Contacts of the helix formed by residues 67 - 85 (chain A) in PDB entry 4BN2
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 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 4.1 2.0 - - - +
65A ASP 4.2 8.3 - - - +
66A THR* 1.3 73.5 - - - +
68A GLN* 1.3 66.1 + - - +
69A GLU* 3.6 11.0 + - - +
70A SER* 3.0 34.6 + - - -
71A VAL* 3.1 15.2 + - - +
69B GLU* 5.9 0.7 - - - -
73B ALA* 4.8 18.8 - - + -
77B LYS* 6.6 0.7 - - - -
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Residues in contact with GLN 68 (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 ARG* 2.9 30.9 + - - +
67A THR* 1.3 72.1 - - - +
69A GLU* 1.3 64.8 + - - +
71A VAL* 3.0 16.0 + - - +
72A PHE* 3.1 12.6 + - - +
103A PHE* 2.9 42.9 + - + +
104A THR* 4.6 1.6 - - - +
107A GLY* 4.2 0.2 - - - -
117A ASN 3.8 6.8 + - - +
118A LEU* 2.7 45.9 + - + +
119A ARG 3.3 16.2 - - - +
120A GLY* 3.7 11.0 - - - -
121A VAL* 5.7 1.0 + - - +
124A ARG* 3.5 10.5 + - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 3.2 8.6 + - - +
68A GLN* 1.3 80.3 - - - +
70A SER* 1.3 64.7 + - - +
72A PHE* 3.2 6.1 + - + +
73A ALA* 3.1 26.7 + - + +
124A ARG* 3.2 27.6 - - - +
67B THR* 2.5 36.1 + - + +
69B GLU* 3.3 22.5 - - - +
70B SER* 3.0 36.8 + - - -
73B ALA* 5.3 2.9 - - - +
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Residues in contact with SER 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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60A HIS* 5.9 1.7 - - - -
66A THR* 3.5 19.7 - - - +
67A THR* 3.0 25.9 + - - -
69A GLU* 1.3 77.7 - - - +
71A VAL* 1.3 64.6 + - - +
73A ALA* 3.2 7.6 + - - +
74A THR* 2.9 32.3 + - - -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.5 37.7 - - + +
62A ALA* 5.7 1.8 - - + -
66A THR* 4.1 10.8 - - + -
67A THR 3.4 13.7 - - - +
68A GLN* 3.0 9.8 + - - +
70A SER* 1.3 78.0 - - - +
72A PHE* 1.3 64.5 + - - +
74A THR* 3.2 4.6 + - - -
75A VAL* 2.9 29.9 + - + +
104A THR* 4.5 7.0 - - + +
121A VAL* 3.8 23.6 - - + -
323A ILE* 4.4 16.2 - - + -
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Residues in contact with PHE 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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68A GLN 3.1 3.4 + - - -
69A GLU* 3.2 10.5 + - + +
71A VAL* 1.3 80.9 - - - +
73A ALA* 1.3 68.1 + - + +
76A ALA* 2.9 45.0 + - + +
77A LYS* 3.2 18.8 + - + -
80A VAL* 4.4 3.8 - - + -
121A VAL* 3.7 13.4 - - + +
124A ARG* 3.4 49.1 - - + +
125A SER* 3.2 34.1 - - - -
128A TYR* 3.6 35.9 - + + -
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Residues in contact with ALA 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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69A GLU* 3.1 18.2 + - + +
70A SER* 3.6 8.7 - - - +
72A PHE* 1.3 79.5 - - + +
74A THR* 1.3 62.9 + - - +
77A LYS* 3.8 35.0 + - + +
78A SER 5.1 0.5 + - - -
67B THR* 6.5 0.9 - - + -
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Residues in contact with THR 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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16A PHE* 3.7 37.5 - - + -
60A HIS* 3.7 34.4 + - + +
70A SER* 2.9 22.8 + - - -
71A VAL* 3.7 5.2 - - - -
73A ALA* 1.3 79.6 - - - +
75A VAL* 1.3 63.0 + - + +
78A SER* 5.7 3.0 - - - -
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Residues in contact with VAL 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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16A PHE* 3.6 46.9 - - + -
71A VAL* 2.9 21.9 + - + +
72A PHE 3.1 0.4 + - - -
74A THR* 1.3 85.8 - - + +
76A ALA* 1.3 63.5 + - + +
77A LYS 3.7 0.2 - - - -
78A SER* 4.5 6.1 + - - -
79A ILE* 3.8 16.8 + - - +
91A ILE* 4.2 11.0 - - + -
121A VAL* 5.7 1.6 - - + -
321A ALA* 4.1 14.3 - - + +
323A ILE* 4.0 32.3 - - + -
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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
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72A PHE* 2.9 42.6 + - + +
75A VAL* 1.3 73.5 - - + +
77A LYS* 1.3 66.5 + - - +
78A SER 3.1 2.9 - - - -
79A ILE* 3.0 4.2 + - - +
80A VAL* 2.9 25.8 + - + +
