Contacts of the helix formed by residues 73 - 86 (chain A) in PDB entry 1B0K
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 ASP 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLN* 1.3 72.1 - - - +
74A ALA* 1.4 58.9 + - - +
75A THR 3.4 0.4 + - - -
76A ALA* 4.0 4.6 + - - -
77A GLN* 3.1 30.1 + - - +
97A ILE* 4.9 1.1 - - + -
98A HIS 2.9 10.3 + - - +
99A CYS* 3.4 26.7 - - - -
100A ASP 3.4 1.3 + - - -
101A HIS* 3.0 32.3 + - - +
102A LEU* 3.7 19.1 + - + +
124A TYR* 3.5 21.5 + - - -
127A LEU* 3.6 26.0 - - + -
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Residues in contact with ALA 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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72A GLN* 2.9 14.3 + - - +
73A ASP* 1.4 82.6 + - - +
75A THR* 1.4 57.1 + - - +
77A GLN* 4.6 4.6 + - - +
101A HIS* 3.7 21.8 - - + -
102A LEU* 5.0 5.4 - - + -
577A LEU* 4.2 13.2 - - + -
580A ARG* 3.3 47.0 + - + +
646A HIS* 4.4 2.1 - - - -
756A FLC 3.8 4.5 - - - +
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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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72A GLN* 3.2 12.1 + - - +
74A ALA* 1.4 76.5 - - - +
76A ALA* 1.3 65.7 + - - +
77A GLN 3.3 2.9 + - - -
78A MET* 3.8 5.5 + - - +
79A ALA* 3.2 20.1 + - - +
164A THR* 2.8 47.9 + - - +
183A GLY* 5.2 3.2 - - - -
580A ARG* 4.0 5.4 - - - +
643A SER* 5.5 2.0 - - - +
644A ARG* 4.4 15.3 - - + +
645A GLU* 4.7 6.2 - - + +
646A HIS* 4.9 7.8 - - + -
756A FLC 3.8 23.3 - - - +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 3.8 25.1 - - + -
72A GLN 3.0 21.5 + - - +
73A ASP* 4.1 4.5 - - - -
74A ALA 3.7 0.4 - - - -
75A THR* 1.3 77.9 + - - +
77A GLN* 1.3 66.0 + - - +
79A ALA* 3.7 5.1 - - - +
80A MET* 3.0 28.9 + - - +
97A ILE* 4.3 9.6 - - + -
127A LEU* 3.9 17.7 - - + -
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Residues in contact with GLN 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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73A ASP 3.1 22.6 + - - +
74A ALA* 4.6 1.3 - - - +
75A THR 3.3 1.0 - - - -
76A ALA* 1.3 77.6 - - - +
78A MET* 1.3 57.7 + - - +
80A MET* 3.5 2.9 + - - +
81A LEU* 2.9 33.7 + - - +
102A LEU* 4.0 10.7 - - - +
123A VAL* 3.6 33.0 - - - +
126A PHE* 4.0 17.4 - - + -
127A LEU* 4.2 17.5 - - + -
537A ARG 4.2 1.0 - - - +
538A LEU* 3.6 19.4 - - + +
577A LEU 5.0 2.8 + - - -
580A ARG* 3.8 24.1 + - + +
581A GLY* 3.6 18.6 + - - -
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Residues in contact with MET 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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75A THR 3.8 2.8 + - - +
76A ALA 3.3 0.2 - - - -
77A GLN* 1.3 78.6 - - - +
79A ALA* 1.4 64.2 + - - +
81A LEU* 4.2 10.1 - - + -
82A GLN* 3.2 26.1 + - - +
541A LEU* 4.1 26.9 - - + -
580A ARG 3.6 16.9 + - - +
581A GLY* 4.3 16.8 - - - -
582A HIS 5.0 0.4 - - - -
583A LEU* 4.5 16.8 - - + +
645A GLU* 3.6 15.7 - - - +
646A HIS* 3.7 33.4 - - + +
649A LEU* 3.7 25.6 - - + -
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Residues in contact with ALA 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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71A MET* 3.9 25.1 - - - -
75A THR 3.2 19.1 + - - +
76A ALA 3.4 1.1 + - - +
78A MET* 1.4 73.8 - - - +
80A MET* 1.3 57.8 + - - +
82A GLN* 3.4 3.9 + - - +
83A PHE* 3.0 22.6 + - - +
164A THR* 4.8 3.6 - - + -
183A GLY* 3.9 30.7 - - - +
186A ALA* 5.0 2.2 - - + -
187A VAL* 3.5 13.9 - - + +
190A MET* 5.0 1.8 - - + -
645A GLU* 4.0 1.6 + - - -
