Contacts of the helix formed by residues 49 - 58 (chain A) in PDB entry 2BKG
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 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 2.0 - - - -
40A VAL 4.7 0.9 - - - -
41A ASN* 3.9 26.0 + - + +
42A ALA 3.1 9.0 - - - +
43A GLU* 4.2 10.3 - - + +
47A GLY 4.4 1.3 - - - +
48A ASP* 1.3 77.3 - - - +
50A PRO* 1.3 77.5 - - - +
51A LEU* 3.5 9.7 + - - +
52A HIS* 3.0 26.3 + - + +
53A LEU* 3.1 21.1 + - - +
72A ASP 5.2 0.3 + - - -
75A ALA* 3.9 26.0 - - + +
76A LEU 6.0 0.2 - - - +
83A PRO* 5.1 0.3 - - - +
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Residues in contact with PRO 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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18A LEU* 3.9 22.4 - - + -
19A LEU* 3.6 17.7 - - + +
22A ALA* 3.7 24.2 - - + +
40A VAL 3.3 20.9 - - - +
42A ALA* 3.1 16.4 - - + +
49A THR* 1.3 88.9 - - - +
51A LEU* 1.3 54.4 + - - +
53A LEU* 3.2 4.5 + - + +
54A ALA* 3.0 31.2 + - - +
66A LEU* 3.5 18.7 - - + +
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Residues in contact with LEU 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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40A VAL 5.2 1.0 + - - +
41A ASN* 6.0 0.4 - - - +
49A THR* 3.1 9.0 + - - +
50A PRO* 1.3 76.4 - - - +
52A HIS* 1.3 66.4 + - - +
54A ALA* 4.8 0.2 - - - -
55A ALA* 3.0 27.1 + - - +
63A VAL* 3.7 45.8 - - + +
66A LEU* 3.4 14.4 - - + +
67A LEU* 3.9 15.0 - - + -
71A ALA* 4.1 12.6 - - + -
72A ASP 3.6 25.1 - - - +
73A VAL* 3.8 12.6 - - - -
83A PRO* 3.8 17.9 - - + -
99A LEU* 4.0 9.2 - - + -
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Residues in contact with HIS 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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47A GLY 4.1 4.7 - - - -
48A ASP* 3.3 28.0 - - + +
49A THR* 3.0 35.1 + - - +
51A LEU* 1.3 78.1 - - - +
53A LEU* 1.3 58.1 + - - +
55A ALA* 3.4 1.1 + - - +
56A ARG* 2.9 32.1 + - - +
75A ALA* 3.0 38.8 + - + -
76A LEU 3.9 1.6 - - - -
77A ASP* 3.6 11.5 + - + -
81A SER 2.8 27.4 + - - -
82A THR 3.8 0.2 - - - -
83A PRO* 3.6 23.3 - - + +
86A LEU* 3.6 18.4 - - + +
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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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19A LEU* 3.2 46.2 - - + +
23A ARG* 3.9 41.3 - - + +
44A ASP* 3.7 10.5 - - + +
48A ASP* 3.6 24.2 - - + -
49A THR 3.1 13.7 + - - +
50A PRO* 3.2 5.8 + - + +
52A HIS* 1.3 80.6 - - - +
54A ALA* 1.3 63.0 + - - +
56A ARG* 3.2 36.3 + - - +
57A VAL* 3.1 28.1 + - - +
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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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22A ALA 4.1 7.5 + - - +
50A PRO 3.0 16.6 + - - +
51A LEU 4.2 1.3 - - - +
53A LEU* 1.3 75.3 - - - +
55A ALA* 1.3 59.5 + - - +
57A VAL* 4.1 7.0 - - - -
58A GLY* 2.9 24.4 + - - -
59A HIS* 3.0 12.8 + - + +
62A ILE* 3.6 33.7 - - + -
63A VAL* 3.9 16.8 - - + +
66A LEU* 4.5 1.8 - - + -
95A ILE* 4.0 1.4 - - - +
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Residues in contact with ALA 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 LEU* 3.0 21.4 + - + +
52A HIS 3.8 3.4 - - - +
54A ALA* 1.3 77.4 - - - +
56A ARG* 1.3 62.6 + - - +
63A VAL* 3.8 9.4 - - + +
83A PRO* 3.7 30.5 - - + +
86A LEU* 5.0 0.2 - - + -
87A ALA* 3.5 14.0 - - + +
92A HIS* 3.2 18.2 + - - -
95A ILE* 3.9 20.0 - - + +
99A LEU* 4.4 1.3 - - + -
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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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23A ARG* 3.9 15.1 - - - +
44A ASP* 5.0 1.2 + - - -
48A ASP* 4.1 20.3 + - - -
52A HIS 2.9 15.4 + - - +
53A LEU* 3.2 37.2 + - - +
54A ALA 3.3 0.2 - - - -
55A ALA* 1.3 77.4 - - - +
57A VAL* 1.3 58.9 + - + +
77A ASP* 5.1 1.4 + - - -
86A LEU* 4.0 34.9 - - + +
90A ARG* 3.3 35.1 - - + +
92A HIS* 2.9 21.7 - - - -
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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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23A ARG* 3.7 17.9 - - + +
53A LEU 3.1 19.3 + - - +
54A ALA* 3.9 4.9 - - - +
56A ARG* 1.3 77.5 - - + +
58A GLY* 1.3 60.0 + - - +
59A HIS* 3.2 42.5 + - + +
92A HIS* 3.6 8.2 + - - -
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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 2.9 4.9 + - - -
56A ARG 3.3 2.6 - - - -
57A VAL* 1.3 79.6 - - - +
59A HIS* 1.3 65.0 + - - +
60A LEU* 3.2 8.1 + - - +
92A HIS* 3.5 17.8 - - - -
95A ILE* 3.4 21.7 - - - +
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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