Contacts of the helix formed by residues 57 - 76 (chain A) in PDB entry 1CBM
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 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE 3.0 25.1 + - - -
47A ASP* 3.6 21.8 + - - +
48A LEU* 4.1 4.8 - - - +
53A ALA 3.1 11.1 + - - +
54A VAL* 3.3 8.4 + - - +
55A MET 4.6 0.2 - - - +
56A GLY* 1.3 72.9 - - - +
58A PRO* 1.3 69.4 - - - +
59A LYS* 2.7 38.2 + - - +
60A VAL* 3.1 30.3 + - + +
61A LYS* 2.9 28.2 + - - +
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Residues in contact with PRO 58 (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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56A GLY 3.2 9.8 - - - +
57A ASN* 1.3 86.6 - - - +
59A LYS* 1.3 63.8 + - + +
61A LYS* 3.5 20.3 - - + +
62A ALA* 2.8 30.3 + - - +
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.8 21.5 + - - -
45A PHE* 3.5 42.0 + - + +
57A ASN* 2.7 22.1 + - - +
58A PRO* 1.3 76.4 - - + +
60A VAL* 1.3 55.7 + - - +
62A ALA* 3.3 5.8 + - - +
63A HIS* 2.9 32.6 + - - +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY* 4.1 6.0 - - - +
28A LEU* 3.5 13.3 - - + +
29A GLY* 3.9 28.9 - - - +
32A LEU* 4.2 11.9 - - + -
45A PHE* 4.1 15.5 - - + -
48A LEU* 4.1 17.0 - - + -
54A VAL 3.8 14.8 - - - +
55A MET* 5.7 1.1 - - - +
57A ASN* 3.1 36.6 + - + +
59A LYS* 1.3 75.3 - - - +
61A LYS* 1.3 56.7 + - + +
64A GLY* 2.8 32.1 + - - -
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Residues in contact with LYS 61 (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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21A ASP 5.2 5.9 - - - +
25A GLY* 4.0 18.9 + - - -
55A MET 4.3 14.6 - - - +
56A GLY* 4.1 13.2 + - - -
57A ASN 2.9 13.6 + - - +
58A PRO* 3.5 28.1 - - + +
59A LYS 3.3 0.2 - - - -
60A VAL* 1.3 78.0 - - + +
62A ALA* 1.3 63.9 + - - +
64A GLY* 3.2 2.1 + - - -
65A LYS* 3.0 22.2 + - - +
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Residues in contact with ALA 62 (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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58A PRO 2.8 21.1 + - - +
59A LYS* 3.7 7.2 - - - +
61A LYS* 1.3 74.6 - - - +
63A HIS* 1.3 61.8 + - - +
65A LYS* 3.2 16.9 + - - +
66A LYS* 3.4 19.8 + - - +
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Residues in contact with HIS 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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28A LEU* 3.9 10.5 - - + -
42A PHE* 4.1 8.1 - + - -
45A PHE* 3.7 20.3 - + + -
59A LYS 2.9 18.2 + - - +
60A VAL 3.8 3.1 - - - +
62A ALA* 1.3 75.1 - - - +
64A GLY* 1.3 61.5 + - - +
66A LYS* 2.8 40.1 + - + +
67A VAL* 2.9 12.9 + - + +
147A HEM 3.2 68.5 + + + +
148A CMO 3.1 28.1 + - - -
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Residues in contact with GLY 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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24A GLY* 3.2 39.2 - - - -
25A GLY* 4.0 0.2 - - - -
28A LEU* 3.8 9.8 - - - +
60A VAL 2.8 21.3 + - - -
61A LYS 3.6 1.3 - - - -
63A HIS* 1.3 71.8 - - - +
65A LYS* 1.3 62.0 + - - +
67A VAL* 3.2 6.0 + - - +
68A LEU 3.1 18.5 + - - -
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Residues in contact with LYS 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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20A VAL* 4.0 22.4 - - + +
21A ASP* 3.7 41.8 + - + +
24A GLY* 4.7 0.7 - - - -
25A GLY 4.3 0.8 - - - +
61A LYS 3.0 12.4 + - - +
62A ALA* 3.4 11.9 - - - +
63A HIS 3.1 0.4 - - - -
64A GLY* 1.3 77.9 - - - +
66A LYS* 1.3 56.0 + - + +
68A LEU* 3.4 3.0 + - - +
69A GLY* 3.1 23.4 + - - -
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Residues in contact with LYS 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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62A ALA* 3.4 15.9 + - - +
63A HIS* 2.8 32.6 + - - +
65A LYS* 1.3 73.4 - - + +
67A VAL* 1.3 66.5 + - - +
69A GLY* 3.4 3.2 + - - +
70A ALA 3.3 14.7 + - - -
147A HEM 3.5 49.6 + - + +
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Residues in contact with VAL 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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24A GLY* 5.5 2.0 - - - +