91A ILE* 3.6 26.9 - - + -
121A VAL* 4.1 7.2 - - + -
125A SER* 4.0 5.2 - - - +
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Residues in contact with LYS 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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72A PHE* 3.2 21.3 + - + +
73A ALA* 3.8 32.5 + - + +
75A VAL 3.7 0.6 - - - -
76A ALA* 1.3 76.2 - - - +
78A SER* 1.3 65.2 + - - +
80A VAL* 3.3 3.3 + - - +
81A GLU* 3.1 44.8 + - - +
128A TYR* 3.4 35.0 + - + +
65B ASP* 4.2 32.0 + - - +
67B THR* 6.5 0.9 - - + -
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Residues in contact with SER 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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14A LYS* 4.0 21.9 + - - -
73A ALA 5.1 1.2 + - - -
74A THR 5.7 2.7 - - - -
75A VAL 4.5 9.4 - - - -
77A LYS* 1.3 79.8 - - - +
79A ILE* 1.3 65.6 + - - +
81A GLU* 3.0 17.0 + - - +
82A SER* 2.9 24.1 + - - -
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Residues in contact with ILE 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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14A LYS* 5.4 9.9 - - - +
75A VAL 3.8 16.4 - - - +
76A ALA 3.0 8.6 + - - +
78A SER* 1.3 78.4 - - - +
80A VAL* 1.3 58.6 + - + +
82A SER* 3.3 6.2 + - - +
83A CYS* 2.8 27.2 + - - -
89A GLY* 4.2 11.7 - - - -
90A THR 4.3 3.4 - - - +
91A ILE* 4.2 21.8 - - + -
247A LEU* 3.6 27.4 - - + -
319A LYS* 3.5 34.5 - - + +
320A THR 4.6 1.1 - - - +
321A ALA* 4.4 15.0 - - + +
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Residues in contact with VAL 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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72A PHE* 4.4 2.7 - - + -
76A ALA* 2.9 20.6 + - + +
77A LYS 3.6 5.8 - - - +
79A ILE* 1.3 76.1 - - + +
81A GLU* 1.3 66.2 + - - +
83A CYS* 2.8 24.8 + - + +
84A MET* 3.0 7.4 + - - +
91A ILE* 6.1 0.7 - - + -
125A SER* 4.4 25.8 - - - +
128A TYR* 3.9 25.1 - - + -
129A LEU* 3.9 34.5 - - + -
132A LEU* 3.9 8.7 - - + -
247A LEU* 5.0 10.5 - - + -
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Residues in contact with GLU 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 LYS* 3.1 37.6 + - - +
78A SER* 3.0 13.5 + - - +
80A VAL* 1.3 79.5 - - - +
82A SER* 1.3 62.6 + - - +
84A MET* 3.0 16.5 + - - +
85A SER* 3.2 11.7 + - - -
128A TYR* 2.9 29.8 + - + +
132A LEU* 4.4 13.2 - - + -
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Residues in contact with SER 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 SER* 2.9 14.4 + - - -
79A ILE* 3.3 14.7 + - - +
81A GLU* 1.3 76.3 - - - +
83A CYS* 1.3 61.2 + - - +
85A SER* 3.1 18.6 + - - -
87A TYR* 3.1 29.8 + - - +
88A ASN 5.1 0.9 + - - -
89A GLY* 5.8 0.2 - - - -
319A LYS* 3.3 37.4 - - - +
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Residues in contact with CYS 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 ILE 2.8 19.1 + - - -
80A VAL* 2.8 16.5 + - + +
82A SER* 1.3 79.8 + - - +
84A MET* 1.3 55.1 + - + +
86A GLY* 2.9 17.0 + - - -
87A TYR 3.5 9.9 - - - -
88A ASN 4.7 0.2 - - - -
89A GLY* 4.2 9.6 - - - -
230A ILE* 4.1 17.3 - - + +
245A SER* 3.4 31.4 - - - +
247A LEU* 3.6 39.0 - - + -
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Residues in contact with MET 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 VAL 3.0 11.7 + - - +
81A GLU* 3.0 9.2 + - - +
83A CYS* 1.3 74.8 - - - +
85A SER* 1.3 58.5 + - - +
86A GLY* 3.2 1.4 + - - -
129A LEU* 3.8 24.7 - - + -
132A LEU* 3.7 34.5 - - + +
133A ILE* 3.9 27.4 - - + +
136A GLU* 4.7 7.9 - - + +
146A PHE* 3.6 37.5 - - + -
230A ILE* 4.7 7.2 - - - -
232A SER* 5.1 4.2 + - - -
243A ARG* 4.3 9.5 + - - +
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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 GLU 3.2 3.2 + - - -
82A SER* 3.1 25.3 + - - -
83A CYS 3.1 0.4 - - - -
84A MET* 1.3 78.4 - - - +
86A GLY* 1.3 57.1 + - - +
87A TYR* 3.6 12.8 - - - -
243A ARG* 3.4 26.7 + - - +
355A VAL* 3.5 20.7 - - - +
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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