Contacts of the helix formed by residues 37 - 50 (chain C) in PDB entry 2JG1
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 GLY 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C THR* 4.2 3.4 - - - -
8C ASN 4.3 10.8 - - - -
10C SER* 3.6 14.2 + - - -
12C ASP* 3.1 12.1 + - - -
36C GLY* 1.3 78.1 - - - +
38C LYS* 1.3 67.3 + - - +
39C GLY 3.4 2.2 - - - -
40C LEU 3.2 7.2 + - - -
41C ASN* 3.4 8.8 + - - -
88C ARG* 4.4 2.9 - - - -
1312C TA6 3.4 18.5 + - - -
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Residues in contact with LYS 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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6C THR* 4.3 2.8 - - - +
37C GLY* 1.3 71.9 - - - -
39C GLY* 1.3 61.3 + - - +
41C ASN 3.2 2.9 + - - -
42C VAL* 3.1 23.6 + - - +
101C GLU* 5.8 0.2 + - - -
103C LEU* 5.9 0.6 - - - +
134C SER* 3.6 18.9 + - - -
135C GLY* 3.8 20.2 - - - +
163C ASP* 4.3 15.9 - - - +
164C CYS* 6.1 1.8 - - - +
165C SER* 6.0 1.1 - - - -
188C GLU* 4.7 10.2 + - - -
254C ASP* 3.3 28.6 - - - +
1311C MG 3.8 7.1 - - - -
1312C TA6 2.8 72.1 + - - +
1313C ANP 3.2 13.9 + - - -
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Residues in contact with GLY 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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4C THR* 3.9 6.5 + - - -
5C LEU 4.3 5.8 - - - -
6C THR* 3.0 21.7 + - - +
37C GLY 3.4 0.6 - - - -
38C LYS* 1.3 78.6 - - - +
40C LEU* 1.3 50.4 + - - +
42C VAL* 3.5 9.2 - - - +
43C THR* 2.7 35.0 + - - -
132C ALA 5.7 0.9 - - - -
134C SER* 3.5 21.5 + - - -
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Residues in contact with LEU 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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6C THR* 3.2 15.1 + - - +
9C PRO* 4.1 13.0 - - + -
35C ALA* 3.6 16.6 - - + +
36C GLY 3.4 28.9 - - - +
37C GLY 3.2 1.8 + - - -
38C LYS 3.2 0.6 - - - -
39C GLY* 1.3 74.5 - - - +
41C ASN* 1.3 61.0 + - - +
42C VAL 3.3 0.4 - - - -
43C THR* 3.7 17.8 - - - +
44C ARG* 3.0 34.5 + - - +
55C ALA* 3.9 20.2 - - + -
56C SER 5.7 0.4 - - - +
67C ILE* 3.6 31.9 - - + -
71C LEU* 4.2 14.1 - - + -
80C PHE* 4.2 9.0 - - + -
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Residues in contact with ASN 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 ASP* 4.1 1.7 + - - +
34C THR* 4.9 0.2 + - - -
36C GLY* 4.0 7.9 - - - -
37C GLY 3.4 6.6 + - - -
38C LYS 3.2 1.5 + - - +
40C LEU* 1.3 77.5 - - - +
42C VAL* 1.3 62.1 + - - +
44C ARG* 2.9 28.8 + - - +
45C VAL* 3.2 29.5 + - - +
251C GLY* 4.2 2.2 - - - +
254C ASP* 2.9 28.5 + - + +
290C THR* 3.8 25.7 - - - +
291C GLY* 4.3 11.1 - - - +
1312C TA6 2.8 30.3 + - - -
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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
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4C THR* 4.2 9.4 - - + -
38C LYS 3.1 15.8 + - - +
39C GLY* 3.5 9.2 - - - +
40C LEU 3.3 0.2 - - - -
41C ASN* 1.3 77.1 - - - +
43C THR* 1.3 56.9 + - - +
45C VAL 3.5 0.2 + - - -
46C LEU* 3.0 45.3 + - + +
132C ALA* 4.4 8.1 - - + -
134C SER* 3.7 20.0 - - - +
254C ASP* 3.5 27.3 - - + +
257C VAL* 3.8 14.8 - - + +
258C ALA* 3.6 18.4 - - - +
261C THR* 5.0 0.2 - - - +
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Residues in contact with THR 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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4C THR* 2.6 30.6 + - - -
39C GLY 2.7 18.6 + - - -
40C LEU* 3.7 16.8 - - + +
41C ASN 3.4 0.2 - - - -
42C VAL* 1.3 75.4 - - - +
44C ARG* 1.3 58.5 - - - +
46C LEU* 3.4 5.7 + - - +
47C ALA* 2.9 27.7 + - - +
