Contacts of the helix formed by residues 74 - 82 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73U SER* 1.3 83.0 - - - +
75U LEU* 1.3 64.1 + - - +
76U LYS* 3.9 3.9 - - - +
77U GLU* 2.7 36.2 + - - +
78U PHE* 3.1 29.3 + - - -
25X VAL* 3.8 4.0 - - - -
29X GLN* 4.0 1.6 - - - +
86X GLU* 3.4 27.6 - - + +
87X ALA* 3.7 36.6 - - - +
88X PRO* 3.8 6.8 - - + +
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Residues in contact with LEU 75 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74U THR* 1.3 67.7 - - - +
76U LYS* 1.3 66.9 + - - +
78U PHE* 3.0 8.6 + - - +
79U LEU* 3.0 27.4 + - - +
21X ASN 3.9 9.6 - - - +
22X VAL* 3.8 17.5 - - + -
25X VAL* 3.7 31.4 - - + -
75X LEU* 3.8 23.6 - - + +
78X PHE* 3.6 39.3 - - + -
79X LEU* 3.7 26.9 - - + -
86X GLU* 3.0 15.1 + - - +
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Residues in contact with LYS 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74U THR* 3.1 5.1 - - - +
75U LEU* 1.3 80.3 - - - +
77U GLU* 1.3 64.5 + - + +
79U LEU* 3.7 2.8 + - - +
80U GLU* 3.2 47.9 + - - +
79X LEU* 3.9 13.9 - - + +
86X GLU* 3.2 15.9 + - - +
88X PRO* 5.4 13.8 - - + +
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Residues in contact with GLU 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72U PHE* 3.9 34.2 - - + -
73U SER* 3.2 19.8 + - - -
74U THR* 2.7 32.0 + - - +
76U LYS* 1.3 82.9 - - + +
78U PHE* 1.3 61.5 + - - +
80U GLU* 3.7 15.0 + - - +
81U ASN* 2.9 32.1 + - - +
88X PRO* 3.5 27.1 - - + +
89X TYR 4.8 3.6 + - - +
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Residues in contact with PHE 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U VAL* 4.0 4.9 - - + -
18U ALA* 3.6 28.1 - - - +
21U ASN* 3.4 45.1 - - + -
22U VAL* 4.7 1.1 - - + -
72U PHE* 3.3 43.5 - - + -
73U SER* 4.0 1.3 - - - -
74U THR 3.1 22.3 + - - -
75U LEU* 3.0 11.7 + - - +
77U GLU* 1.3 75.8 - - - +
79U LEU* 1.3 64.8 + - - +
81U ASN 3.2 1.9 + - - -
82U ALA* 3.0 29.0 + - - +
25X VAL* 3.6 36.6 - - + -
32X TRP* 5.1 4.5 - + - -
75X LEU* 3.7 14.4 - - + -
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Residues in contact with LEU 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U VAL* 4.8 6.3 - - + -
75U LEU 3.0 12.6 + - - +
76U LYS* 3.9 3.6 - - - +
78U PHE* 1.3 77.6 - - - +
80U GLU* 1.3 61.2 + - - +
81U ASN 3.3 0.7 + - - -
82U ALA* 3.7 14.0 + - + +
86U GLU* 3.6 32.3 - - + +
75X LEU* 3.9 17.6 - - + +
76X LYS* 3.9 34.8 - - + +
79X LEU* 4.5 11.0 - - + -
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Residues in contact with GLU 80 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76U LYS* 3.2 49.7 + - - +
77U GLU* 3.7 18.9 - - - +
79U LEU* 1.3 77.0 - - - +
81U ASN* 1.3 65.6 + - - +
82U ALA 3.8 0.6 - - - +
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Residues in contact with ASN 81 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U HIS* 2.9 37.1 + - + -
18U ALA* 4.2 7.4 - - + +
72U PHE* 3.3 43.2 - - + -
77U GLU* 2.9 26.3 + - - +
78U PHE 3.2 0.4 + - - -
80U GLU* 1.3 85.5 + - - +
82U ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U HIS* 4.3 0.4 - - - -
18U ALA* 4.1 9.0 - - - +
19U ASN* 3.5 14.1 - - - +
22U VAL* 3.7 25.6 - - + -
78U PHE 3.0 16.7 + - - +
79U LEU* 3.7 10.5 + - + +
80U GLU 5.4 0.2 - - - +
81U ASN* 1.3 77.5 - - - +
83U SER* 1.3 59.9 + - - +
84U VAL 4.0 9.6 - - - +
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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