Contacts of the helix formed by residues 39 - 50 (chain D) in PDB entry 5MR4
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 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D PRO 3.6 3.6 + - - +
38D VAL* 1.3 78.0 - - - +
40D CYS* 1.3 57.1 + - - +
41D VAL* 3.0 22.3 + - - +
42D ARG* 3.0 18.1 + - - +
43D ALA* 2.9 25.8 + - - +
93D CYS* 3.8 1.8 - - - -
94D ARG 3.3 17.5 - - - +
95D CYS* 5.0 1.1 - - - -
96D LYS* 5.9 0.4 - - + +
99D MET* 4.0 23.5 - - + +
105D CYS* 4.5 0.2 - - - -
129D GLU* 4.7 7.4 - - - +
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Residues in contact with CYS 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 1.3 73.6 - - - +
41D VAL* 1.3 60.9 + - - +
43D ALA* 3.8 0.8 - - - +
44D ASN* 3.0 30.0 + - - +
93D CYS* 2.1 61.5 - - - -
94D ARG* 3.5 8.2 + - - -
95D CYS* 4.3 0.4 - - - -
105D CYS* 3.5 23.7 - - - +
108D ILE* 3.5 13.0 - - + +
109D TYR* 3.9 23.6 - - - -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 3.0 9.4 + - - +
40D CYS* 1.3 77.2 - - - +
42D ARG* 1.3 61.0 + - - +
44D ASN* 3.7 3.8 + - - +
45D GLU* 3.3 31.9 + - + +
99D MET* 4.4 5.4 - - + -
100D LYS 5.5 0.4 - - - +
101D LYS* 3.7 45.1 - - + +
104D GLN* 4.2 9.6 - - + -
105D CYS* 3.6 33.2 - - + +
108D ILE* 4.0 7.9 - - + -
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 3.8 23.5 - - + +
39D ASP* 3.0 23.0 + - - +
41D VAL* 1.3 73.8 - - - +
43D ALA* 1.3 65.6 + - - +
44D ASN 3.2 0.2 - - - -
45D GLU* 3.1 44.8 + - - +
46D LEU* 3.1 56.1 + - + +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 3.5 12.9 - - + +
39D ASP 2.9 19.0 + - - +
40D CYS 3.8 4.7 - - - +
42D ARG* 1.3 74.7 - - - +
44D ASN* 1.3 57.7 + - - +
46D LEU* 3.6 8.1 + - - +
47D CYS* 3.1 26.2 + - - +
89D PRO 5.2 1.6 - - - +
90D LEU* 4.0 22.2 - - + +
93D CYS* 3.9 18.2 - - + -
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Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D CYS 3.0 18.0 + - - +
41D VAL 3.8 4.7 + - - +
42D ARG 3.2 0.2 - - - -
43D ALA* 1.3 76.3 - - - +
45D GLU* 1.3 62.4 + - - +
47D CYS* 3.6 7.1 - - - +
48D ALA* 2.8 34.4 + - - +
57D TYR* 3.1 36.5 - - - -
61D ARG* 4.6 12.3 + - - +
90D LEU* 4.1 4.4 - - - +
108D ILE* 3.7 25.6 - - + +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D VAL* 3.3 29.4 + - + +
42D ARG* 3.1 39.6 + - - +
44D ASN* 1.3 78.4 - - - +
46D LEU* 1.3 57.8 + - - +
48D ALA* 3.4 6.5 + - - +
49D ALA* 3.1 29.1 + - - +
101D LYS* 4.3 8.7 + - - -
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 4.5 12.8 - - + -
42D ARG* 3.1 54.2 + - + +
43D ALA* 3.7 11.2 - - - +
44D ASN 3.4 0.2 - - - -
45D GLU* 1.3 78.7 - - - +
47D CYS* 1.3 58.4 + - - +
49D ALA* 3.9 5.4 + - + +
50D GLU* 3.6 27.0 + - - +
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Residues in contact with CYS 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D ALA 3.1 18.4 + - - +
44D ASN* 3.6 6.1 - - - +
45D GLU 3.3 0.2 - - - -
46D LEU* 1.3 75.7 - - - +
48D ALA* 1.3 64.9 + - - +
49D ALA 3.2 0.2 - - - -
50D GLU 3.2 10.2 + - - +
53D CYS* 2.1 62.8 - - - +
54D SER* 3.1 21.9 + - - -
57D TYR* 4.1 15.7 - - - -
90D LEU* 3.7 18.6 - - + -
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASN* 2.8 28.3 + - - +
45D GLU* 3.4 7.6 + - - +
47D CYS* 1.3 74.9 - - - +
49D ALA* 1.3 59.4 + - - +
54D SER* 3.5 21.0 + - - +
58D ARG* 5.5 0.2 + - - -
61D ARG* 5.7 6.1 - - - +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU 3.1 15.0 + - - +
46D LEU* 4.1 8.1 - - + +
47D CYS 3.2 0.2 - - - -
48D ALA* 1.3 77.3 - - - +
50D GLU* 1.3 67.0 + - - +
51D SER* 3.9 1.4 + - - -
54D SER* 5.1 0.2 - - - -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU 3.6 16.9 + - - +
47D CYS* 3.2 5.6 + - - +
49D ALA* 1.3 83.5 - - - +
51D SER* 1.3 60.6 + - - +
52D ASN 3.6 0.9 - - - +
53D CYS* 3.6 10.9 + - + +
54D SER* 2.6 36.5 + - - -
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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