Contacts of the helix formed by residues 33 - 46 (chain C) in PDB entry 3CJS
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 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C LEU* 5.3 0.2 - - - -
31C GLY 3.8 1.6 + - - -
32C ALA* 1.3 70.0 - - - +
34C ILE* 1.3 63.0 + - - +
35C MET* 3.2 12.3 + - - +
36C GLU* 2.9 46.2 + - - +
37C PHE* 3.0 22.3 + - - +
63C ARG 4.4 3.8 + - - +
65C PHE* 3.9 5.4 - - + -
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Residues in contact with ILE 34 (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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19C PRO* 3.9 35.4 - - + -
23C VAL* 4.2 11.9 - - + -
24C GLY* 3.5 33.0 - - - +
27C LEU* 4.0 14.1 - - + -
28C GLY* 4.2 9.6 - - - +
32C ALA 3.2 9.4 + - - +
33C ASN* 1.3 71.8 + - - +
35C MET* 1.3 60.9 + - + +
37C PHE* 3.2 7.0 + - - +
38C VAL* 2.9 29.5 + - + +
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Residues in contact with MET 35 (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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19C PRO* 3.2 37.0 - - + -
33C ASN* 3.2 8.2 + - - +
34C ILE* 1.3 80.2 - - + +
36C GLU* 1.3 64.2 + - - +
38C VAL* 3.2 21.8 + - + +
39C LYS* 2.9 26.1 + - - +
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Residues in contact with GLU 36 (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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15A PRO* 5.7 0.2 - - - +
33C ASN* 2.9 39.7 + - - +
35C MET* 1.3 75.9 - - - +
37C PHE* 1.3 58.7 + - - +
39C LYS* 3.5 4.5 + - - +
40C ALA* 3.0 32.1 + - + +
64C SER* 6.1 0.3 - - - -
65C PHE* 3.8 21.0 - - + -
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Residues in contact with PHE 37 (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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10C LEU* 4.7 0.2 - - + -
12C LEU* 3.8 26.9 - - + -
17C ALA* 5.3 0.7 - - + -
23C VAL* 3.9 24.2 - - + -
27C LEU* 3.9 22.0 - - + -
33C ASN 3.0 12.8 + - - +
34C ILE 3.6 5.4 - - - +
36C GLU* 1.3 73.7 - - - +
38C VAL* 1.3 61.4 + - + +
40C ALA* 3.8 0.4 - - - +
41C PHE* 2.8 56.8 + + + +
55C VAL* 4.4 3.1 - - + -
57C ILE* 3.6 38.8 - - + -
65C PHE* 3.4 32.2 - + + -
67C PHE* 3.9 18.4 - + - -
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Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ALA* 3.3 31.2 - - + +
18C THR* 3.6 30.5 - - - +
19C PRO* 3.9 4.0 - - + -
23C VAL* 3.8 14.4 - - + -
34C ILE* 2.9 21.6 + - + +
35C MET* 3.2 19.7 + - + +
37C PHE* 1.3 77.0 - - + +
39C LYS* 1.3 58.3 + - - +
41C PHE* 4.0 0.3 - - - +
42C ASN* 2.9 37.0 + - - +
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Residues in contact with LYS 39 (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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11A GLU 3.8 13.8 + - - -
12A ALA* 4.0 6.2 + - - +
14A ASP* 3.5 16.1 - - - +
15A PRO* 2.3 48.8 - - + +
35C MET 2.9 17.2 + - - +
36C GLU* 3.9 4.9 - - - +
38C VAL* 1.3 77.9 - - - +
40C ALA* 1.3 58.2 + - - +
42C ASN* 3.9 3.9 - - - +
43C ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 40 (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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15A PRO* 3.7 22.2 - - + +
16A ILE* 4.6 2.4 - - - +
36C GLU* 3.0 21.2 + - + +
