Contacts of the helix formed by residues 65 - 82 (chain A) in PDB entry 4BC4
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 VAL 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER 3.4 3.0 + - - -
64A PRO* 1.3 70.0 - - - +
66A LEU* 1.3 66.7 + - + +
68A TRP* 3.1 24.4 + - + +
69A VAL* 3.2 10.4 + - - +
102A ILE* 4.1 12.8 - - + -
129A PHE* 3.5 50.0 - - + -
131A ILE 3.9 5.4 - - - +
132A SER* 3.0 23.4 + - - +
134A CYS* 3.5 13.9 - - - -
199A PHE* 3.7 28.7 - - + -
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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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46A PHE* 4.1 10.1 - - + -
64A PRO* 3.2 2.5 - - + +
65A VAL* 1.3 74.9 - - + +
67A MSE 1.3 58.8 + - - +
69A VAL* 3.8 10.7 - - + +
70A GLN* 3.0 30.1 + - - +
122A HIS* 3.5 32.6 - - + +
125A LEU* 3.8 13.5 - - + +
126A GLN* 3.6 30.5 - - + +
129A PHE* 3.8 31.2 - - + -
132A SER* 5.0 1.8 + - - -
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Residues in contact with MSE 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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39A PHE* 3.7 39.0 - - + -
43A LEU* 3.8 13.8 - - + +
46A PHE* 3.6 48.0 - - + -
48A THR* 3.8 21.3 - - - -
51A GLY 3.5 24.2 - - - +
63A SER* 4.2 0.2 - - - -
64A PRO* 3.1 25.3 + - + +
66A LEU* 1.3 73.8 - - - +
68A TRP* 1.3 79.3 + - + +
70A GLN 3.4 0.7 + - - -
71A ALA* 2.9 29.5 + - - +
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Residues in contact with TRP 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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15A PHE* 4.2 18.7 - + + -
16A SER 5.0 0.2 - - - -
17A THR 5.1 0.2 + - - -
20A VAL* 5.2 1.6 - - + -
39A PHE* 3.6 33.5 - + - -
63A SER* 3.5 29.5 + - - -
64A PRO 3.6 2.9 + - - -
65A VAL* 3.1 16.9 + - + +
67A MSE 1.3 85.2 - - + +
69A VAL* 1.3 61.1 + - - +
71A ALA* 3.4 7.5 + - - +
72A LEU* 3.2 19.8 + - - +
97A GLN* 3.4 25.3 - - - +
102A ILE* 3.6 24.0 - - + -
134A CYS* 3.8 28.9 - - + -
135A PRO 5.2 0.9 - - - -
136A VAL* 3.9 9.6 - - + -
196A VAL* 3.7 20.6 - - + -
199A PHE* 3.8 31.0 - + + -
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Residues in contact with VAL 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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65A VAL 3.2 13.4 + - - +
66A LEU* 3.8 12.8 - - + +
67A MSE 3.3 0.2 - - - -
68A TRP* 1.3 73.9 - - - +
70A GLN* 1.3 63.7 + - - +
72A LEU* 3.0 15.1 + - - +
73A ASP* 3.1 12.2 + - - +
121A LEU* 3.6 19.0 - - + +
122A HIS* 3.5 31.9 - - - +
125A LEU* 4.4 9.2 - - + -
129A PHE* 4.4 16.4 - - + -
199A PHE* 3.8 23.8 - - + -
203A LEU* 4.2 15.5 - - + -
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Residues in contact with GLN 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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43A LEU* 3.8 17.2 - - + +
45A GLU* 4.0 13.9 + - - +
46A PHE* 3.8 21.8 - - - -
66A LEU 3.0 17.2 + - - +
69A VAL* 1.3 76.6 - - - +
71A ALA* 1.3 63.4 + - - +
73A ASP* 3.1 14.1 + - + +
74A ILE* 2.9 36.8 + - + +
120A ARG* 6.5 0.7 - - - -
122A HIS* 4.0 23.7 + - + +
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Residues in contact with ALA 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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20A VAL* 3.8 11.0 - - + -
37A VAL* 3.9 22.2 - - + +
39A PHE* 3.7 26.2 - - + -
43A LEU* 4.0 6.0 - - + +
67A MSE 2.9 18.1 + - - +
68A TRP 3.6 6.1 - - - +
69A VAL 3.2 0.2 - - - -
70A GLN* 1.3 76.8 - - - +
72A LEU* 1.3 56.7 + - - +
74A ILE* 3.3 2.9 + - - +
75A ILE* 2.9 32.2 + - - +
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Residues in contact with LEU 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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13A TRP* 3.7 21.8 - - + -
15A PHE* 4.2 16.2 - - + -
20A VAL* 4.9 1.5 - - - +
68A TRP 3.2 10.6 + - - +
69A VAL* 3.0 11.9 + - - +
71A ALA* 1.3 72.5 - - - +
73A ASP* 1.3 66.8 + - - +
75A ILE* 3.3 6.3 - - - +
76A LEU* 3.1 35.6 + - + +
121A LEU* 3.5 26.2 - - + -
203A LEU* 3.8 26.0 - - + -
204A PHE* 3.7 31.9 - - + -
262A TYR* 4.1 6.3 - - - +
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Residues in contact with ASP 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 VAL 3.1 10.5 + - - +
