Contacts of the helix formed by residues 57 - 76 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C PHE* 2.8 26.0 + - - +
47C ASP 3.5 19.6 + - - +
48C LEU* 3.8 8.5 - - - +
53C ALA 3.2 17.8 + - - +
54C VAL* 3.2 12.4 + - - +
55C MET 3.3 0.2 - - - -
56C GLY* 1.3 74.0 - - - +
58C PRO* 1.3 72.9 - - - +
59C LYS* 2.8 36.8 + - - +
60C VAL* 3.0 26.2 + - + +
61C LYS* 3.0 14.3 + - - +
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Residues in contact with PRO 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLY 3.1 10.3 - - - +
57C ASN* 1.3 89.6 - - - +
59C LYS* 1.3 58.8 + - + +
61C LYS* 3.4 9.4 + - + +
62C ALA* 3.0 29.5 + - - +
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Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C SER* 3.5 38.7 + - - +
45C PHE* 3.8 30.3 - - + +
57C ASN* 2.8 11.7 + - - +
58C PRO* 1.3 79.8 - - + +
60C VAL* 1.3 59.0 + - - +
62C ALA* 4.0 4.6 - - - +
63C HIS* 2.9 32.6 + - - +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY* 4.0 20.3 - - - +
28C LEU* 3.7 9.2 - - + +
29C GLY* 4.0 16.6 - - - +
32C LEU* 4.2 17.3 - - + -
45C PHE* 3.8 24.5 - - + -
48C LEU* 4.2 7.0 - - + -
54C VAL 3.7 16.6 - - - +
55C MET 4.9 4.3 - - - +
57C ASN* 3.0 26.7 + - + +
59C LYS* 1.3 76.4 - - - +
61C LYS* 1.3 60.5 + - - +
64C GLY* 2.8 27.4 + - - -
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASP 4.9 6.5 - - - +
25C GLY* 4.2 17.6 + - - -
55C MET 3.2 26.4 + - - +
56C GLY* 3.3 24.0 - - - +
57C ASN 3.0 12.0 + - - +
58C PRO* 3.8 8.5 - - + +
60C VAL* 1.3 77.3 - - + +
62C ALA* 1.3 62.0 + - - +
64C GLY* 3.4 1.2 + - - -
65C LYS* 3.3 28.6 + - - +
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Residues in contact with ALA 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PRO 3.0 18.1 + - - +
59C LYS* 4.0 5.8 - - - +
61C LYS* 1.3 77.1 - - - +
63C HIS* 1.3 63.5 + - - +
65C LYS* 3.3 25.6 + - - +
66C LYS* 3.4 17.4 + - + +
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Residues in contact with HIS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.9 11.2 - - + -
42C PHE* 4.2 8.3 - + - -
45C PHE* 3.7 18.2 - + + -
59C LYS 2.9 18.0 + - - +
62C ALA* 1.3 76.1 - - - +
64C GLY* 1.3 58.2 + - - +
66C LYS* 2.9 48.2 + - + +
67C VAL* 3.2 17.2 + - + +
147C HEM 3.3 62.3 + + + +
148C CMO 3.3 23.9 + - - -
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Residues in contact with GLY 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY* 3.3 39.9 - - - -
25C GLY* 3.7 0.7 - - - -
28C LEU* 3.9 9.1 - - - +
60C VAL 2.8 16.4 + - - -
61C LYS 3.4 0.6 + - - -
62C ALA 3.3 0.2 - - - -
63C HIS* 1.3 74.4 - - - +
65C LYS* 1.3 61.7 + - - +
67C VAL* 3.3 7.6 + - - +
68C LEU* 3.0 19.1 + - - +
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Residues in contact with LYS 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 3.8 23.5 - - + +
21C ASP* 3.2 48.7 + - - +
24C GLY* 4.4 0.6 - - - -
25C GLY 4.5 0.4 - - - +
61C LYS* 3.3 19.4 + - - +
62C ALA* 3.3 13.7 + - - +
63C HIS 3.2 1.0 - - - -
64C GLY* 1.3 76.3 - - - +
66C LYS* 1.3 59.8 + - + +
68C LEU* 3.4 2.5 + - - +
69C GLY* 3.0 24.3 + - - -
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA* 3.4 19.8 + - + +
63C HIS* 2.9 32.3 + - - +
65C LYS* 1.3 77.3 - - + +
67C VAL* 1.3 61.5 + - - +
69C GLY* 3.3 2.8 + - - +
70C ALA 3.2 16.1 + - - -
147C HEM 3.5 55.7 + - + +
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Residues in contact with VAL 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLY* 5.6 2.9 - - - +
27C ALA* 6.5 0.9 - - + -
