Contacts of the helix formed by residues 62 - 74 (chain A) in PDB entry 4BPU
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 ASN 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A TYR* 4.0 13.0 - - + +
40A PHE* 3.8 16.1 - - - -
41A GLN* 4.9 0.4 - - - +
60A PHE* 3.4 1.1 - - - +
61A ASN* 1.3 88.3 - - - +
63A GLN* 1.3 64.5 + - - +
64A SER* 3.5 26.3 - - - +
65A ASP* 3.0 22.2 + - - +
66A LEU* 3.1 11.8 + - - +
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Residues in contact with GLN 63 (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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23A TYR* 3.7 12.5 - - + +
24A SER* 3.5 35.6 + - - +
27A TYR* 3.6 42.8 - - + +
62A ASN* 1.3 77.4 - - - +
64A SER* 1.3 58.3 + - - +
66A LEU* 3.2 10.8 + - + +
67A GLU* 2.9 58.9 + - + +
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Residues in contact with SER 64 (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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62A ASN* 3.2 18.5 - - - +
63A GLN* 1.3 79.3 - - - +
65A ASP* 1.3 58.4 + - - +
67A GLU* 3.1 11.8 + - - +
68A LYS* 2.8 31.1 + - - +
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Residues in contact with ASP 65 (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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59A SER 4.6 1.2 - - - +
60A PHE* 3.6 14.2 - - + -
61A ASN* 3.1 42.1 + - + +
62A ASN* 3.0 19.7 + - - +
64A SER* 1.3 77.9 - - - +
66A LEU* 1.3 56.0 - - - +
68A LYS* 3.5 15.6 + - - +
69A GLU* 2.9 40.8 + - - +
89A ASN* 5.7 0.7 + - - -
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Residues in contact with LEU 66 (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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23A TYR* 4.2 16.6 - - + +
26A TYR* 3.8 29.4 - - + -
27A TYR* 5.6 2.5 - - + -
40A PHE* 4.3 16.4 - - + -
45A PHE* 4.7 12.1 - - + -
47A PHE* 5.2 0.7 - - + -
60A PHE* 3.5 38.5 - - + +
62A ASN 3.1 10.9 + - - +
63A GLN* 3.4 12.3 - - + +
64A SER 3.1 0.2 - - - -
65A ASP* 1.3 75.0 - - - +
67A GLU* 1.3 67.1 + - - +
69A GLU 3.3 0.2 + - - -
70A MET* 2.8 55.6 + - + +
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Residues in contact with GLU 67 (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* 5.3 3.2 + - - +
23A TYR* 3.5 41.8 - - + +
63A GLN* 2.9 47.9 + - - +
64A SER* 3.5 10.7 - - - +
66A LEU* 1.3 75.1 - - - +
68A LYS* 1.3 57.3 + - - +
70A MET* 4.0 0.5 - - - +
71A GLN* 2.9 51.6 + - - +
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Residues in contact with LYS 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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64A SER* 2.8 16.8 + - - +
65A ASP* 3.5 19.0 + - - +
67A GLU* 1.3 79.1 - - - +
69A GLU* 1.3 78.9 + - - +
71A GLN* 3.1 7.8 + - - +
72A ALA* 2.8 35.4 + - + +
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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
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47A PHE* 4.7 5.8 - - + -
58A GLN* 5.4 6.0 + - - +
60A PHE* 3.5 29.6 - - + -
65A ASP* 2.9 32.8 + - - +
68A LYS* 1.3 97.1 + - + +
70A MET* 1.3 57.9 + - - +
72A ALA* 3.7 8.2 - - - +
73A ALA* 2.8 35.3 + - - +
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Residues in contact with MET 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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17A TYR* 3.6 18.1 - - + -
21A PHE* 3.9 17.7 - - + -
23A TYR* 3.5 38.4 - - + +
26A TYR* 5.4 2.5 - - - -
45A PHE* 6.3 0.4 - - - -
47A PHE* 3.7 26.5 - - + -
66A LEU* 2.8 39.1 + - + +
69A GLU* 1.3 75.7 - - - +
71A GLN* 1.3 58.2 + - - +
74A ASN* 2.7 35.9 + - - +
75A PRO* 3.6 7.8 - - + +
78A ILE* 3.6 28.9 - - + -
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Residues in contact with GLN 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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14A LYS 5.6 0.7 - - - +
17A TYR* 3.3 32.9 + - + +
18A ARG* 2.9 52.9 + - + +
23A TYR* 3.9 5.3 + - - +
67A GLU* 2.9 45.2 + - - +
68A LYS* 3.7 5.2 - - - +
70A MET* 1.3 75.3 - - - +
72A ALA* 1.3 59.4 + - - +
74A ASN* 2.9 29.7 + - - +
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Residues in contact with ALA 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 LYS* 2.8 23.6 + - + +
69A GLU* 3.7 15.3 - - - +
71A GLN* 1.3 80.4 - - - +
73A ALA* 1.3 61.0 + - - +
74A ASN* 4.4 4.2 + - - -
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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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47A PHE* 4.5 13.2 - - + -
49A LEU* 3.8 29.9 - - + +
55A ILE* 6.3 0.7 - - + -
69A GLU* 2.8 21.1 + - - +
70A MET 4.1 0.7 - - - +
72A ALA* 1.3 77.1 - - - +
74A ASN* 1.3 73.4 + - - +
75A PRO* 3.6 6.2 - - + -
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Residues in contact with ASN 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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10A PRO 5.4 1.6 - - - +
13A LEU* 3.9 14.9 - - + +
14A LYS* 3.4 44.6 - - + +
17A TYR* 3.7 19.8 - - + +
49A LEU* 4.6 1.4 - - - +
50A LYS 5.6 0.3 + - - -
70A MET 2.7 17.3 + - - +
71A GLN* 2.9 28.2 + - - +
72A ALA 4.4 4.6 + - - -
73A ALA* 1.3 75.7 - - - +
75A PRO* 1.3 69.2 - - - +
76A TYR* 3.9 8.0 + - - -
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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