70A GLN* 3.1 12.8 + - + +
72A LEU* 1.3 76.4 - - - +
74A ILE* 1.3 63.4 + - + +
76A LEU* 3.5 3.2 + - - +
77A GLU* 3.1 32.3 + - - +
120A ARG* 3.6 26.2 - - + +
121A LEU* 2.8 37.2 + - - +
122A HIS* 2.9 34.8 + - - +
261A TYR* 4.1 3.3 + - - -
266A TYR* 4.2 8.0 + - - -
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Residues in contact with ILE 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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37A VAL* 3.6 21.1 - - + -
42A ASP* 4.6 11.9 - - + +
43A LEU* 3.8 35.9 - - + -
70A GLN* 2.9 34.7 + - + +
71A ALA 3.7 3.6 - - - +
72A LEU 3.3 0.2 - - - -
73A ASP* 1.3 78.1 - - + +
75A ILE* 1.3 56.3 + - - +
77A GLU* 3.3 6.8 + - - +
78A LYS* 2.9 36.7 + - + +
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Residues in contact with ILE 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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13A TRP* 3.6 27.1 - - + -
20A VAL* 3.6 32.5 - - + +
22A VAL* 3.8 18.4 - - + +
35A GLU* 3.6 34.8 - - + +
36A SER* 3.8 3.1 - - - -
37A VAL* 3.6 19.7 - - + +
71A ALA 2.9 12.6 + - - +
72A LEU* 3.3 15.5 - - - +
74A ILE* 1.3 77.3 - - - +
76A LEU* 1.3 59.3 + - - +
78A LYS* 3.2 3.7 + - - +
79A MSE 2.9 34.5 + - + +
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Residues in contact with LEU 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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13A TRP* 3.9 26.0 - - + -
72A LEU* 3.1 40.6 + - + +
73A ASP* 4.0 2.2 - - - +
75A ILE* 1.3 74.8 - - - +
77A GLU* 1.3 57.0 + - - +
79A MSE 3.5 6.1 + - - +
80A LYS* 3.0 27.9 + - - +
86A PHE* 4.0 25.8 - - + -
121A LEU* 5.2 2.5 - - + -
204A PHE* 4.9 1.8 - - + -
262A TYR* 3.7 28.0 - - + -
266A TYR* 3.6 31.7 - - + +
268A PHE* 4.3 12.8 - - + -
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Residues in contact with GLU 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 20.4 + - - +
74A ILE* 3.8 5.8 - - - +
76A LEU* 1.3 72.5 - - - +
78A LYS* 1.3 59.6 + - - +
80A LYS* 3.4 9.5 + - + +
81A ALA* 2.8 30.7 + - - +
120A ARG* 3.0 47.8 + - - +
265A ARG* 3.1 20.2 + - - +
266A TYR* 3.7 17.7 + - + +
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Residues in contact with LYS 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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33A TYR* 4.8 0.9 - - - -
35A GLU* 2.9 36.5 + - + +
36A SER* 2.9 26.5 + - - +
37A VAL* 4.6 10.4 - - + +
41A ARG* 4.4 13.3 - - - +
42A ASP* 4.9 3.0 + - - -
74A ILE* 2.9 21.6 + - + +
75A ILE* 3.5 5.2 - - - +
77A GLU* 1.3 76.5 - - - +
79A MSE 1.4 62.1 + - - +
81A ALA* 3.4 7.2 + - - +
82A SER* 3.1 24.7 + - - -
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Residues in contact with MSE 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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11A LEU* 4.1 18.8 - - + -
13A TRP* 4.0 16.6 - - - -
22A VAL* 4.0 19.7 - - + -
33A TYR* 3.2 36.6 - - + +
35A GLU* 4.4 8.7 - - + -
75A ILE* 2.9 21.7 + - + +
76A LEU* 3.7 6.7 - - - +
78A LYS* 1.4 75.3 - - - +
80A LYS* 1.3 61.5 + - - +
82A SER* 2.9 18.2 + - - -
84A PHE* 3.0 39.7 + - + -
86A PHE* 3.6 32.8 - - + -
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Residues in contact with LYS 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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76A LEU 3.0 17.5 + - - +
77A GLU* 3.6 9.2 - - + +
79A MSE 1.3 76.1 - - - +
81A ALA* 1.3 61.7 + - - +
83A GLY* 3.1 14.8 + - - +
84A PHE 4.6 4.3 - - - +
86A PHE* 4.0 15.1 - - + -
265A ARG* 3.5 25.4 + - - +
266A TYR* 3.8 26.3 - - + +
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Residues in contact with ALA 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 GLU 2.8 21.0 + - - +
78A LYS* 3.4 8.5 + - - +
80A LYS* 1.3 73.7 - - - +
82A SER* 1.4 59.6 + - - +
83A GLY 3.2 1.1 + - - -
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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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33A TYR* 3.5 27.1 + - - -
35A GLU* 5.5 4.3 - - - -
78A LYS* 3.1 14.4 + - - -
79A MSE 2.9 12.9 + - - -
81A ALA* 1.4 75.1 - - - +
83A GLY* 1.3 56.6 + - - +
84A PHE 3.9 2.3 + - - -
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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