Contacts of the helix formed by residues 40 - 51 (chain A) in PDB entry 6P7B
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 ASN 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 1.3 84.5 + - - +
41A TRP* 1.3 61.2 + - - +
42A GLU 3.3 2.7 - - - -
43A ARG* 3.2 35.4 + - + +
44A SER* 2.9 28.0 + - - +
14E T 4.7 2.8 - - - +
15E T 4.1 30.0 + - - +
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Residues in contact with TRP 41 (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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10A ILE* 5.0 7.9 - - + -
37A TRP* 3.4 28.9 - - + +
39A LYS 3.5 0.2 - - - -
40A ASN* 1.3 75.5 - - - +
42A GLU* 1.3 85.0 + - + +
44A SER* 3.8 5.3 - - - -
45A VAL* 2.7 41.9 + - + +
70A LYS* 3.7 29.5 - - + +
71A ILE* 3.8 30.1 - - + -
74A PHE* 3.6 35.4 - + + -
73C TYR* 3.6 30.3 - + - -
15E T 5.3 5.3 - - - -
16E T 2.8 21.9 + - - -
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Residues in contact with GLU 42 (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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40A ASN 3.3 0.6 - - - -
41A TRP* 1.3 112.0 + - + +
43A ARG* 1.3 65.9 + - + +
45A VAL* 3.4 1.7 + - - +
46A ALA* 2.9 26.3 + - - +
74A PHE* 3.5 40.5 - - + -
73C TYR* 4.3 0.7 - - - -
76C LYS* 3.5 34.0 + - - +
80C TYR* 3.9 18.7 - - + -
16E T 5.4 0.2 + - - -
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Residues in contact with ARG 43 (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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40A ASN* 3.2 34.5 + - + +
42A GLU* 1.3 78.0 - - + +
44A SER* 1.3 59.2 + - - +
46A ALA* 3.8 2.3 - - - +
47A ARG* 2.9 36.7 + - + +
80C TYR* 3.2 22.9 + - + +
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Residues in contact with SER 44 (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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36A ASP 4.0 8.8 + - - -
37A TRP* 3.4 25.8 - - - -
39A LYS 3.1 13.9 + - - -
40A ASN* 2.9 18.5 + - - +
41A TRP* 3.8 4.3 - - - -
43A ARG* 1.3 76.3 - - - +
45A VAL* 1.3 59.2 + - - +
47A ARG* 3.3 5.0 + - - +
48A ASP* 2.9 37.4 + - - +
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Residues in contact with VAL 45 (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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37A TRP* 3.6 43.3 - - + -
41A TRP* 2.7 29.9 + - + +
42A GLU 3.8 3.1 - - - +
44A SER* 1.3 73.4 - - - +
46A ALA* 1.3 59.1 + - - +
48A ASP 3.3 0.2 + - - -
49A LEU* 2.9 54.6 + - + +
71A ILE* 4.0 12.1 - - + -
74A PHE* 4.1 15.3 - - + -
75A ILE* 3.7 16.8 - - + -
78A PHE* 5.9 2.2 - - + -
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Residues in contact with ALA 46 (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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42A GLU 2.9 17.4 + - - +
43A ARG* 3.8 3.8 - - - +
45A VAL* 1.3 79.0 - - - +
47A ARG* 1.3 53.2 + - + +
50A THR* 2.5 38.5 + - - +
74A PHE* 4.8 2.4 - - + -
78A PHE* 3.9 31.8 - - + -
80C TYR* 3.9 21.8 - - + -
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Residues in contact with ARG 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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43A ARG* 2.9 22.1 + - + +
44A SER* 3.7 6.1 - - - +
46A ALA* 1.3 77.0 - - + +
48A ASP* 1.3 67.6 + - - +
50A THR* 3.4 5.6 + - - -
51A ARG* 3.2 34.0 + - - +
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Residues in contact with ASP 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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4A CYS* 5.8 0.9 - - - -
15A TYR* 4.1 28.2 + - + -
35A SER* 2.7 31.4 + - - -
37A TRP* 2.7 29.4 + - + +
44A SER* 2.9 17.0 + - - +
45A VAL 4.1 1.3 - - - +
47A ARG* 1.3 78.6 - - - +
49A LEU* 1.3 64.0 + - + +
51A ARG* 3.4 37.9 + - - +
52A TYR* 4.8 2.8 + - - -
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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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4A CYS* 4.2 14.9 - - - -
6A VAL* 3.9 26.9 - - + -
15A TYR* 5.3 6.1 - - + -
37A TRP* 4.8 13.2 - - + -
45A VAL* 2.9 41.7 + - + +
46A ALA* 4.8 1.8 - - - +
48A ASP* 1.3 81.7 - - + +
50A THR* 1.3 60.3 + - + +
51A ARG 3.3 1.0 + - - -
52A TYR* 4.5 2.8 + - - +
54A PRO* 3.4 26.2 - - - +
57A VAL* 4.8 6.5 - - + -
75A ILE* 3.6 26.0 - - + -
78A PHE* 5.5 0.9 - - + -
79A PHE* 3.8 27.9 - - + -
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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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46A ALA 2.5 25.4 + - - +
47A ARG* 3.4 8.1 + - - -
49A LEU* 1.3 76.3 - - - +
51A ARG* 1.3 66.9 + - - +
52A TYR 3.4 1.7 + - - -
53A ASN* 3.5 20.3 + - - +
54A PRO* 4.8 1.6 - - - -
78A PHE* 3.6 30.5 - - + -
79A PHE* 4.2 9.0 - - + -
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Residues in contact with ARG 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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15A TYR* 4.0 11.4 + - - -
47A ARG* 3.2 23.5 + - - +
48A ASP* 3.4 35.0 + - - +
49A LEU 3.3 1.4 - - - -
50A THR* 1.3 80.4 - - - +
52A TYR* 1.3 98.2 + - + +
53A ASN* 3.7 3.3 + - - -
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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