Contacts of the helix formed by residues 43 - 58 (chain A) in PDB entry 7BQQ
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A MET* 2.9 38.4 + - - +
40A ALA 3.2 14.9 - - - +
41A ASN 3.6 0.2 - - - -
42A ASP* 1.3 103.2 + - - +
44A PRO* 1.3 70.0 - - + +
45A GLU* 3.4 17.9 + - + +
46A VAL* 3.5 20.0 + - + +
47A SER 3.5 3.5 + - - -
104A GLN* 4.8 7.4 - - - +
107A LYS* 5.5 9.0 + - - +
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Residues in contact with PRO 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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40A ALA 4.8 0.7 - - - +
42A ASP 4.5 2.7 - - - +
43A ASN* 1.3 85.9 - - + +
45A GLU* 1.3 59.0 + - + +
47A SER* 3.3 8.6 + - - -
48A GLU* 2.8 37.7 + - - +
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Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASN* 4.2 21.1 - - + +
44A PRO* 1.3 83.1 - - + +
46A VAL* 1.3 65.9 + - + +
48A GLU* 3.5 26.2 - - - +
49A GLN* 3.8 8.0 + - - +
98A LEU 4.6 2.9 - - - +
100A ILE* 6.2 0.9 - - + -
104A GLN* 4.8 12.7 - - - +
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Residues in contact with VAL 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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36A LEU 4.9 1.3 - - - +
39A MET* 3.7 27.8 - - + +
40A ALA* 3.9 17.3 - - + +
43A ASN* 3.5 12.1 + - + +
44A PRO 3.3 0.2 - - - -
45A GLU* 1.3 77.2 - - + +
47A SER* 1.3 59.8 + - - +
49A GLN* 3.0 20.8 + - - +
50A LEU* 3.0 15.4 + - + +
98A LEU* 4.2 37.9 - - + -
100A ILE* 4.2 7.9 - - + -
104A GLN* 3.5 27.8 - - - +
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Residues in contact with SER 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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40A ALA* 3.6 34.5 + - - +
43A ASN 3.5 3.4 + - - -
44A PRO* 3.3 11.6 + - - -
46A VAL* 1.3 79.1 - - - +
48A GLU* 1.3 59.0 + - - +
50A LEU* 3.3 10.5 + - - +
51A ARG* 3.2 25.2 + - - +
61A PRO* 5.1 1.6 - - - +
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Residues in contact with GLU 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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44A PRO* 2.8 19.0 + - - +
45A GLU* 3.5 29.2 + - - +
47A SER* 1.3 72.3 - - - +
49A GLN* 1.3 60.3 + - + +
51A ARG* 3.5 11.2 - - - +
52A GLU* 3.2 28.4 + - - +
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Residues in contact with GLN 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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45A GLU 4.1 5.8 - - - +
46A VAL 3.0 9.6 + - - +
48A GLU* 1.3 79.5 - - + +
50A LEU* 1.3 64.1 + - - +
52A GLU* 3.0 29.4 + - - +
53A LEU* 3.1 29.7 + - + +
56A ARG* 5.1 4.6 - - - +
96A ASP 4.6 4.4 + - - -
97A ASP* 2.9 30.3 + - - +
98A LEU* 3.6 25.8 - - - +
99A GLY* 4.8 2.7 - - - -
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Residues in contact with LEU 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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36A LEU* 5.0 2.0 - - + +
37A GLN* 3.8 10.8 - - - +
40A ALA* 3.3 28.7 - - + -
46A VAL* 3.0 21.7 + - + +
47A SER* 3.3 11.0 + - - +
49A GLN* 1.3 74.7 - - - +
51A ARG* 1.3 55.8 + - - +
53A LEU* 3.5 2.4 + - + -
54A ALA* 3.1 30.0 + - - +
61A PRO* 3.8 22.0 - - + +
64A VAL* 3.8 12.6 - - + +
65A ILE* 3.6 32.5 - - + -
68A LEU* 5.4 0.7 - - + -
98A LEU* 3.5 29.8 - - + -
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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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47A SER* 3.2 13.1 + - - +
48A GLU* 3.5 12.8 - - - +
49A GLN 3.2 0.2 - - - -
50A LEU* 1.3 75.2 - - - +
52A GLU* 1.3 59.6 + - - +
54A ALA* 3.4 1.6 + - - +
55A LYS* 2.9 51.5 + - + +
61A PRO* 3.9 31.2 - - + +
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Residues in contact with GLU 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 GLU 3.2 15.3 + - - +
49A GLN* 3.0 31.1 + - - +
51A ARG* 1.3 75.7 - - - +
53A LEU* 1.3 58.4 + - + +
55A LYS* 3.8 8.1 - - - +
56A ARG* 3.0 45.1 + - - +
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Residues in contact with LEU 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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49A GLN* 3.1 25.3 + - - +
50A LEU* 3.9 5.2 - - - +
52A GLU* 1.3 74.2 - - - +
54A ALA* 1.3 61.4 + - - +
56A ARG* 3.3 26.3 + - - +
57A LYS* 3.1 40.0 + - - +
64A VAL* 4.0 17.3 - - + -
68A LEU* 3.9 28.0 - - + -
97A ASP* 3.6 42.4 - - + +
98A LEU* 4.4 8.1 - - + -
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Residues in contact with ALA 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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50A LEU 3.1 18.5 + - - +
51A ARG* 3.8 4.3 - - - +
53A LEU* 1.3 77.0 - - - +
55A LYS* 1.3 56.2 + - + +
57A LYS 3.3 0.9 + - - -
58A GLY 2.8 25.6 + - - -
59A THR* 2.9 21.0 + - - +
60A SER 3.4 35.2 - - - +
61A PRO* 3.5 7.0 - - + -
64A VAL* 3.7 11.3 - - + +
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Residues in contact with LYS 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 ARG* 2.9 41.2 + - + +
52A GLU* 3.9 9.0 - - - +
54A ALA* 1.3 69.7 - - + +
56A ARG* 1.3 63.2 + - + +
57A LYS 3.6 0.2 + - - -
58A GLY* 3.7 11.7 + - - +
59A THR 4.2 14.5 + - - +
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Residues in contact with ARG 56 (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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49A GLN* 5.1 5.1 - - - +
52A GLU* 3.0 32.2 + - - +
53A LEU* 3.6 25.0 - - - +
55A LYS* 1.3 76.3 - - - +
57A LYS* 1.3 62.8 + - + +
58A GLY 3.9 0.2 + - - -
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Residues in contact with LYS 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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53A LEU* 3.1 30.2 + - - +
54A ALA 3.9 3.4 - - - +
56A ARG* 1.3 82.0 - - + +
58A GLY* 1.3 58.7 + - - +
59A THR* 3.5 12.9 - - + -
64A VAL* 3.8 20.9 - - + -
67A ASP* 5.8 12.6 + - - +
68A LEU* 6.2 2.5 - - - -
93A LYS* 5.9 3.2 - - - +
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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 ALA 2.8 7.7 + - - -
55A LYS* 3.7 11.9 + - - -
56A ARG 3.6 3.0 - - - -
57A LYS* 1.3 77.5 - - - +
59A THR* 1.3 55.7 + - - -
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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