Contacts of the helix formed by residues 70 - 83 (chain A) in PDB entry 1B4C
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 PHE 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LEU* 5.5 11.2 - - + -
11A ILE* 5.8 3.4 - - + -
14A PHE* 3.3 63.9 - + + -
25A HIS 5.0 4.3 + - - +
69A ASP* 1.3 74.7 - - - +
71A GLN* 1.3 69.1 + - + +
73A PHE* 2.9 23.6 + + - +
74A MET* 2.9 38.9 + - + -
81B THR* 6.4 1.6 - - + -
82B THR* 4.1 22.9 - - + -
87B PHE* 4.3 28.7 - + + -
88B PHE* 5.7 0.9 - - + -
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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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69A ASP* 3.3 13.9 - - + +
70A PHE* 1.3 82.8 - - + +
72A GLU* 1.3 62.9 + - + +
74A MET* 3.4 6.4 + - - +
75A ALA* 3.3 21.3 + - - +
78B SER* 5.5 6.9 + - - +
79B MET* 5.4 8.1 - - - +
82B THR* 4.1 32.2 + - + +
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Residues in contact with GLU 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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32A LEU* 5.2 0.4 - - - -
63A ASP* 4.0 5.7 - - - +
65A ASP* 4.9 7.9 - - - +
67A GLU 3.8 5.8 - - - +
68A CYS* 3.5 25.6 - - + -
69A ASP* 3.2 37.0 + - + +
70A PHE 3.1 0.6 - - - -
71A GLN* 1.3 79.9 - - + +
73A PHE* 1.3 57.9 + - - +
75A ALA* 3.8 5.0 - - - +
76A PHE* 2.9 53.3 + - + -
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Residues in contact with PHE 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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10A LEU* 6.6 0.2 - - + -
14A PHE* 4.3 29.2 - + + -
27A LEU* 5.1 3.8 - - + -
32A LEU* 3.8 42.3 - - + +
35A LEU* 4.9 20.6 - - + -
36A ILE* 5.6 3.6 - - + -
39A GLU* 5.4 13.2 - - + -
40A LEU* 6.0 1.8 - - + -
69A ASP 3.4 9.4 + - - +
70A PHE* 2.9 25.8 + + - +
72A GLU* 1.3 78.8 - - - +
74A MET* 1.3 71.9 + - + +
76A PHE* 4.6 2.2 - - + +
77A VAL* 2.8 57.7 + - + +
3B LEU* 5.4 9.0 - - + -
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Residues in contact with MET 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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7A MET* 5.7 4.7 - - - -
10A LEU* 3.9 29.8 - - + -
70A PHE* 2.9 39.5 + - + +
71A GLN* 4.0 5.2 - - - +
72A GLU 3.4 0.2 - - - -
73A PHE* 1.3 83.4 - - + +
75A ALA* 1.3 61.6 + - - +
77A VAL* 3.9 21.0 - - + +
78A SER* 3.2 21.4 + - - -
7B MET* 5.4 5.8 - - + -
10B LEU* 5.8 0.7 - - + -
74B MET* 4.4 30.9 - - + +
78B SER* 3.8 29.8 - - - -
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Residues in contact with ALA 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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71A GLN 3.3 15.8 + - - +
72A GLU* 3.8 7.0 - - - +
73A PHE 3.1 0.6 - - - -
74A MET* 1.3 74.8 - - - +
76A PHE* 1.3 68.7 + - + +
77A VAL 3.0 1.1 - - - -
78A SER* 2.8 27.8 + - - -
79A MET* 3.0 22.6 + - + +
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Residues in contact with PHE 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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32A LEU* 4.9 9.2 - - + -
36A ILE* 5.7 4.0 - - + -
56A VAL* 4.4 11.4 - - + -
59A THR* 3.6 34.8 - - + -
60A LEU* 3.2 48.9 - - + -
63A ASP* 6.5 0.4 - - - -
68A CYS* 5.2 5.2 - - - -
72A GLU* 2.9 47.4 + - + +
73A PHE* 4.3 3.4 - - - +
75A ALA* 1.3 79.1 - - + +
