Contacts of the helix formed by residues 31 - 46 (chain C) in PDB entry 2JBG
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 ASP 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C THR* 1.3 74.3 - - - +
32C ASP* 1.3 65.8 + - - +
33C VAL 3.4 2.2 - - - -
34C LEU* 3.5 11.9 - - + +
35C ASP* 2.9 44.4 + - - +
520D ARG* 2.8 35.8 + - - -
525D LYS* 2.6 36.9 + - - +
528D LYS* 4.6 4.4 + - - -
540D SER* 4.9 4.3 + - - -
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Residues in contact with ASP 32 (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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30C THR* 3.4 26.3 + - - +
31C ASP* 1.3 79.8 + - - +
33C VAL* 1.3 66.1 + - + +
35C ASP* 4.3 2.7 - - - +
36C VAL* 3.7 20.3 + - - +
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Residues in contact with VAL 33 (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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21C GLU* 5.1 1.8 - - - +
25C GLU* 3.5 36.5 + - + +
30C THR* 5.2 0.6 + - - -
31C ASP 3.4 0.2 - - - -
32C ASP* 1.3 78.7 - - + +
34C LEU* 1.3 68.1 + - - +
36C VAL* 3.1 9.3 + - + +
37C LEU* 3.1 31.9 + - + +
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Residues in contact with LEU 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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22C ILE* 3.7 31.0 - - + +
25C GLU* 3.8 23.6 + - + +
26C ASN* 3.2 27.8 - - - +
30C THR 5.0 0.2 - - - +
31C ASP* 3.4 22.1 + - - +
33C VAL* 1.3 79.8 - - - +
35C ASP* 1.3 59.1 + - - +
37C LEU* 3.0 6.4 + - - +
38C LEU* 2.8 42.1 + - + +
55C TYR* 3.7 17.5 - - - +
520D ARG* 3.2 19.5 - - - +
528D LYS* 4.1 7.2 - - - -
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Residues in contact with ASP 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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31C ASP* 2.9 39.8 + - - +
32C ASP* 4.3 4.0 - - - +
34C LEU* 1.3 73.2 - - - +
36C VAL* 1.3 59.0 + - + +
38C LEU* 3.3 7.4 + - - +
39C GLU* 3.0 37.1 + - + +
528D LYS* 2.9 30.5 + - - -
537D LYS* 4.5 9.4 - - - +
539D THR* 4.4 6.7 + - - +
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Residues in contact with VAL 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 5.4 10.8 - - + -
32C ASP 3.7 15.7 - - - +
33C VAL* 3.1 9.9 + - + +
35C ASP* 1.3 75.3 - - + +
37C LEU* 1.3 70.5 + - + +
39C GLU* 3.2 19.3 + - - +
40C HIS* 3.0 21.6 + - + +
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Residues in contact with LEU 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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1C MET* 4.7 9.4 - - + -
3C LEU* 4.3 30.1 - - + -
18C LEU* 4.9 4.6 - - + +
21C GLU* 3.7 33.7 - - + +
22C ILE* 4.0 18.9 - - + +
25C GLU* 3.8 27.4 - - + -
33C VAL* 3.1 19.9 + - + +
34C LEU* 3.0 6.1 + - - +
36C VAL* 1.3 79.6 - - + +
38C LEU* 1.3 58.9 + - - +
40C HIS* 3.3 7.5 + - - +
41C PHE* 3.0 26.5 + - - +
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Residues in contact with LEU 38 (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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22C ILE* 3.7 28.3 - - + -
34C LEU* 2.8 28.4 + - + +
35C ASP* 3.7 7.2 - - - +
37C LEU* 1.3 75.4 - - - +
39C GLU* 1.3 60.8 + - - +
41C PHE* 3.2 3.6 + - + +
42C VAL* 2.9 33.7 + - - +
51C THR* 4.1 17.7 - - + -
54C ILE* 3.8 20.6 - - + -
55C TYR* 3.6 28.3 - - + +
528D LYS* 3.7 29.2 - - - +
