Contacts of the helix formed by residues 69 - 76 (chain A) in PDB entry 1BIK
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 GLU 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A TYR* 3.6 34.3 + - + +
51A CYS* 4.0 20.4 + - + +
68A THR* 1.3 71.5 - - - +
70A LYS* 1.3 60.2 + - - +
72A CYS* 3.6 3.7 - - - +
73A LEU* 2.8 41.4 + - + +
112A TYR* 3.0 32.3 + - - -
114A GLY 4.8 3.5 - - - +
115A CYS* 5.2 0.7 - - - -
116A GLN 5.8 0.7 - - - -
117A GLY 4.2 11.1 + - - +
118A ASN 4.3 1.0 - - - +
121A LYS* 2.8 28.1 + - - +
123A TYR* 4.0 3.2 + - - +
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Residues in contact with LYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 3.1 10.6 - - - +
69A GLU* 1.3 79.3 - - - +
71A GLU* 1.3 54.2 + - - +
73A LEU* 3.6 0.9 - - - +
74A GLN* 2.8 73.9 + - - +
123A TYR* 3.5 51.7 + - + -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PHE* 3.5 24.1 - - + -
67A VAL* 3.7 27.0 + - - +
68A THR* 3.3 19.4 + - - +
70A LYS* 1.3 79.7 - - - +
72A CYS* 1.3 64.5 + - - +
74A GLN* 3.9 6.1 - - - +
75A THR* 2.9 32.9 + - - +
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Residues in contact with CYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR* 4.2 3.8 - - + -
43A PHE 3.9 2.2 - - - -
44A TYR* 3.7 25.6 - - - -
51A CYS* 2.0 48.9 - - + -
66A PHE* 3.6 29.4 - - + -
68A THR 3.2 13.2 + - - +
69A GLU* 3.6 3.4 - - - +
71A GLU* 1.3 81.1 - - - +
73A LEU* 1.3 55.4 + - - +
75A THR* 3.6 1.2 - - - -
76A CYS* 2.8 33.6 + - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 4.9 7.6 - - + -
50A ALA* 5.0 0.7 - - - -
51A CYS* 3.4 28.0 - - - +
69A GLU* 2.8 23.9 + - + +
70A LYS 3.8 2.2 - - - +
72A CYS* 1.3 74.5 - - - +
74A GLN* 1.3 61.3 + - - +
77A ARG* 2.9 61.8 + - + +
118A ASN 3.9 6.5 - - - +
119A GLY* 3.8 23.1 - - - +
121A LYS* 3.8 25.8 - - + +
123A TYR* 3.8 21.8 - - + +
131A TYR* 4.7 0.2 + - - -
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LYS* 2.8 61.9 + - - +
71A GLU* 4.2 5.2 + - - +
73A LEU* 1.3 71.8 - - - +
75A THR* 1.3 62.2 + - - +
77A ARG* 4.3 7.2 - - - +
123A TYR* 3.8 12.1 - - + +
127A GLU* 3.4 32.9 + - - +
131A TYR* 3.9 13.3 + - - -
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 6.5 0.4 - - - -
26A CYS* 3.8 8.6 - - - -
66A PHE* 3.6 29.2 - - + -
71A GLU* 2.9 25.0 + - - +
72A CYS 3.6 2.0 - - - -
74A GLN* 1.3 82.4 - - - +
76A CYS* 1.3 65.5 + - - +
77A ARG 4.9 1.3 - - - +
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Residues in contact with CYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A CYS* 2.0 53.9 - - - +
44A TYR* 3.1 50.7 - - + -
66A PHE* 4.0 12.6 - - - -
72A CYS 2.8 18.9 + - - +
75A THR* 1.3 79.3 - - - +
77A ARG* 1.3 66.1 + - - +
78A THR* 3.6 8.1 + - - +
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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