77A VAL* 1.3 64.4 + - + +
79A MET* 4.0 23.6 - - + +
80A VAL* 3.2 29.8 + - + +
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Residues in contact with VAL 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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32A LEU* 6.1 0.2 - - + -
36A ILE* 6.4 0.7 - - + -
40A LEU* 5.0 18.1 - - + +
73A PHE* 2.8 66.9 + - + +
74A MET* 3.9 18.4 - - + +
76A PHE* 1.3 79.7 - - + +
78A SER* 1.3 57.4 + - - +
80A VAL* 4.0 4.3 - - - +
81A THR* 2.5 35.6 + - - +
7B MET* 4.0 27.1 - - + -
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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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74A MET* 3.2 12.3 + - - -
75A ALA* 2.8 16.2 + - - -
77A VAL* 1.3 77.7 - - - +
79A MET* 1.3 72.7 + - - +
81A THR* 2.9 5.8 + - - -
82A THR* 2.5 47.3 + - - +
7B MET* 5.9 1.3 - - - -
71B GLN* 5.4 7.8 + - - +
74B MET* 3.9 29.2 - - - -
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Residues in contact with MET 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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52A VAL* 4.4 7.4 - - + +
56A VAL* 4.6 16.4 - - + -
75A ALA* 3.0 31.3 + - + +
76A PHE* 4.0 26.7 - - + +
78A SER* 1.3 86.5 + - - +
80A VAL* 1.3 54.0 + - - +
82A THR* 3.2 8.1 - - - -
83A ALA* 2.4 40.2 + - - +
71B GLN* 5.4 7.9 - - - +
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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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36A ILE* 5.5 10.5 - - + -
40A LEU* 3.8 32.1 - - + +
43A PHE* 6.1 1.0 - - + +
47A ILE* 4.6 23.0 - - + +
53A VAL* 5.0 13.0 - - + -
56A VAL* 3.8 33.2 - - + +
57A MET* 6.5 0.7 - - + -
76A PHE* 3.2 18.3 + - + +
77A VAL* 4.0 4.3 - - - +
78A SER 3.2 0.4 - - - -
79A MET* 1.3 76.3 - - - +
81A THR* 1.3 64.5 + - - +
83A ALA* 3.2 19.4 - - - +
84A CYS* 4.1 1.7 + - - +
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Residues in contact with THR 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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40A LEU* 4.4 11.5 - - - +
43A PHE* 5.7 12.8 - - + -
77A VAL* 2.5 25.1 + - - +
78A SER* 2.9 6.1 + - - -
80A VAL* 1.3 79.7 - - - +
82A THR* 1.3 65.0 + - + +
83A ALA 3.3 0.7 + - - -
84A CYS* 3.5 15.9 + - - +
87A PHE* 4.4 14.7 - - + +
7B MET* 3.5 35.0 - - + +
11B ILE* 5.5 13.0 - - + -
70B PHE* 6.3 2.2 - - + -
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Residues in contact with THR 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* 2.5 36.6 + - - +
79A MET* 3.1 13.5 + - - -
81A THR* 1.3 70.9 - - + +
83A ALA* 1.3 65.8 + - - +
84A CYS 3.0 11.3 + - - +
85A HIS* 3.6 5.0 + - - -
87A PHE* 4.6 16.3 - - + -
70B PHE* 4.0 30.7 - - + -
71B GLN* 4.1 32.2 + - + +
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Residues in contact with ALA 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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47A ILE* 5.1 4.9 - - + -
49A GLU* 3.3 22.7 - - + +
52A VAL* 3.4 32.3 - - + +
53A VAL* 4.4 13.0 - - + -
79A MET 2.4 30.6 + - - +
80A VAL* 3.2 14.4 - - - +
81A THR 3.1 0.6 - - - -
82A THR* 1.3 69.8 - - - +
84A CYS* 1.3 58.1 + - - +
85A HIS* 2.7 10.4 + - - +
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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