28C LEU* 5.0 5.6 - - + -
63C HIS* 3.2 22.0 + - + +
64C GLY* 3.3 9.8 + - - +
66C LYS* 1.3 75.4 - - - +
68C LEU* 1.3 59.1 + - - +
70C ALA* 3.2 5.0 + - - +
71C PHE* 3.0 53.2 + - + -
106C LEU* 4.2 16.2 - - + -
147C HEM 4.0 24.4 - - + +
148C CMO 3.3 32.5 - - - +
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP* 3.2 37.5 - - + -
18C VAL* 4.2 9.0 - - + -
20C VAL* 3.2 55.0 - - + +
23C VAL* 4.3 13.2 - - + -
24C GLY* 3.6 17.3 - - - +
64C GLY 3.0 16.7 + - - +
65C LYS* 3.8 4.0 - - - +
67C VAL* 1.3 79.0 - - - +
69C GLY* 1.3 62.9 - - - +
71C PHE* 3.2 10.3 + - + +
72C SER* 3.0 24.0 + - - -
110C LEU* 4.9 7.2 - - + -
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Residues in contact with GLY 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 6.0 2.2 - - - +
65C LYS 3.0 15.6 + - - -
66C LYS* 3.3 4.0 + - - -
67C VAL 3.2 0.4 - - - -
68C LEU* 1.3 76.1 - - - +
70C ALA* 1.3 54.8 + - - +
72C SER* 3.2 10.7 + - - -
73C ASP* 3.0 29.2 + - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LYS 3.2 11.2 + - - +
67C VAL 3.2 9.0 + - - +
69C GLY* 1.3 74.1 - - - +
71C PHE* 1.3 64.2 + - - +
73C ASP* 3.2 11.5 + - - +
74C GLY 3.0 16.6 + - - -
85C PHE* 3.3 15.3 - - + -
88C LEU* 3.8 29.4 - - + -
147C HEM 3.9 16.8 - - + -
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Residues in contact with PHE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TRP* 4.1 16.8 - + + -
67C VAL* 3.0 41.7 + - + -
68C LEU* 3.2 11.4 + - + +
70C ALA* 1.3 74.7 - - - +
72C SER* 1.3 59.1 + - - +
74C GLY* 2.9 4.2 + - - +
75C LEU* 2.9 31.4 + - + +
85C PHE* 4.8 3.1 - - - -
106C LEU* 4.9 4.9 - - + -
107C GLY* 4.9 8.1 - - - -
110C LEU* 4.0 31.9 - - + -
133C VAL* 5.5 4.6 - - + +
134C VAL* 4.3 13.5 - - + -
137C VAL* 3.7 35.1 - - + +
147C HEM 3.6 37.9 - - + +
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Residues in contact with SER 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TRP* 2.9 33.3 + - - +
20C VAL* 5.1 7.3 - - - +
68C LEU 3.0 14.5 + - - -
69C GLY* 3.2 10.9 + - - -
71C PHE* 1.3 71.6 - - - +
73C ASP* 1.3 69.5 + - - +
75C LEU* 3.1 6.0 + - - +
76C ALA* 3.0 23.8 + - - +
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Residues in contact with ASP 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLY 3.0 15.5 + - - +
70C ALA* 3.2 14.6 + - - +
72C SER* 1.3 78.4 - - - +
74C GLY* 1.3 62.4 + - - +
76C ALA* 3.3 3.8 + - - -
77C HIS* 2.7 41.6 + - - +
84C THR* 3.9 21.6 - - + +
85C PHE* 5.0 1.1 - - + -
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Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ALA 3.0 6.9 + - - -
71C PHE 2.9 8.4 + - - -
73C ASP* 1.3 76.0 - - - +
75C LEU* 1.3 64.3 + - - +
77C HIS 2.9 22.5 + - - -
78C LEU* 3.4 6.1 + - - +
81C LEU* 3.6 13.1 - - - +
84C THR* 4.7 1.6 - - - -
85C PHE* 3.7 27.1 - - - -
137C VAL* 5.0 4.0 - - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 4.4 10.4 + - - -
11C VAL* 3.5 29.2 - - + -
12C THR* 5.5 8.9 - - + +
15C TRP* 3.3 60.8 - - + +
71C PHE* 2.9 14.0 + - + +
72C SER 3.1 6.3 + - - +
74C GLY* 1.3 77.4 - - - +
76C ALA* 1.3 61.4 - - - +
77C HIS 3.4 0.7 + - - -
78C LEU* 3.6 23.9 + - + +
130C TYR* 4.6 4.5 - - + +
133C VAL* 3.7 30.9 - - + +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 5.5 3.4 + - - +
72C SER 3.0 15.2 + - - +
73C ASP* 3.8 5.8 - - - +
74C GLY 3.1 0.4 - - - -
75C LEU* 1.3 78.6 - - - +
77C HIS* 1.3 76.9 + - + +
78C LEU 3.8 0.9 - - - -
79C ASP* 5.0 2.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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