28A LEU* 4.7 7.2 - - + -
63A HIS* 2.9 24.1 + - + +
64A GLY* 3.2 11.0 + - - +
66A LYS* 1.3 76.8 - - - +
68A LEU* 1.3 62.4 + - + +
70A ALA* 3.1 14.6 + - - +
71A PHE* 3.1 29.5 + - + -
106A LEU* 4.0 15.0 - - + -
147A HEM 3.7 30.5 - - + -
148A CMO 3.1 33.0 - - - +
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Residues in contact with LEU 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 TRP* 3.4 26.9 - - + -
18A VAL* 3.8 16.8 - - + -
20A VAL* 3.4 44.4 - - + +
23A VAL* 4.2 9.2 - - + -
24A GLY* 4.0 15.2 - - - +
64A GLY 3.1 14.8 + - - +
65A LYS 3.9 4.7 - - - +
67A VAL* 1.3 76.9 - - + +
69A GLY* 1.3 57.3 + - - +
71A PHE* 3.2 10.1 + - + +
72A SER* 2.9 32.5 + - - -
110A LEU* 4.1 22.0 - - + -
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Residues in contact with GLY 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 LYS 3.1 13.5 + - - -
66A LYS* 3.4 5.4 + - - -
67A VAL 3.1 0.8 - - - -
68A LEU* 1.3 79.3 - - - +
70A ALA* 1.3 58.4 + - - +
72A SER* 3.3 8.4 + - - -
73A ASP* 3.0 28.0 + - - +
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Residues in contact with ALA 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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66A LYS 3.3 11.0 + - - +
67A VAL 3.1 9.4 + - - +
69A GLY* 1.3 72.7 - - - +
71A PHE* 1.3 61.6 - - - +
73A ASP* 3.1 13.9 - - - +
74A GLY 2.9 23.6 + - - -
85A PHE* 3.7 13.4 - - + -
88A LEU* 3.8 28.7 - - + -
147A HEM 3.9 16.4 - - + -
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Residues in contact with PHE 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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15A TRP* 4.3 13.5 - + + -
67A VAL* 3.1 34.6 + - + -
68A LEU* 3.4 14.6 - - + +
70A ALA* 1.3 76.4 - - - +
72A SER* 1.3 61.7 + - - +
74A GLY* 3.1 3.1 + - - -
75A LEU* 3.1 29.1 + - + +
85A PHE* 5.1 3.6 - - - -
106A LEU* 4.8 6.3 - - + -
107A GLY* 5.0 10.1 - - - -
110A LEU* 4.0 31.2 - - + -
133A VAL* 5.4 5.3 - - + +
134A VAL* 4.1 17.7 - - + -
137A VAL* 3.9 32.6 - - + +
147A HEM 3.8 35.0 - - + -
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Residues in contact with SER 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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15A TRP* 3.1 31.6 + - - +
20A VAL* 5.0 6.9 - - - +
68A LEU* 2.9 18.0 + - - +
69A GLY* 3.6 10.4 - - - -
70A ALA 3.3 0.2 - - - -
71A PHE* 1.3 74.9 - - - +
73A ASP* 1.3 63.2 + - - +
75A LEU* 3.4 7.0 + - - +
76A ALA* 3.2 21.5 + - - +
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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 GLY 3.0 18.9 + - - +
70A ALA* 3.1 18.4 + - + +
72A SER* 1.3 76.3 - - - +
74A GLY* 1.3 58.0 + - - +
76A ALA* 3.1 6.0 + - - -
77A HIS* 2.5 38.5 + - + -
84A THR* 4.1 13.1 - - + +
85A PHE* 5.5 0.7 - - + -
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Residues in contact with GLY 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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70A ALA 2.9 14.5 + - - -
71A PHE 3.1 2.8 + - - -
73A ASP* 1.3 74.6 - - - +
75A LEU* 1.3 55.6 + - - +
77A HIS 2.8 19.3 + - - -
78A LEU* 3.0 14.6 + - - +
81A LEU* 3.1 29.7 - - - +
84A THR* 4.1 4.5 - - - -
85A PHE* 3.8 14.1 - - - -
133A VAL* 6.0 0.2 - - - -
137A VAL* 5.4 2.5 - - - -
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Residues in contact with LEU 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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11A VAL* 4.8 13.9 - - + +
12A THR* 5.8 8.2 - - + +
15A TRP* 3.4 60.1 - - + +
71A PHE* 3.1 15.4 + - + +
72A SER 3.6 8.5 - - - +
73A ASP 3.2 0.4 - - - -
74A GLY* 1.3 76.5 - - - +
76A ALA* 1.3 59.6 + - - +
77A HIS 3.5 0.5 + - - -
78A LEU* 4.0 17.5 + - + +
130A TYR* 4.7 11.7 - - + +
133A VAL* 3.6 37.2 - - + +
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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 SER 3.2 11.3 + - - +
73A ASP* 3.1 11.3 + - - +
74A GLY 3.0 0.6 - - - -
75A LEU* 1.3 79.8 - - - +
77A HIS* 1.3 76.5 + - + +
78A LEU 3.8 0.9 - - - -
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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