Contacts of the helix formed by residues 75 - 81 (chain A) in PDB entry 1BMZ
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 5.3 0.2 - - - -
73A ILE* 2.8 29.3 + - + +
74A ASP* 1.3 70.4 - - - +
76A LYS* 1.3 67.5 + - - +
78A TYR* 3.3 9.0 + - - +
79A TRP* 3.2 36.2 + - - -
86A PRO* 5.3 0.6 - - - +
88A HIS* 4.0 10.9 + - - +
89A GLU 3.9 0.2 + - - -
90A HIS* 3.2 20.9 + - - +
91A ALA* 3.9 12.8 - - + -
111A LEU* 3.7 35.9 - - + -
116A TYR* 5.7 2.2 - - + -
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Residues in contact with LYS 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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74A ASP* 3.3 4.9 + - - +
75A THR* 1.3 82.5 + - - +
77A SER* 1.3 63.1 + - - +
79A TRP* 3.4 0.7 + - - -
80A LYS* 3.1 51.4 + - + +
86A PRO* 3.3 42.7 + - + +
87A PHE 4.2 4.9 + - - -
88A HIS 3.6 13.2 + - - +
89A GLU* 3.2 48.8 + - - +
96B THR* 5.2 4.1 + - - -
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Residues in contact with SER 77 (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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29A ALA* 6.2 1.1 - - - -
74A ASP* 2.8 34.9 + - - -
76A LYS* 1.3 77.6 - - - +
78A TYR* 1.3 64.7 + - - +
80A LYS* 3.3 9.1 + - - +
81A ALA* 3.1 23.6 + - - +
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Residues in contact with TYR 78 (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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18A ASP* 2.7 33.1 + - + -
21A ARG* 3.4 17.4 + - - -
25A ALA* 3.5 28.8 - - + -
26A ILE 3.8 17.3 - - - -
27A ASN 5.4 1.3 - - - -
28A VAL* 3.5 25.4 - - + -
74A ASP 3.5 8.8 + - - +
75A THR* 3.3 11.7 - - - +
76A LYS 3.2 0.2 - - - -
77A SER* 1.3 82.8 - - - +
79A TRP* 1.3 87.4 + + - +
81A ALA* 3.3 12.5 + - + +
82A LEU* 3.4 32.2 + - + +
111A LEU* 4.2 10.5 - - + -
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Residues in contact with TRP 79 (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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18A ASP* 3.5 28.7 - - - -
20A VAL* 3.6 24.2 - - + -
75A THR* 3.2 31.2 + - - +
76A LYS 4.1 0.2 - - - +
78A TYR* 1.3 87.7 - + - +
80A LYS* 1.3 65.0 + - - +
82A LEU* 3.0 19.3 + - + +
84A ILE* 2.9 61.4 + - + +
86A PRO* 3.7 28.5 - - + -
111A LEU* 3.3 40.5 - - + +
112A SER 3.4 27.9 + - - -
113A PRO* 4.0 8.1 - - + -
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Residues in contact with LYS 80 (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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76A LYS* 3.1 52.9 + - + +
77A SER* 3.5 8.5 - - - +
79A TRP* 1.3 75.3 - - - +
81A ALA* 1.3 55.5 + - - +
83A GLY* 2.7 25.9 + - - -
84A ILE 3.6 8.9 + - - +
85A SER* 3.5 17.4 + - - +
86A PRO* 3.2 27.2 + - + +
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Residues in contact with ALA 81 (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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77A SER 3.1 8.9 + - - +
78A TYR* 3.5 11.4 - - - +
79A TRP 3.2 0.2 - - - -
80A LYS* 1.3 78.9 - - - +
82A LEU* 1.3 65.9 + - + +
83A GLY 3.1 2.6 + - - -
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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