53C VAL* 4.1 15.7 - - + +
55C ALA* 4.0 14.1 - - + +
71C LEU* 5.1 1.3 - - + -
76C ILE* 3.7 30.1 - - + -
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Residues in contact with ARG 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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34C THR* 3.7 14.9 - - - +
35C ALA* 2.9 30.3 + - - +
40C LEU 3.0 15.6 + - - +
41C ASN* 2.9 30.3 + - - +
42C VAL 3.4 0.4 - - - -
43C THR* 1.3 77.2 - - - +
45C VAL* 1.3 61.7 + - - +
47C ALA* 3.5 4.0 + - - +
48C GLN* 3.1 27.5 + - - +
70C LYS* 5.7 4.0 - - - -
71C LEU* 4.1 16.2 - - + -
74C ALA* 6.3 1.1 - - - -
76C ILE* 3.9 24.0 - - + +
289C GLN* 3.4 22.6 + - - -
290C THR 2.9 16.0 + - - -
291C GLY 3.0 22.9 + - - +
292C TYR* 5.0 1.6 - - - +
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Residues in contact with VAL 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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41C ASN 3.2 18.4 + - - +
42C VAL 4.0 2.2 - - - +
44C ARG* 1.3 74.1 - - - +
46C LEU* 1.3 59.0 + - - +
48C GLN* 3.1 11.1 + - - +
49C VAL* 2.8 30.8 + - + +
255C SER* 3.6 27.4 - - - +
258C ALA* 3.8 18.6 - - + -
280C LEU* 4.1 18.8 - - + -
291C GLY 3.7 21.3 - - - +
292C TYR 4.1 2.0 - - - +
293C VAL* 4.3 21.8 - - + -
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Residues in contact with LEU 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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2C ILE* 3.8 39.0 - - + -
4C THR* 4.0 2.5 - - + -
42C VAL* 3.0 36.6 + - + +
43C THR 3.6 4.5 - - - +
45C VAL* 1.3 77.3 - - - +
47C ALA* 1.3 50.9 + - - +
49C VAL* 3.2 7.9 + - + +
50C GLY 2.8 30.0 + - - -
51C GLU* 3.1 27.6 + - + -
53C VAL* 3.9 28.9 - - + -
258C ALA* 3.5 31.6 - - + +
261C THR* 4.9 2.7 - - - -
262C SER* 4.3 2.9 - - - +
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Residues in contact with ALA 47 (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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43C THR 2.9 17.2 + - - +
44C ARG 3.5 6.1 - - - +
45C VAL 3.3 0.2 - - - -
46C LEU* 1.3 75.6 - - - +
48C GLN* 1.3 62.1 + - - +
50C GLY* 3.3 12.5 + - - +
51C GLU 4.5 7.9 - - - -
53C VAL* 4.3 7.3 - - + +
74C ALA 5.9 0.4 - - - +
76C ILE* 3.8 28.7 - - + -
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Residues in contact with GLN 48 (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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44C ARG 3.1 17.4 + - - +
45C VAL* 3.1 13.4 + - - +
47C ALA* 1.3 72.6 - - - +
49C VAL* 1.3 66.0 + - - +
50C GLY* 3.3 1.6 + - - -
291C GLY 4.3 1.4 - - - +
292C TYR* 3.3 35.4 + - + -
293C VAL* 2.9 55.7 + - + +
295C LEU* 3.3 20.1 - - + +
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Residues in contact with VAL 49 (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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45C VAL* 2.8 19.3 + - + +
46C LEU* 3.4 12.6 - - + +
48C GLN* 1.3 76.6 - - + +
50C GLY* 1.3 57.1 + - - +
51C GLU* 3.8 23.6 - - + +
262C SER* 4.2 13.7 - - - +
276C LYS* 5.3 7.4 - - - +
280C LEU* 3.9 37.7 - - + -
293C VAL* 5.4 0.2 - - + -
295C LEU* 4.2 14.3 - - + +
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Residues in contact with GLY 50 (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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46C LEU 2.8 4.4 + - - -
47C ALA 3.3 11.2 + - - -
48C GLN 3.2 3.9 - - - -
49C VAL* 1.3 80.1 - - - +
51C GLU* 1.3 65.5 + - - +
52C PRO* 3.9 4.0 - - - +
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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