Contacts of the helix formed by residues 37 - 50 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A THR* 4.0 13.7 - - - -
8A ASN 5.1 3.6 - - - -
9A PRO* 4.8 2.2 - - - -
10A SER* 4.3 2.3 + - - -
12A ASP* 4.6 1.4 + - - -
36A GLY* 1.3 74.7 - - - -
38A LYS* 1.3 65.6 + - - -
39A GLY 3.3 2.5 - - - -
40A LEU* 3.0 13.0 + - - +
41A ASN* 3.0 20.1 + - - +
44A ARG* 4.9 0.6 - - - +
88A ARG* 6.2 0.7 - - - -
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Residues in contact with LYS 38 (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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6A THR* 4.9 0.4 - - - +
37A GLY* 1.3 69.8 - - - -
39A GLY* 1.3 61.5 + - - +
41A ASN* 3.2 9.2 + - - +
42A VAL* 3.1 23.9 + - - +
134A SER* 3.6 18.4 - - - -
135A GLY* 4.3 22.2 - - - +
163A ASP* 5.2 6.5 - - - +
254A ASP* 3.4 31.6 + - - +
1311A MG 4.0 1.4 - - - -
1312A ANP 3.1 31.2 + - - -
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Residues in contact with GLY 39 (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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4A THR* 3.9 6.7 + - - -
5A LEU 3.9 8.7 + - - -
6A THR* 3.2 21.0 + - - +
37A GLY 3.3 0.6 - - - -
38A LYS* 1.3 78.0 - - - +
40A LEU* 1.3 52.7 + - - +
42A VAL* 3.5 6.2 + - - +
43A THR* 2.6 36.4 + - - -
132A ALA 5.8 0.7 - - - -
134A SER* 3.6 19.2 + - - -
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Residues in contact with LEU 40 (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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6A THR* 3.3 16.5 + - + +
9A PRO* 4.2 9.9 - - + -
35A ALA* 4.2 13.7 - - + +
36A GLY 3.4 24.0 - - - +
37A GLY 3.0 8.3 + - - +
39A GLY* 1.3 76.7 - - - +
41A ASN* 1.3 60.1 + - - +
43A THR* 3.4 11.2 + - - +
44A ARG* 2.9 49.4 + - - +
55A ALA* 4.4 5.4 - - + -
67A ILE* 4.2 20.9 - - + -
71A LEU* 4.1 29.1 - - + +
80A PHE* 4.2 12.3 - - + -
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Residues in contact with ASN 41 (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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36A GLY* 5.9 0.2 - - - -
37A GLY 3.0 18.0 + - - +
38A LYS* 3.4 10.1 - - - +
40A LEU* 1.3 72.7 - - - +
42A VAL* 1.3 64.9 + - - +
44A ARG* 3.0 26.5 + - - +
45A VAL* 3.1 30.2 + - - +
251A GLY* 4.6 0.8 - - - -
254A ASP* 3.0 30.4 + - + +
290A THR* 3.8 37.0 - - - +
291A GLY* 4.4 9.6 - - - +
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Residues in contact with VAL 42 (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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4A THR* 4.0 11.0 - - + -
38A LYS 3.1 12.9 + - - +
39A GLY* 3.5 9.2 - - - +
40A LEU 3.3 0.2 - - - -
41A ASN* 1.3 77.3 - - - +
43A THR* 1.3 65.2 + - - +
45A VAL* 3.3 1.8 + - - +
46A LEU* 3.0 40.6 + - + +
132A ALA* 4.3 14.8 - - + -
134A SER* 3.7 17.7 - - - +
254A ASP* 3.4 32.3 - - + +
257A VAL* 3.9 10.1 - - + -
258A ALA* 3.8 16.4 - - - +
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Residues in contact with THR 43 (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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4A THR* 2.7 24.6 + - - -
39A GLY 2.6 22.0 + - - -
40A LEU* 3.4 13.5 - - - +
41A ASN 3.3 0.2 - - - -
42A VAL* 1.3 76.7 - - - +
44A ARG* 1.3 57.1 + - - +
46A LEU* 3.3 6.9 + - - +
47A ALA* 3.0 26.9 + - - +
53A VAL* 4.2 14.6 - - + +
55A ALA* 4.1 16.4 - - + +
