Contacts of the helix formed by residues 59 - 68 (chain B) in PDB entry 2KBX
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 CYS 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B CYS* 2.8 14.2 - - - -
41B CYS* 4.1 1.6 - - - -
45B PHE* 3.3 36.1 - - + -
49B LEU 4.5 1.1 - - - +
50B PHE* 4.2 4.9 - - - +
51B TYR* 4.1 6.5 - - + -
58B TYR* 1.3 77.3 - - - +
60B GLU* 1.3 67.7 + - + +
61B HIS* 2.9 18.7 + - + +
62B ASP* 2.6 20.5 + - - -
63B PHE* 3.0 12.8 + - - +
299B ZN 2.3 35.2 - - - -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 3.0 55.4 + - + -
59B CYS* 1.3 74.0 - - + +
61B HIS* 1.3 64.6 + - + +
63B PHE* 3.4 14.0 - - + -
64B GLN* 2.7 53.1 + - - +
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B CYS* 3.7 12.8 - - + +
60B GLU* 1.3 90.3 - - + +
62B ASP* 1.3 79.8 + - - +
64B GLN* 3.4 13.3 + - - +
65B MET* 3.3 29.1 + - + +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B GLN* 3.2 27.4 + - - +
41B CYS* 3.3 10.3 - - - -
58B TYR* 3.2 12.9 - - + +
59B CYS* 2.6 29.3 + - - -
61B HIS* 1.3 89.2 - - + +
63B PHE* 1.3 67.4 + - - +
65B MET* 2.9 19.9 + - + +
66B LEU* 3.0 16.5 + - + +
299B ZN 2.0 30.0 - - - -
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 5.0 0.4 - + + -
53B PHE* 2.8 74.7 - + + -
58B TYR* 3.5 21.0 - - + +
59B CYS 3.0 16.3 + - - +
60B GLU* 3.4 19.7 - - + -
62B ASP* 1.3 79.9 - - - +
64B GLN* 1.3 82.4 + - + +
66B LEU* 3.2 3.1 + - - +
67B PHE* 2.7 48.6 + + + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLU* 2.7 42.2 + - - +
61B HIS* 3.4 15.1 - - - +
63B PHE* 1.3 92.5 - - + +
65B MET* 1.3 54.5 + - - +
67B PHE* 4.1 3.1 - - - +
68B ALA* 2.3 48.2 + - + +
69B PRO 4.9 1.3 - - - +
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Residues in contact with MET 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 5.1 1.2 - - - +
35A PHE* 5.3 0.3 - - - -
65A ARG* 4.2 28.3 + - - +
66A GLY* 3.8 31.6 - - - +
40B GLN* 6.2 1.6 - - - -
61B HIS* 3.3 25.7 + - + +
62B ASP* 2.9 14.4 + - + +
64B GLN* 1.3 79.6 - - - +
66B LEU* 1.3 66.7 + - + +
68B ALA 2.6 21.9 - - - +
69B PRO 4.4 2.2 - - - -
70B CYS* 4.2 23.1 - - + -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 4.2 1.0 + - - -
35A PHE* 3.1 43.0 - - + -
65A ARG* 6.3 0.4 - - - +
66A GLY* 4.5 21.1 - - - -
40B GLN* 4.1 17.0 - - - +
56B ARG* 5.2 1.8 - - - +
58B TYR* 3.1 54.1 - - + +
62B ASP 3.0 12.5 + - - +
63B PHE* 3.9 3.1 - - - +
65B MET* 1.3 86.8 - - + +
67B PHE* 1.3 70.3 + - + +
68B ALA 3.3 0.3 + - - -
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 3.8 11.5 + - - -
40A TRP* 6.0 7.0 - + - -
53B PHE* 3.7 30.7 - + + -
54B GLU* 4.5 22.4 - - + -
58B TYR* 6.1 1.3 - + - -
63B PHE* 2.7 55.1 + + + +
64B GLN* 4.0 1.6 - - - +
66B LEU* 1.3 82.2 - - + +
68B ALA* 1.3 59.9 + - + +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 3.5 10.1 - - - -
65A ARG* 4.4 1.0 + - - -
64B GLN* 2.3 35.0 + - + +
65B MET 2.6 24.3 - - - +
66B LEU 3.2 1.0 + - - -
67B PHE* 1.3 73.0 - - + +
69B PRO* 1.3 83.3 - - + +
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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