Contacts of the helix formed by residues 59 - 69 (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 HIS 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA 3.4 9.5 + - - -
23A ARG 2.9 27.4 + - - -
24A ALA* 3.5 5.9 + - - -
25A GLY* 3.4 20.2 - - - -
54A ALA* 3.0 10.6 + - + +
57A VAL* 3.2 27.9 + - + +
58A GLY* 1.3 76.4 - - - +
60A LEU* 1.3 64.5 + - - +
61A GLU* 3.3 20.4 - - - +
62A ILE* 3.1 14.1 + - + +
63A VAL* 3.0 22.7 + - - +
95A ILE* 4.2 2.5 - - - -
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Residues in contact with LEU 60 (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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58A GLY 3.2 8.7 + - - +
59A HIS* 1.3 72.7 - - - +
61A GLU* 1.3 63.6 + - - +
63A VAL* 3.3 2.6 + - + +
64A GLU* 3.0 46.7 + - + +
94A GLU* 3.8 31.0 - - + +
95A ILE* 3.8 27.6 - - + -
98A VAL* 3.8 24.5 - - + -
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Residues in contact with GLU 61 (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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25A GLY 4.3 8.8 - - - +
27A ASP* 4.4 17.3 - - + +
59A HIS* 3.7 27.2 - - - +
60A LEU* 1.3 82.7 + - - +
62A ILE* 1.3 75.8 + - + +
64A GLU* 3.4 12.2 + - - +
65A VAL* 3.1 23.4 + - - +
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Residues in contact with ILE 62 (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* 3.8 25.1 - - + +
25A GLY* 3.9 24.0 - - - -
26A GLN 4.6 0.2 - - - +
27A ASP* 3.5 42.4 - - + +
30A VAL* 4.0 19.5 - - + -
54A ALA* 3.6 20.4 - - + -
59A HIS* 3.1 14.3 + - + +
61A GLU* 1.3 80.1 - - + +
63A VAL* 1.3 66.8 + - - +
65A VAL* 3.2 5.5 + - + +
66A LEU* 2.9 38.5 + - + +
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Residues in contact with VAL 63 (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* 3.7 24.2 - - + +
54A ALA* 3.9 5.4 - - + +
55A ALA* 3.8 32.5 - - + +
59A HIS 3.0 17.5 + - - +
60A LEU* 3.5 9.4 - - + +
62A ILE* 1.3 77.5 - - - +
64A GLU* 1.3 62.4 + - - +
66A LEU* 3.4 3.9 + - - +
67A LEU* 3.0 30.9 + - + +
95A ILE* 4.0 14.6 - - + -
98A VAL* 3.7 28.7 - - + -
99A LEU* 4.2 6.5 - - + -
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Residues in contact with GLU 64 (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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60A LEU* 3.0 46.8 + - + +
61A GLU* 3.7 9.4 - - - +
62A ILE 3.2 0.2 - - - -
63A VAL* 1.3 75.0 - - - +
65A VAL* 1.3 64.1 + - - +
67A LEU* 3.3 5.9 + - - +
68A LYS* 3.0 50.0 + - + +
98A VAL* 4.3 16.3 - - + +
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Residues in contact with VAL 65 (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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27A ASP* 5.9 1.8 - - + +
30A VAL* 3.8 28.3 - - + -
31A ARG* 5.5 16.6 - - + +
34A MET* 6.2 1.8 - - + -
61A GLU 3.1 14.4 + - - +
62A ILE* 3.3 16.6 - - + +
64A GLU* 1.3 77.6 - - - +
66A LEU* 1.3 66.0 + - - +
68A LYS* 3.2 9.5 + - + +
69A ASN* 2.8 43.9 + - - +
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Residues in contact with LEU 66 (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* 4.6 9.0 - - + -
30A VAL* 4.5 16.2 - - + -
34A MET* 4.9 3.6 - - + -
40A VAL* 3.8 21.0 - - + +
50A PRO* 3.5 26.0 - - + +
51A LEU* 3.4 37.7 - - + +
54A ALA* 4.5 0.4 - - + -
62A ILE* 2.9 36.1 + - + +
63A VAL* 3.7 3.6 - - - +
65A VAL* 1.3 77.8 - - + +
67A LEU* 1.3 62.4 + - - +
69A ASN* 2.9 14.5 + - - +
70A GLY 3.3 0.5 + - - -
71A ALA* 3.1 29.1 + - + +
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Residues in contact with LEU 67 (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* 3.9 26.2 - - + -
63A VAL* 3.0 36.9 + - + +
64A GLU* 3.7 5.2 - - - +
66A LEU* 1.3 77.1 - - - +
68A LYS* 1.3 60.0 + - - +
70A GLY* 3.4 10.7 + - - -
71A ALA* 4.1 12.9 - - + +
73A VAL* 4.0 22.2 - - + -
98A VAL* 4.1 13.7 - - + +
99A LEU* 4.2 9.6 - - + -
102A TYR* 3.7 56.6 - - + -
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Residues in contact with LYS 68 (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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64A GLU* 3.0 53.6 + - + +
65A VAL* 3.2 11.1 + - + +
67A LEU* 1.3 77.3 - - - +
69A ASN* 1.3 63.0 + - - +
70A GLY 3.2 2.9 + - - -
98A VAL* 5.4 0.4 - - - +
101A LYS* 5.6 2.5 - - - +
102A TYR* 3.1 34.5 + - - +
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Residues in contact with ASN 69 (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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34A MET* 4.0 42.3 - - + +
40A VAL* 3.8 15.6 - - + +
65A VAL* 2.8 40.5 + - - +
66A LEU* 2.9 8.6 + - - +
68A LYS* 1.3 83.1 + - - +
70A GLY* 1.3 58.4 + - - -
71A ALA 3.5 0.6 + - - -
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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