Contacts of the helix formed by residues 104 - 112 (chain A) in PDB entry 3BNF
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 TYR 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A THR 3.9 0.2 - - - -
68A LYS* 2.4 38.8 + - - +
70A SER 3.3 25.8 - - - -
71A ASP* 3.3 13.2 - - + +
100A ARG* 3.4 38.8 - - - +
101A GLY 2.8 12.6 + - - +
103A TYR* 1.3 91.4 - + + +
105A ALA* 1.3 63.0 + - - -
106A LEU 3.3 2.7 - - - -
107A GLN* 3.2 3.9 + - - -
108A ASP* 2.8 25.8 + - - +
494A GLY 3.5 19.7 - - - -
495A VAL* 3.7 20.2 - - + +
507A LYS* 2.7 27.0 + - + -
510A HEM 3.1 7.1 - - - +
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Residues in contact with ALA 105 (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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101A GLY 3.7 0.4 + - - -
102A HIS 3.1 4.8 + - - +
104A TYR* 1.3 76.3 - - - +
106A LEU* 1.3 63.7 + - - +
108A ASP* 3.8 1.2 - - - +
109A ASN 3.1 18.7 + - - -
134A LYS* 3.5 15.8 - - + +
165A THR* 3.5 3.8 + - - +
166A ILE* 3.6 35.0 - - + -
510A HEM 3.0 40.1 + - + -
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Residues in contact with LEU 106 (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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104A TYR 3.3 0.2 - - - -
105A ALA* 1.3 73.3 - - - +
107A GLN* 1.3 67.8 + - - +
109A ASN* 3.2 6.9 + - - +
110A ILE* 3.0 47.4 + - + +
131A TRP* 3.5 31.4 - - + -
134A LYS* 4.0 11.6 + - + +
135A SER* 4.1 8.7 - - - -
162A ILE* 3.6 24.5 - - + +
163A VAL* 4.2 16.4 - - + +
164A ASN 3.9 9.0 - - - +
165A THR* 3.1 28.4 + - - +
478A LYS* 5.1 4.0 - - - +
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Residues in contact with GLN 107 (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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104A TYR* 3.2 5.7 + - - +
106A LEU* 1.3 81.1 - - - +
108A ASP* 1.3 60.1 + - - +
110A ILE* 3.1 9.4 + - - +
111A ASN* 2.8 57.8 + - - +
470A LYS* 3.6 1.2 - - - +
474A GLU* 2.9 24.2 + - - -
478A LYS* 3.0 27.3 + - - -
492A LEU* 5.0 0.5 - - - +
495A VAL* 3.4 48.7 - - + +
496A ASP* 3.6 21.9 + - + +
507A LYS* 5.0 0.2 - - - +
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Residues in contact with ASP 108 (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 ILE* 4.4 7.9 - - - +
100A ARG* 2.9 43.0 + - - +
104A TYR* 2.8 19.2 + - - +
105A ALA 3.8 2.2 - - - +
107A GLN* 1.3 74.6 - - - +
109A ASN* 1.3 53.4 + - - +
111A ASN* 3.8 9.2 + - - +
112A THR* 2.8 37.6 + - - -
498A LYS 4.7 0.5 - - - +
499A SER* 5.9 0.2 - - - -
508A HEM 3.5 17.3 - - + +
510A HEM 2.4 35.6 - - - +
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Residues in contact with ASN 109 (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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105A ALA 3.1 13.7 + - - +
106A LEU* 3.2 12.6 - - - +
108A ASP* 1.3 75.4 - - - +
110A ILE* 1.3 56.5 + - - +
112A THR* 3.5 3.1 - - - +
115A THR* 2.9 32.7 + - - +
130A CYS 3.0 24.4 + - - +
131A TRP* 3.4 18.2 - - - -
134A LYS* 3.7 12.8 - - + +
155A TRP* 2.8 26.5 + - - +
508A HEM 3.4 39.7 - - - +
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Residues in contact with ILE 110 (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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106A LEU* 3.0 37.0 + - + +
107A GLN* 3.5 12.6 - - - +
109A ASN* 1.3 75.5 - - - +
111A ASN* 1.3 56.8 + - - +
115A THR* 3.4 0.9 + - - -
131A TRP* 4.5 12.1 - - + -
155A TRP* 3.7 18.6 - - + -
159A GLY 6.0 0.2 - - - +
162A ILE 5.4 0.4 - - - +
163A VAL* 6.5 0.7 - - + -
466A LYS* 2.8 32.2 + - - -
469A PHE* 3.8 21.3 - - + -
470A LYS* 4.8 0.4 - - - +
474A GLU* 3.6 29.4 - - + +
477A TRP* 4.8 11.0 - - + -
478A LYS* 3.6 21.8 - - - +
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Residues in contact with ASN 111 (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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107A GLN* 2.8 38.3 + - - +
108A ASP* 3.8 9.1 + - - +
110A ILE* 1.3 71.3 - - - +
112A THR* 1.3 70.9 + - - +
466A LYS* 3.2 3.7 - - - +
470A LYS* 2.9 25.2 + - - -
496A ASP* 2.9 19.6 + - - -
498A LYS 3.5 18.2 + - - -
499A SER* 4.1 9.1 - - - -
501A TYR* 2.6 33.7 + - - +
502A TYR* 3.1 13.5 + - - -
507A LYS* 4.4 1.4 - - - +
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Residues in contact with THR 112 (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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95A ASP* 3.5 17.4 - - - +
97A ASN* 5.6 1.8 - - - -
108A ASP 2.8 14.7 + - - +
109A ASN* 3.5 14.1 - - - +
111A ASN* 1.3 72.5 - - - +
113A LEU* 1.3 65.5 + - - +
114A ARG* 2.9 37.2 + - + +
115A THR* 3.1 17.6 + - + +
466A LYS* 3.0 18.5 + - - -
508A HEM 3.4 37.0 + - + -
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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