Contacts of the helix formed by residues 41 - 57 (chain A) in PDB entry 5BNG
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 THR 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 4.4 9.8 - - + +
37A ASP* 2.7 13.3 + - - +
40A LEU* 1.3 91.3 + - + +
42A ILE* 1.3 61.8 + - - +
43A LEU* 3.1 5.7 + - - +
44A GLN* 2.7 52.7 + - + +
45A VAL* 4.2 6.4 + - - +
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Residues in contact with ILE 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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28A GLU* 5.8 0.9 - - - +
31A LYS* 3.8 28.0 - - + +
32A LYS* 4.5 7.9 - - + +
35A ALA* 4.6 5.4 - - + -
37A ASP* 3.9 25.3 + - - +
41A THR* 1.3 71.5 - - - +
43A LEU* 1.3 69.8 + - - +
44A GLN 3.1 1.1 - - - -
45A VAL* 3.1 30.0 + - + -
46A ASN* 3.1 23.5 + - - +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.1 6.0 - - - +
42A ILE* 1.3 84.8 - - - +
44A GLN* 1.3 63.0 + - + +
46A ASN* 3.4 10.6 + - + +
47A ASN* 3.4 36.1 + - - +
7D C 3.8 22.9 - - - +
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Residues in contact with GLN 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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6A PRO* 5.9 5.1 - - - +
40A LEU* 5.7 1.4 - - - +
41A THR* 2.7 41.8 + - + +
42A ILE 3.1 0.6 - - - -
43A LEU* 1.3 80.8 - - + +
45A VAL* 1.3 65.1 - - + +
47A ASN* 3.7 5.0 + - - +
48A TRP* 3.1 26.0 + - - +
5D G 4.0 3.4 + - - -
6D A 2.7 45.5 + - - +
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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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13A MET* 4.2 15.3 - - + -
31A LYS* 3.8 32.1 - - + +
34A LEU* 4.8 4.7 - - + +
35A ALA* 3.7 34.1 - - + +
41A THR 4.3 4.3 - - - +
42A ILE* 3.1 19.5 + - + +
44A GLN* 1.3 77.8 - - + +
46A ASN* 1.3 64.2 + - - +
48A TRP* 3.2 9.0 + - - +
49A PHE* 3.2 43.6 - - + -
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Residues in contact with ASN 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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31A LYS* 2.6 37.5 + - - +
42A ILE* 3.1 40.8 + - - +
43A LEU* 3.4 12.9 + - + +
44A GLN 3.3 0.2 - - - -
45A VAL* 1.3 81.8 - - - +
47A ASN* 1.3 64.8 + - - +
48A TRP 3.1 0.7 + - - -
49A PHE* 3.3 4.0 + - - +
50A ILE* 3.0 38.1 + - + +
53A ARG* 5.5 0.2 + - - -
28C A 4.8 5.4 - - - +
29C G 3.8 5.4 + - - -
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Residues in contact with ASN 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 LEU* 3.4 35.3 + - - +
44A GLN* 4.2 5.4 - - - +
46A ASN* 1.3 78.8 - - - +
48A TRP* 1.3 58.0 + - - +
50A ILE* 3.5 15.9 - - - +
51A ASN* 2.8 44.8 + - - +
5D G 5.9 1.1 - - + -
6D A 4.1 36.1 + - + +
7D C 4.1 23.1 + - - +
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Residues in contact with TRP 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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10A THR* 4.1 27.1 + - + +
13A MET* 3.6 54.9 - - + +
14A ARG* 3.6 27.8 - - + -
17A LEU* 4.4 7.6 - - + -
44A GLN 3.1 15.9 + - - +
45A VAL 3.3 11.0 - - - +
46A ASN 3.1 0.8 - - - -
47A ASN* 1.3 77.9 - - - +
49A PHE* 1.3 63.0 + + - +
51A ASN* 3.7 4.1 - - - +
52A ALA* 2.8 56.9 + - + +
56A ILE* 4.6 6.7 - - + -
5D G 3.3 35.1 + - - -
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Residues in contact with PHE 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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13A MET* 3.4 42.2 - - + -
16A TRP* 3.6 27.1 - + - -
17A LEU* 4.0 22.4 - - + -
24A PRO 5.5 1.6 - - - -
26A PRO* 4.2 17.3 - - + -
31A LYS* 6.3 0.4 - - - -
34A LEU* 3.7 23.3 - - + -
45A VAL* 3.2 34.2 + - + -
46A ASN* 3.3 6.0 + - - +
