Contacts of the helix formed by residues 46 - 58 (chain A) in PDB entry 6K71
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 ARG 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PHE* 4.6 17.4 + - + -
34A LEU* 4.3 16.1 + - + +
36A ARG* 3.2 45.9 + - - +
44A GLY 4.3 2.9 - - - +
45A LEU* 1.3 109.9 + - + +
47A ALA* 1.3 51.7 + - - +
48A ASN 3.5 2.2 - - - -
49A LEU* 3.3 32.8 + - - +
50A THR* 2.6 45.9 + - - +
76A ILE* 5.9 2.5 - - + -
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Residues in contact with ALA 47 (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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44A GLY* 4.9 10.4 + - - +
45A LEU 3.8 1.4 - - - +
46A ARG* 1.3 76.2 - - - +
48A ASN* 1.3 66.2 + - - +
50A THR* 3.2 9.6 + - - -
51A SER* 3.0 23.4 + - - -
73A LEU* 4.0 12.9 - - + +
76A ILE* 5.2 17.9 - - + +
77A SER* 6.1 0.9 - - - +
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Residues in contact with ASN 48 (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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47A ALA* 1.3 82.2 - - - +
49A LEU* 1.3 60.1 + - - +
51A SER* 2.5 28.8 + - - +
52A ALA* 2.9 15.1 + - - +
73A LEU* 5.6 3.0 - - - +
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Residues in contact with LEU 49 (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 PHE* 3.6 22.7 - - + -
36A ARG* 5.4 8.1 - - - +
45A LEU 5.2 1.6 - - - +
46A ARG* 3.3 36.0 + - - +
47A ALA 3.3 0.2 - - - -
48A ASN* 1.3 78.7 - - - +
50A THR* 1.3 56.5 + - - +
52A ALA* 3.4 6.4 + - + +
53A ILE* 2.9 57.9 + - + +
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Residues in contact with THR 50 (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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30A LEU* 4.7 14.5 - - + +
33A PHE* 3.5 24.9 - - + -
46A ARG* 2.6 23.7 + - - +
47A ALA* 3.2 11.7 + - - -
49A LEU* 1.3 75.0 - - - +
51A SER* 1.3 58.2 + - - +
53A ILE* 4.8 1.3 - - - -
54A GLU* 2.8 30.8 + - + +
72A PHE* 4.8 12.3 - - + -
73A LEU* 3.7 16.6 - - + -
76A ILE* 4.4 19.2 - - + +
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Residues in contact with SER 51 (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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47A ALA 3.0 8.8 + - - -
48A ASN* 2.5 34.5 + - - +
50A THR* 1.3 73.6 - - - +
52A ALA* 1.3 62.7 + - - +
54A GLU* 3.2 14.7 - - - +
55A THR* 3.0 28.7 + - - -
73A LEU* 3.7 24.8 - - - +
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Residues in contact with ALA 52 (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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48A ASN 2.9 11.5 + - - +
49A LEU* 3.7 10.3 - - + +
50A THR 3.4 0.2 - - - -
51A SER* 1.3 82.6 + - - +
53A ILE* 1.3 61.0 + - + +
55A THR* 3.2 9.3 + - - -
56A LEU* 2.9 35.1 + - + +
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Residues in contact with ILE 53 (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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4A LYS* 5.0 8.1 - - + -
6A LEU* 3.7 33.0 - - + -
30A LEU* 4.1 11.4 - - + -
33A PHE* 3.5 25.8 - - + -
36A ARG* 4.6 11.7 - - - +
49A LEU* 2.9 35.9 + - + +
50A THR* 4.4 1.6 - - - +
52A ALA* 1.3 76.6 - - + +
54A GLU* 1.3 61.1 + - - +
56A LEU* 3.6 17.2 - - + -
57A CYS* 2.9 34.6 + - - -
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Residues in contact with GLU 54 (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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30A LEU* 4.7 13.6 - - + +
50A THR* 2.8 19.3 + - + +
51A SER* 3.2 26.2 - - - +
53A ILE* 1.3 73.5 - - - +
55A THR* 1.3 68.4 + - - +
57A CYS* 3.7 4.5 - - - +
58A GLY* 2.8 24.9 + - - -
65A VAL* 5.2 2.0 - - - +
66A SER* 3.5 27.5 + - - +
69A GLY* 3.6 26.5 - - - +
70A GLU* 4.3 12.7 - - - +
73A LEU* 4.3 9.5 - - + +
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Residues in contact with THR 55 (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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51A SER 3.0 15.7 + - - -
52A ALA* 3.4 11.9 - - - -
54A GLU* 1.3 86.1 + - - +
56A LEU* 1.3 60.3 + - + +
58A GLY* 3.0 4.7 + - - +
59A VAL* 3.0 31.2 + - + +
66A SER* 6.0 0.2 - - - -
249A LYS* 5.0 14.9 + - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.8 41.0 + - + +
7A ILE* 5.4 4.5 - - - +
52A ALA* 2.9 24.0 + - + +
53A ILE* 3.3 20.4 + - + +
55A THR* 1.3 79.1 - - + +
57A CYS* 1.3 59.5 + - - +
59A VAL* 3.3 29.2 - - + +
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Residues in contact with CYS 57 (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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4A LYS* 5.4 2.2 - - - -
6A LEU* 3.3 36.6 - - - -
7A ILE* 6.3 2.2 - - - -
10A PHE* 3.9 26.0 - - + -
26A ALA* 5.8 0.2 - - + -
29A THR* 4.6 4.3 - - - -
30A LEU* 4.1 24.9 - - + -
53A ILE* 2.9 24.4 + - - +
54A GLU* 4.3 2.0 - - - +
56A LEU* 1.3 78.1 - - - +
58A GLY* 1.3 57.2 + - - +
59A VAL* 3.2 9.2 + - - +
60A ASP* 4.1 6.1 + - - +
65A VAL* 3.3 19.2 - - + +
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Residues in contact with GLY 58 (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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54A GLU 2.8 18.0 + - - -
55A THR* 3.0 6.7 + - - -
57A CYS* 1.3 75.7 - - - +
59A VAL* 1.3 58.4 + - - +
60A ASP* 3.1 13.1 + - - +
62A SER* 5.1 1.5 - - - +
65A VAL* 3.7 13.0 - - - -
66A SER* 3.5 24.4 + - - -
249A LYS* 4.0 15.9 - - - -
250A PHE* 5.8 0.2 - - - -
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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