71A LEU* 5.2 3.1 - - + -
76A ILE* 3.5 34.1 - - + -
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Residues in contact with ARG 44 (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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34A THR* 6.0 1.1 - - - -
35A ALA* 2.9 43.6 + - - +
36A GLY* 4.7 1.2 - - - -
37A GLY 4.4 1.2 + - - -
40A LEU* 2.9 25.4 + - - +
41A ASN* 3.0 39.4 + - - +
43A THR* 1.3 75.6 - - - +
45A VAL* 1.3 57.8 + - - +
47A ALA* 3.4 3.5 + - - +
48A GLN* 3.1 31.9 + - + +
70A LYS* 6.0 0.8 - - - +
71A LEU* 4.9 10.3 - - + +
74A ALA* 5.9 2.2 - - + -
76A ILE* 4.1 22.9 - - + -
290A THR 5.0 3.4 + - - -
291A GLY 4.3 13.7 + - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A ASN 3.1 17.7 + - - +
42A VAL 3.8 3.6 - - - +
44A ARG* 1.3 73.0 - - - +
46A LEU* 1.3 59.0 + - - +
48A GLN* 3.2 10.5 + - - +
49A VAL* 2.9 28.6 + - - +
255A SER* 3.7 21.5 - - - +
258A ALA* 3.6 20.4 - - + -
280A LEU* 4.0 19.5 - - + -
291A GLY* 3.5 29.2 - - - +
292A TYR* 4.0 4.5 - - - +
293A VAL* 4.4 17.0 - - + -
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Residues in contact with LEU 46 (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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2A ILE* 3.9 38.1 - - + -
4A THR* 4.0 2.9 - - + -
42A VAL* 3.0 33.9 + - + +
43A THR 3.5 7.4 - - - +
45A VAL* 1.3 74.2 - - - +
47A ALA* 1.3 58.4 + - - +
49A VAL* 3.3 7.3 + - + +
50A GLY 3.0 23.0 + - - -
51A GLU* 3.1 27.1 + - + -
53A VAL* 3.8 29.4 - - + -
258A ALA* 3.3 33.2 - - + +
261A THR* 4.7 2.7 - - - -
262A SER* 4.2 3.1 - - - +
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Residues in contact with ALA 47 (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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43A THR 3.0 14.0 + - - +
44A ARG 3.6 9.0 - - - +
46A LEU* 1.3 76.2 - - - +
48A GLN* 1.3 61.4 + - - +
50A GLY* 3.2 13.7 + - - -
51A GLU 4.6 2.9 - - - -
53A VAL* 4.4 11.6 - - + +
74A ALA 5.8 0.9 - - - +
76A ILE* 4.0 28.0 - - + -
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Residues in contact with GLN 48 (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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44A ARG 3.1 17.4 + - - +
45A VAL* 3.2 11.6 + - - +
47A ALA* 1.3 73.8 - - + +
49A VAL* 1.3 63.5 - - - +
50A GLY* 3.3 0.5 + - - -
291A GLY 4.5 1.0 - - - +
292A TYR* 3.4 34.7 + - - -
293A VAL* 2.9 54.2 + - + +
295A LEU* 3.3 19.3 - - + +
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Residues in contact with VAL 49 (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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45A VAL* 2.9 17.6 + - + +
46A LEU* 3.6 11.7 - - + +
48A GLN* 1.3 75.1 - - - +
50A GLY* 1.3 57.2 + - - +
51A GLU* 3.7 24.5 - - + +
262A SER* 4.1 13.2 - - - +
276A LYS* 5.0 7.2 - - + +
280A LEU* 3.8 37.0 - - + -
293A VAL* 5.2 1.3 - - + -
295A LEU* 4.1 14.7 - - + +
298A TYR* 6.1 1.1 - - + -
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Residues in contact with GLY 50 (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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46A LEU 3.0 3.4 + - - -
47A ALA 3.2 10.0 + - - -
48A GLN 3.1 4.9 - - - -
49A VAL* 1.3 79.8 - - - +
51A GLU* 1.3 68.1 + - - +
52A PRO* 3.8 4.2 - - - +
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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