Contacts of the helix formed by residues 74 - 82 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25N VAL* 4.1 1.6 - - - -
29N GLN* 4.3 0.4 - - - +
86N GLU* 3.2 30.1 - - + +
87N ALA* 3.4 34.5 - - - +
88N PRO* 3.7 4.9 - - + +
73P SER* 1.3 85.1 - - - +
75P LEU* 1.3 63.5 + - - +
76P LYS* 3.3 4.9 + - - +
77P GLU* 2.6 42.3 + - - +
78P PHE* 3.1 31.5 + - - -
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Residues in contact with LEU 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N ASN 3.8 10.3 - - - +
22N VAL* 4.0 11.2 - - + -
25N VAL* 3.6 33.2 - - + -
75N LEU* 3.9 25.7 - - + +
78N PHE* 3.8 40.8 - - + -
79N LEU* 3.6 22.2 - - + -
86N GLU* 2.7 22.0 + - - +
74P THR* 1.3 71.4 - - - +
76P LYS* 1.3 63.4 + - - +
78P PHE* 3.2 16.7 + - + +
79P LEU* 3.2 17.0 + - - +
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Residues in contact with LYS 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N LEU* 4.1 13.8 - - + +
86N GLU* 3.1 16.2 + - - +
88N PRO* 5.1 17.4 - - + +
74P THR* 3.1 6.7 - - - +
75P LEU* 1.3 80.5 - - - +
77P GLU* 1.3 64.4 + - + +
79P LEU* 3.4 5.2 + - - +
80P GLU* 3.1 48.6 + - - +
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Residues in contact with GLU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N PRO* 4.0 26.5 - - + +
89N TYR 5.1 0.7 + - - -
72P PHE* 3.7 38.5 - - + -
73P SER* 3.2 18.7 + - - -
74P THR* 2.6 36.2 + - - +
76P LYS* 1.3 82.9 - - + +
78P PHE* 1.3 62.1 + - - +
80P GLU* 3.8 12.6 - - - +
81P ASN* 2.9 32.8 + - - +
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Residues in contact with PHE 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N VAL* 3.5 26.7 - - + -
32N TRP* 4.9 4.9 - + - -
75N LEU* 3.7 16.4 - - + -
17P VAL* 3.9 6.7 - - + -
18P ALA* 3.7 29.2 - - - +
21P ASN* 3.4 42.0 - - + -
22P VAL* 4.7 0.4 - - - -
72P PHE* 3.5 39.7 - - + -
73P SER* 3.9 8.3 - - - -
74P THR 3.1 20.8 + - - -
75P LEU* 3.2 10.7 + - + +
77P GLU* 1.3 75.2 - - - +
79P LEU* 1.3 61.2 + - - +
82P ALA* 3.0 35.1 + - - +
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Residues in contact with LEU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75N LEU* 4.0 12.3 - - + -
76N LYS* 3.9 22.4 - - + +
79N LEU* 3.7 30.1 - - + -
22P VAL* 5.1 4.5 - - + -
75P LEU 3.2 7.9 + - - +
76P LYS* 3.7 6.5 - - - +
78P PHE* 1.3 76.9 - - - +
80P GLU* 1.3 67.4 + - + +
81P ASN 3.2 0.7 + - - -
82P ALA* 3.8 12.0 + - + +
86P GLU* 3.2 34.5 - - + +
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Residues in contact with GLU 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76P LYS* 3.1 48.3 + - - +
77P GLU* 3.9 9.7 - - - +
78P PHE 3.3 0.4 - - - -
79P LEU* 1.3 80.7 - - + +
81P ASN* 1.3 71.4 + - - +
82P ALA 5.2 0.2 - - - +
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Residues in contact with ASN 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P HIS* 2.7 42.5 + - + -
18P ALA* 4.0 8.3 - - + -
72P PHE* 3.3 42.9 - - + -
77P GLU* 2.9 25.3 + - - +
79P LEU 3.1 0.4 - - - -
80P GLU* 1.3 89.9 + - - +
82P ALA* 1.3 55.0 + - - +
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Residues in contact with ALA 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P HIS* 4.4 0.2 - - - -
18P ALA* 4.1 8.3 - - - +
19P ASN* 3.4 13.0 - - - +
22P VAL* 3.8 23.3 - - + -
78P PHE 3.0 18.9 + - - +
79P LEU* 3.8 10.0 + - + +
80P GLU 3.8 1.3 - - - +
81P ASN* 1.3 78.5 - - - +
83P SER* 1.3 60.1 + - - +
84P VAL 3.8 12.3 - - - +
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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