48A TRP* 1.3 80.4 - + - +
50A ILE* 1.3 59.6 + - - +
52A ALA* 3.7 5.1 - - - +
53A ARG* 3.0 60.4 + - - +
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Residues in contact with ILE 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 ASN* 3.0 35.7 + - + +
47A ASN* 3.5 18.4 - - - +
48A TRP 3.2 0.2 - - - -
49A PHE* 1.3 79.8 - - - +
51A ASN* 1.3 70.4 + - - +
53A ARG* 3.6 31.4 + - - +
54A ARG* 3.8 10.6 + - - +
29C G 4.4 18.8 - - + +
30C C 4.1 22.7 + - + +
31C T 3.6 31.4 - - + +
7D C 5.6 2.0 - - - +
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Residues in contact with ASN 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 ASN* 2.8 26.0 + - - +
48A TRP* 3.9 4.2 - - - +
50A ILE* 1.3 82.3 - - - +
52A ALA* 1.3 65.7 + - - +
53A ARG 3.1 1.5 + - - -
54A ARG* 3.3 22.7 + - - +
55A ARG* 3.1 50.9 + - - +
5D G 4.3 14.3 + - - +
6D A 3.1 44.4 + - - +
7D C 4.6 2.8 - - - +
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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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17A LEU* 4.2 9.4 - - + -
48A TRP* 2.8 50.4 + - + +
49A PHE* 3.4 6.7 + - - +
51A ASN* 1.3 74.0 - - - +
53A ARG* 1.3 55.5 + - - +
55A ARG* 4.6 1.1 - - - -
56A ILE* 2.7 54.1 + - + +
57A VAL* 3.3 3.4 + - - +
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Residues in contact with ARG 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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17A LEU* 5.7 2.2 - - + -
24A PRO* 3.5 30.6 + - + +
25A TYR* 3.7 19.8 - - + -
26A PRO* 4.0 12.5 - - - +
31A LYS* 6.1 1.0 - - - +
46A ASN 5.5 0.4 + - - -
49A PHE* 3.0 46.1 + - + +
50A ILE* 3.7 19.0 - - - +
52A ALA* 1.3 76.9 - - + +
54A ARG* 1.3 54.9 + - + +
55A ARG 2.9 1.0 + - - -
57A VAL* 2.9 25.2 + - + -
58A GLN* 2.6 47.3 + - + +
29C G 3.5 22.2 + - - -
30C C 2.5 46.7 + - - +
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Residues in contact with ARG 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 ILE 3.8 8.9 + - - +
51A ASN* 3.6 21.8 - - - +
53A ARG* 1.3 75.9 - - + +
55A ARG* 1.3 72.3 + - + +
58A GLN* 3.6 17.8 - - + +
59A PRO* 4.1 10.0 - - - +
31C T 3.5 52.4 + - - +
32C G 3.0 39.1 + - - -
33C T 3.2 23.7 + - - +
6D A 3.5 15.0 - - - +
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Residues in contact with ARG 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 ASN* 3.1 37.8 + - - +
52A ALA* 4.2 1.3 - - - +
53A ARG 2.9 1.2 + - - -
54A ARG* 1.3 101.0 - - + +
56A ILE* 1.3 67.8 + - + +
59A PRO* 3.8 15.4 - - - +
33C T 4.1 7.1 + - - -
34C C 5.1 0.2 - - - +
4D T 3.7 41.1 + - - +
5D G 3.5 41.2 + - - -
6D A 3.8 10.5 - - - +
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Residues in contact with ILE 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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14A ARG* 3.1 37.2 - - - +
17A LEU* 3.8 25.8 - - + -
18A PHE* 3.7 31.0 - - + -
21A LEU* 5.8 0.4 - - + -
48A TRP* 4.6 4.7 - - + -
52A ALA* 2.7 33.3 + - + +
55A ARG* 1.3 82.1 - - + +
57A VAL* 1.3 59.8 + - + +
59A PRO* 4.0 2.8 - - - +
60A MET* 3.4 22.7 + - + +
4D T 5.3 2.9 - - - +
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Residues in contact with VAL 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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17A LEU* 4.6 13.7 - - + -
21A LEU* 3.7 31.4 - - + +
24A PRO* 4.7 14.6 - - + -
52A ALA 3.3 2.2 + - - +
53A ARG* 2.9 30.8 + - + +
56A ILE* 1.3 78.1 - - + +
58A GLN* 1.3 67.1 + - - +
59A PRO* 3.1 2.7 - - - -
60A MET* 2.6 37.2 + - + +
61A ILE* 3.2 28.4 + - + -
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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