* 3.6 21.3 - - + -
48B CYS 3.4 8.8 + - - +
49B ALA 3.1 9.1 + - - +
51B GLU* 1.3 80.3 - - - +
53B MET* 1.3 63.1 + - - +
55B ALA* 3.2 11.6 + - - +
56B CYS* 3.2 11.3 + - - -
61B ILE* 4.1 7.0 - - - +
101B 0KA 4.7 0.3 - - - -
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Residues in contact with MET 53 (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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46B TYR* 5.9 1.8 - - + +
49B ALA 2.8 17.6 + - - +
50B LYS* 3.3 32.3 - - + +
52B ALA* 1.3 71.2 - - - +
54B GLU* 1.3 71.2 + - + +
56B CYS* 3.3 21.0 + - - +
59B SER* 5.3 2.4 - - - -
61B ILE* 3.7 41.1 - - + +
62B THR* 4.2 0.9 - - - -
63B ILE* 3.7 43.5 - - + +
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Residues in contact with GLU 54 (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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50B LYS* 2.5 58.1 + - - +
51B GLU* 4.0 7.3 - - - +
52B ALA 3.4 0.2 - - - -
53B MET* 1.3 83.9 - - + +
55B ALA* 1.3 58.1 + - - +
56B CYS 3.5 2.9 - - - +
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Residues in contact with ALA 55 (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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16B ILE* 4.0 16.2 - - + +
20B LEU* 3.5 32.1 - - + -
51B GLU* 3.2 7.1 + - + +
52B ALA 3.2 5.1 + - - +
54B GLU* 1.3 76.7 - - - +
56B CYS* 1.3 64.7 + - - +
57B PRO* 3.3 9.5 - - - +
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Residues in contact with CYS 56 (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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52B ALA 3.2 7.8 + - - +
53B MET 3.3 16.3 + - - +
54B GLU 4.8 2.8 - - - +
55B ALA* 1.3 75.1 - - - +
57B PRO* 1.3 71.8 - - - +
58B VAL* 3.1 2.8 + - - -
59B SER* 3.5 17.9 + - - +
60B ALA* 3.4 26.0 - - - +
61B ILE* 4.5 5.8 - - + -
101B 0KA 2.2 50.7 - - - -
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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