37C PHE* 3.8 3.4 - - - +
39C LYS* 1.3 73.6 - - - +
41C PHE* 1.3 59.9 + - - +
43C ALA* 3.4 2.6 + - - +
44C ALA* 2.9 30.8 + - - +
65C PHE* 4.7 5.6 - - + -
67C PHE* 3.7 21.8 - - + -
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Residues in contact with PHE 41 (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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12C LEU* 3.6 32.1 - - + -
13C PRO 3.6 18.8 - - - -
17C ALA* 3.6 10.5 - - + -
37C PHE* 2.8 50.3 + + + +
38C VAL* 4.0 2.7 - - - +
40C ALA* 1.3 72.4 - - - +
42C ASN* 1.3 65.8 + - - +
44C ALA* 3.2 1.6 + - - -
45C THR* 2.7 69.0 + - + +
53C VAL* 4.0 12.6 - - + -
55C VAL* 3.9 31.6 - - + -
67C PHE* 3.7 13.8 - + - -
69C THR* 5.9 0.4 - - + -
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Residues in contact with ASN 42 (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 GLY* 3.5 19.3 + - - +
16C LYS* 3.1 7.5 + - - +
17C ALA* 2.8 49.3 + - - +
38C VAL* 2.9 27.9 + - - +
39C LYS* 4.0 5.1 - - - +
41C PHE* 1.3 79.2 - - - +
43C ALA* 1.3 55.4 + - - +
45C THR* 3.7 3.8 + - - -
46C ALA* 2.9 32.8 + - - +
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Residues in contact with ALA 43 (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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12A ALA 3.7 20.8 + - - +
13A LEU* 3.8 23.4 - - - +
15A PRO* 3.8 17.5 - - + -
16A ILE* 3.7 24.6 - - + +
47A TYR* 4.8 0.7 - - - +
39C LYS 3.0 18.1 + - - +
40C ALA 3.8 4.0 - - - +
41C PHE 3.3 0.2 - - - -
42C ASN* 1.3 78.0 - - - +
44C ALA* 1.3 61.3 + - - +
45C THR 3.3 0.7 + - - -
46C ALA* 3.6 6.2 + - - +
47C ASN* 5.2 1.2 + - - +
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Residues in contact with ALA 44 (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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16A ILE* 3.8 5.6 - - + +
47A TYR* 3.4 42.5 - - + +
40C ALA 2.9 18.1 + - - +
41C PHE 3.2 4.2 + - - +
43C ALA* 1.3 76.7 - - - +
45C THR* 1.3 61.9 + - + +
46C ALA 3.6 0.2 - - - -
47C ASN 5.2 0.2 + - - -
48C MET* 3.7 15.4 - - - +
67C PHE* 4.0 21.5 - - + -
69C THR* 5.1 6.5 + - - +
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Residues in contact with THR 45 (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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14C ALA* 3.5 20.3 - - - +
15C GLY* 2.8 27.2 + - - -
41C PHE* 2.7 51.1 + - + +
42C ASN 3.7 0.4 + - - -
44C ALA* 1.3 85.2 - - + +
46C ALA* 1.3 60.1 + - - +
47C ASN 3.1 6.9 + - - -
48C MET* 3.1 33.5 + - - +
49C GLY 4.5 0.5 + - - +
53C VAL* 4.2 8.5 - - + -
67C PHE* 5.9 0.4 - - + -
69C THR* 4.5 5.8 - - + +
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Residues in contact with ALA 46 (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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7A LYS* 3.1 37.1 + - - +
13A LEU* 4.1 13.5 - - + -
15C GLY* 4.4 9.0 - - - -
42C ASN 2.9 17.2 + - - +
43C ALA* 3.6 11.8 + - - +
44C ALA 3.6 0.4 - - - -
45C THR* 1.3 76.9 - - - +
47C ASN* 1.3 65.5 + - - +
48C MET 3.5 1.2 + - - -
49C GLY* 4.7 4.1 + - - -
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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
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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