Contacts of the helix formed by residues 74 - 82 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73M SER* 1.3 82.0 - - - +
75M LEU* 1.3 64.1 + - - +
76M LYS* 4.0 5.0 - - - +
77M GLU* 2.7 36.9 + - - +
78M PHE* 3.1 30.1 + - - -
25O VAL* 3.7 3.7 - - - +
29O GLN* 3.9 1.1 - - - +
86O GLU* 3.3 26.9 - - + +
87O ALA 3.5 36.3 - - - +
88O PRO* 3.5 8.0 - - + +
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Residues in contact with LEU 75 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74M THR* 1.3 69.5 - - - +
76M LYS* 1.3 65.0 + - - +
78M PHE* 3.0 11.1 + - + +
79M LEU* 2.8 26.2 + - - +
21O ASN* 4.2 5.6 - - + +
22O VAL* 4.0 20.6 - - + +
25O VAL* 3.4 35.9 - - + -
75O LEU* 4.0 27.9 - - + +
78O PHE* 3.9 36.1 - - + -
79O LEU* 3.8 15.0 - - + -
86O GLU* 2.8 20.5 + - - +
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Residues in contact with LYS 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74M THR* 4.0 6.1 - - - +
75M LEU* 1.3 77.4 - - - +
77M GLU* 1.3 57.9 + - + +
79M LEU* 3.2 4.7 + - - +
80M GLU* 2.6 62.2 + - - +
79O LEU* 3.6 13.5 - - + +
86O GLU* 3.0 16.3 + - + +
88O PRO* 4.9 19.3 - - + -
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Residues in contact with GLU 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M ALA* 4.4 0.9 - - - +
71M PRO 5.3 0.3 - - - +
72M PHE* 3.8 35.7 - - + -
73M SER* 3.1 22.1 + - - -
74M THR* 2.7 34.3 + - - +
76M LYS* 1.3 76.1 - - + +
78M PHE* 1.3 63.0 + - - +
80M GLU* 3.5 14.5 + - - +
81M ASN* 3.0 31.3 + - - +
88O PRO* 3.6 30.6 - - + +
89O TYR 4.9 4.4 + - - +
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Residues in contact with PHE 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M VAL* 3.8 11.0 - - + -
18M ALA* 3.5 26.3 - - - +
21M ASN* 3.5 35.9 - - + -
22M VAL* 4.8 0.9 - - + -
72M PHE* 3.2 42.2 - - + -
73M SER* 4.0 1.3 - - - -
74M THR 3.1 24.9 + - - -
75M LEU* 3.0 14.6 + - + +
77M GLU* 1.3 75.9 - - - +
79M LEU* 1.3 62.0 + - - +
82M ALA* 3.1 31.2 + - - +
25O VAL* 3.6 27.4 - - + -
32O TRP* 5.1 4.9 - + - -
75O LEU* 3.8 14.1 - - + -
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Residues in contact with LEU 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M VAL* 5.4 4.5 - - + -
75M LEU 2.8 14.3 + - - +
76M LYS* 3.7 4.7 - - - +
78M PHE* 1.3 76.8 - - - +
80M GLU* 1.3 64.1 + - + +
81M ASN 3.4 0.3 + - - -
82M ALA* 4.0 9.0 + - + +
86M GLU* 3.9 22.9 - - + +
75O LEU* 4.0 19.1 - - + +
76O LYS* 3.6 34.3 - - + +
79O LEU* 4.8 10.5 - - + -
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Residues in contact with GLU 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76M LYS* 2.6 67.5 + - - +
77M GLU* 3.8 12.1 - - - +
78M PHE 3.4 0.2 - - - -
79M LEU* 1.3 77.3 - - + +
81M ASN* 1.3 72.6 + - - +
82M ALA 3.7 1.1 + - - +
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Residues in contact with ASN 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M HIS* 2.9 27.3 - - + -
18M ALA* 3.9 6.5 - - + +
72M PHE* 3.5 42.5 - - + -
77M GLU* 3.0 24.6 + - - +
78M PHE 3.9 0.7 - - - -
79M LEU 3.2 0.4 - - - -
80M GLU* 1.3 94.6 + - - +
82M ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M HIS* 4.3 0.2 - - - -
18M ALA* 3.7 10.3 - - - +
19M ASN* 3.5 14.4 - - - +
22M VAL* 3.7 24.5 - - + -
78M PHE 3.1 18.5 + - - +
79M LEU* 4.0 6.8 + - + +
80M GLU 3.7 2.0 - - - +
81M ASN* 1.3 78.2 - - - +
83M SER* 1.3 60.2 + - - +
84M VAL 4.1 8.8 - - - +
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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