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 4.6 14.4 - - - -
76A ALA 3.0 20.5 + - - +
77A GLN 3.8 2.7 - - - +
79A ALA* 1.3 73.8 - - - +
81A LEU* 1.3 60.5 + - - +
83A PHE* 3.4 12.5 - - + +
84A ILE* 2.8 34.5 + - + +
91A VAL* 5.5 0.4 - - + -
97A ILE* 4.4 19.1 - - + -
126A PHE* 4.4 13.9 - - + -
127A LEU* 4.6 5.4 - - + -
130A ALA* 4.1 19.1 - - + +
131A GLY 5.1 0.4 - - - +
134A TYR* 3.6 38.1 - - + -
136A VAL* 5.0 7.2 - - + -
190A MET* 4.3 20.9 - - - +
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Residues in contact with LEU 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 GLN 2.9 30.9 + - - +
78A MET* 3.5 21.5 + - + +
79A ALA 3.5 0.2 - - - -
80A MET* 1.3 71.6 - - - +
82A GLN* 1.3 60.0 + - - +
84A ILE* 3.6 9.1 + - + +
85A SER* 3.1 23.4 + - - -
126A PHE* 4.2 19.0 - - + -
531A VAL* 5.0 2.7 - - + -
538A LEU* 5.1 4.7 - - + -
539A GLN 3.6 29.4 - - - +
540A LEU* 3.8 28.9 - - + -
541A LEU* 4.5 11.3 + - + +
581A GLY* 3.7 21.1 - - - +
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Residues in contact with GLN 82 (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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78A MET* 3.2 18.5 + - + +
79A ALA 3.6 7.4 - - - +
81A LEU* 1.3 74.7 - - - +
83A PHE* 1.3 63.1 + - - +
85A SER* 3.2 15.0 + - - -
86A SER* 3.3 9.4 + - - -
183A GLY 4.1 2.0 - - - -
184A ALA* 3.9 18.1 - - - +
187A VAL* 4.2 10.2 - - + +
541A LEU* 3.8 20.4 - - + -
645A GLU* 2.8 40.8 + - - -
649A LEU* 4.8 5.7 - - - +
675A GLN* 3.7 20.6 + - - +
745A LEU* 3.7 33.3 - - + +
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Residues in contact with PHE 83 (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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79A ALA 3.0 15.1 + - - +
80A MET* 3.1 21.3 + - + +
82A GLN* 1.3 73.5 - - - +
84A ILE* 1.3 64.5 + - - +
86A SER* 2.6 33.4 + - - -
87A GLY 3.8 1.6 + - - -
88A LEU* 3.6 30.4 + - + +
90A LYS 3.8 17.7 - - - -
91A VAL* 4.3 7.2 - - + -
134A TYR* 3.5 44.4 - + + -
187A VAL* 4.2 13.0 - - + +
190A MET* 3.8 46.4 - - + -
191A ALA* 4.2 6.1 - - + -
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Residues in contact with ILE 84 (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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80A MET* 2.8 21.8 + - + +
81A LEU* 3.6 13.2 - - + +
83A PHE* 1.3 75.8 - - - +
85A SER* 1.3 62.4 + - - +
86A SER 3.2 0.9 + - - -
87A GLY* 3.4 10.9 + - - -
126A PHE* 4.2 28.5 - - + -
130A ALA* 5.3 2.2 - - + -
134A TYR* 3.6 35.2 - - + +
529A VAL* 4.7 16.8 - - + -
531A VAL* 5.7 0.4 - - + -
540A LEU* 4.9 17.5 - - + -
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Residues in contact with SER 85 (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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81A LEU 3.1 13.4 + - - -
82A GLN* 3.2 12.7 + - - -
84A ILE* 1.3 78.5 - - - +
86A SER* 1.3 61.2 + - - +
87A GLY* 3.3 0.9 + - - -
541A LEU* 4.4 20.7 + - - +
745A LEU* 4.6 12.1 - - - -
749A LYS* 3.4 19.9 + - - +
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Residues in contact with SER 86 (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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82A GLN 3.3 9.3 + - - -
83A PHE* 2.6 29.9 + - - -
85A SER* 1.3 76.5 - - - +
87A GLY* 1.3 58.0 + - - +
88A LEU* 3.3 22.3 + - - +
187A VAL* 5.1 2.9 - - - -
191A ALA* 5.9 0.2 - - - -
745A LEU* 4.1 17.5 - - - +
748A MET* 4.2 16.8 - - - -
749A LYS* 2.7 25.1 + - - -
752A GLN* 2.9 17.5 + - - +
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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