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Residues in contact with GLU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ASP* 3.0 26.5 + - + +
36C VAL* 3.2 26.6 + - - +
38C LEU* 1.3 76.2 - - - +
40C HIS* 1.3 57.8 + - - +
42C VAL* 3.3 7.5 + - - +
43C LYS* 2.9 31.1 + - - +
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Residues in contact with HIS 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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3C LEU* 3.5 39.5 - - + +
4C LYS 2.6 24.0 + - - -
5C ASN* 4.8 1.2 - - - -
10C TYR* 3.0 28.4 + - - -
18C LEU* 4.3 5.7 - - - +
36C VAL* 3.0 12.7 + - + +
37C LEU* 3.6 10.8 - - - +
38C LEU 3.2 0.2 - - - -
39C GLU* 1.3 77.4 - - - +
41C PHE* 1.3 63.8 + - - +
43C LYS* 3.3 12.2 + - + +
44C ILE* 3.0 48.7 + - + +
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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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15C PHE* 3.5 38.4 - + - -
18C LEU* 5.0 4.7 - - + +
19C LEU* 4.0 12.6 - - + -
22C ILE* 4.1 13.9 - - + -
37C LEU 3.0 13.8 + - - +
38C LEU* 3.6 8.3 - - + +
40C HIS* 1.3 78.8 + - - +
42C VAL* 1.3 72.1 + - + +
44C ILE* 3.6 7.3 - - - +
45C THR* 3.0 45.2 + - + +
50C GLY 3.5 24.0 - - - -
51C THR* 4.9 2.2 - - + -
53C LEU* 4.1 12.6 - - + -
54C ILE* 3.7 36.8 - - + -
68C ILE* 4.3 2.2 - - + -
72C ILE* 3.9 10.5 - - + -
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU 2.9 21.8 + - - +
39C GLU* 3.6 6.7 - - - +
41C PHE* 1.3 77.7 - - + +
43C LYS* 1.3 65.1 + - - +
45C THR* 3.4 5.3 + - - -
46C GLU* 3.2 21.8 + - - -
47C HIS 4.5 4.4 + - - +
50C GLY* 3.9 13.5 - - - -
51C THR* 3.7 37.2 - - + +
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Residues in contact with LYS 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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5C ASN 6.0 1.3 - - - +
39C GLU 2.9 18.3 + - - +
40C HIS* 3.6 13.2 - - + +
41C PHE 3.3 0.2 - - - -
42C VAL* 1.3 79.6 - - - +
44C ILE* 1.3 66.2 + - + +
46C GLU* 3.4 16.1 - - - +
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Residues in contact with ILE 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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4C LYS 3.9 2.7 - - - +
5C ASN 3.5 24.2 - - - +
6C SER* 4.2 9.7 - - - +
7C ILE* 3.2 21.7 + - + +
10C TYR* 3.7 28.7 - - + -
15C PHE* 3.9 21.1 - - + -
18C LEU* 4.3 4.9 - - + -
40C HIS* 3.0 44.3 + - + +
41C PHE* 3.6 5.2 - - - +
43C LYS* 1.3 78.8 - - + +
45C THR* 1.3 72.2 + - + +
46C GLU* 3.5 9.4 - - - +
76C ARG* 3.6 2.4 + - - -
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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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7C ILE* 4.1 9.0 - - + -
15C PHE* 3.8 11.2 - - + -
41C PHE* 3.0 41.8 + - + +
42C VAL* 3.4 7.1 + - - -
44C ILE* 1.3 77.1 - - + +
46C GLU* 1.3 72.6 + - - +
47C HIS* 3.0 21.6 + - - +
50C GLY* 5.3 1.2 - - - -
72C ILE* 3.7 33.2 - - + -
75C TRP* 4.0 6.8 - - - -
76C ARG* 3.0 18.9 + - - +
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Residues in contact with GLU 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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42C VAL 3.2 11.3 + - - -
43C LYS 3.4 16.6 - - - +
44C ILE 3.5 5.5 - - - +
45C THR* 1.3 80.9 + - - +
47C HIS* 1.3 63.1 + - - +
48C PRO* 3.6 2.3 - - - +
75C TRP* 3.3 18.8 - - + -
76C ARG* 2.7 29.3 + - - +
81C LYS* 4.0 22.7 + - - +
82C PRO* 5.7 0.2 - - - +
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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