Contacts of the helix formed by residues 74 - 82 (chain K) in PDB entry 2BKC
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 74 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25I VAL* 3.8 4.3 - - - -
29I GLN* 4.0 0.9 - - - +
86I GLU* 3.3 27.1 - - + -
87I ALA* 3.5 37.0 - - - +
88I PRO* 3.7 3.8 - - + +
73K SER* 1.3 79.8 - - - +
75K LEU* 1.3 63.5 + - - +
76K LYS* 3.7 4.1 + - - +
77K GLU* 2.8 39.7 + - - +
78K PHE* 3.1 28.9 + - - -
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Residues in contact with LEU 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ASN* 4.0 8.1 - - + +
22I VAL* 3.9 19.7 - - + +
25I VAL* 3.5 32.8 - - + -
75I LEU* 3.9 26.7 - - + +
78I PHE* 3.6 36.8 - - + -
79I LEU* 3.7 19.7 - - + -
86I GLU* 2.8 19.5 + - - +
74K THR* 1.3 71.3 - - - +
76K LYS* 1.3 56.2 + - - +
78K PHE* 3.2 9.4 + - + +
79K LEU* 2.9 33.8 + - - +
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Residues in contact with LYS 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I LEU* 3.8 18.6 - - + +
86I GLU* 3.1 14.3 + - - +
88I PRO* 5.7 14.0 - - + +
74K THR* 3.2 4.5 - - - +
75K LEU* 1.3 78.6 - - - +
77K GLU* 1.3 69.8 + - + +
79K LEU* 3.4 2.5 + - - +
80K GLU* 3.0 60.5 + - - +
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Residues in contact with GLU 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88I PRO* 3.8 26.5 - - + +
89I TYR 5.4 0.3 + - - -
72K PHE* 3.5 36.5 - - + -
73K SER* 3.1 21.9 + - - -
74K THR* 2.8 38.5 + - - +
76K LYS* 1.3 84.2 - - + +
78K PHE* 1.3 62.5 + - - +
80K GLU* 3.4 11.3 + - - +
81K ASN* 3.0 31.2 + - - +
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Residues in contact with PHE 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I VAL* 3.5 33.4 - - + -
32I TRP* 4.9 5.4 - + - -
75I LEU* 3.9 14.8 - - + -
17K VAL* 3.8 8.3 - - + -
18K ALA* 3.7 31.7 - - - +
21K ASN* 3.5 41.5 - - + -
22K VAL* 5.0 0.9 - - + -
72K PHE* 3.4 36.3 - - + -
73K SER* 3.9 1.8 - - - -
74K THR 3.1 22.8 + - - -
75K LEU* 3.2 10.1 + - + +
77K GLU* 1.3 75.7 - - - +
79K LEU* 1.3 57.7 + - - +
81K ASN 3.2 0.3 + - - -
82K ALA* 2.9 36.1 + - - +
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Residues in contact with LEU 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I LEU* 4.0 12.1 - - + +
76I LYS* 3.8 31.0 - - + +
79I LEU* 3.8 24.5 - - + -
22K VAL* 5.2 4.9 - - + -
75K LEU 2.9 14.5 + - - +
76K LYS* 3.7 4.0 - - - +
78K PHE* 1.3 75.3 - - - +
80K GLU* 1.3 63.8 + - + +
81K ASN 3.3 0.7 + - - -
82K ALA* 3.9 10.3 + - - +
86K GLU* 3.6 28.9 - - + +
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Residues in contact with GLU 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K LYS* 3.0 59.8 + - - +
77K GLU* 3.7 9.2 - - - +
79K LEU* 1.3 76.2 - - + +
81K ASN* 1.3 66.8 + - - +
82K ALA 5.0 0.7 - - - +
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Residues in contact with ASN 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS* 3.1 26.7 + - + -
18K ALA* 4.0 7.9 - - + -
72K PHE* 3.3 45.1 - - + -
77K GLU* 3.0 25.1 + - - +
79K LEU 3.2 0.2 - - - -
80K GLU* 1.3 86.7 + - - +
82K ALA* 1.3 65.7 + - - +
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Residues in contact with ALA 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K HIS* 4.3 0.7 - - - -
18K ALA* 4.0 12.1 - - - -
19K ASN* 3.4 13.9 - - - +
22K VAL* 3.9 24.0 - - + -
78K PHE 2.9 17.4 + - - +
79K LEU* 3.9 8.5 + - - +
80K GLU 3.8 1.5 - - - +
81K ASN* 1.3 80.5 - - - +
83K SER* 1.3 60.6 + - - +
84K VAL 4.0 9.5 - - - +
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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