Contacts of the helix formed by residues 35 - 53 (chain c) in PDB entry 3J7Y
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 PHE 35 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2275A U 3.3 5.0 + - - +
2284A C 3.4 60.1 - + - -
34c GLY* 1.3 74.8 - - - +
36c ARG* 1.3 71.1 + - + +
37c ALA* 3.2 3.9 - - - +
38c ALA* 3.2 13.5 + - - +
39c PHE* 2.9 31.6 + + + +
38i LEU* 5.1 13.6 - - + +
39i PRO* 3.5 33.0 - - + -
40i PRO 5.8 1.6 - - - -
41i PRO* 5.9 5.6 - - + -
42i LYS* 6.1 3.6 - - + -
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Residues in contact with ARG 36 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2273A A 5.7 0.2 + - - -
2274A A 3.6 37.8 + - - +
2275A U 3.3 29.6 + - - +
2284A C 3.3 34.1 + - - +
2285A U 4.5 27.9 + - - +
2286A A 4.3 24.0 + - - -
16R ASP* 5.1 0.4 - - - -
35c PHE* 1.3 80.5 - - + +
37c ALA* 1.3 58.6 + - - +
39c PHE* 3.2 6.0 + - - +
40c ARG* 2.9 32.1 + - - +
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Residues in contact with ALA 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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2274A A 5.0 1.4 + - - +
2275A U 4.4 0.8 + - - -
15R THR* 3.3 48.7 - - - +
16R ASP* 3.6 24.1 + - + +
35c PHE 3.2 2.8 - - - +
36c ARG* 1.3 79.5 - - - +
38c ALA* 1.3 56.9 + - - +
40c ARG* 3.2 4.8 + - - +
41c PHE 2.9 24.6 + - - -
34i ILE* 3.7 14.5 - - + +
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Residues in contact with ALA 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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35c PHE* 3.2 15.2 + - - +
37c ALA* 1.3 79.0 - - - +
39c PHE* 1.3 56.3 + - - +
41c PHE* 3.2 8.9 + - - +
42c GLN* 2.9 33.9 + - + +
34i ILE* 4.8 4.2 - - - +
35i ARG* 4.2 38.8 - - + +
37i THR 5.7 0.2 - - - -
38i LEU* 4.5 17.7 - - + +
39i PRO* 4.5 0.7 - - + -
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Residues in contact with PHE 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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2283A C 4.0 35.7 - + - -
2284A C 3.6 46.9 - + + +
35c PHE* 2.9 20.1 + + + +
36c ARG* 3.4 12.3 - - - +
38c ALA* 1.3 75.1 - - - +
40c ARG* 1.3 62.0 + - + +
42c GLN* 3.2 10.9 + - + +
43c LYS* 2.9 68.2 + - + +
46c GLU* 6.2 0.4 - - - -
38i LEU* 4.7 19.4 - - + +
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Residues in contact with ARG 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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2273A A 5.4 5.3 + - - -
2274A A 5.4 6.3 + - - -
16R ASP* 3.6 28.4 + - - +
19R PHE* 3.3 42.6 - - + +
36c ARG 2.9 14.1 + - - +
37c ALA 3.3 7.6 - - - +
39c PHE* 1.3 84.0 - - + +
41c PHE* 1.3 57.4 + - - +
43c LYS* 3.2 10.1 + - + +
44c GLU* 2.9 31.5 + - - +
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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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1813A C 4.1 23.1 - + - -
18R TYR* 3.8 34.1 - + - -
19R PHE* 3.7 4.3 - - - -
37c ALA 2.9 5.9 + - - -
38c ALA 3.5 8.5 - - - +
40c ARG* 1.3 76.7 - - - +
42c GLN* 1.3 58.3 + - - +
44c GLU* 3.2 7.7 + - + +
45c LEU* 2.9 61.2 + - + +
34i ILE* 3.4 50.9 - - + -
35i ARG 3.3 19.7 - - - +
36i LEU* 3.4 26.5 - - + -
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Residues in contact with GLN 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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1811A A 5.7 5.3 - - - +
38c ALA 2.9 15.4 + - - +
39c PHE* 3.4 13.9 - - + +
41c PHE* 1.3 77.8 - - + +
43c LYS* 1.3 56.3 + - - +
45c LEU* 3.2 15.7 + - + +
46c GLU* 2.9 46.7 + - - +
49c ARG* 4.2 5.3 + - - +
35i ARG 5.7 0.4 - - - +
36i LEU 2.8 28.9 + - - +
37i THR* 4.5 1.8 - - - +
38i LEU* 3.7 42.3 - - + +
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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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2283A C 5.4 2.2 - - - -
2284A C 3.7 8.2 + - - -
74b ARG* 3.7 28.7 - - - +
39c PHE* 2.9 45.5 + - + +
40c ARG* 3.2 13.0 + - + +
42c GLN* 1.3 76.5 - - - +
44c GLU* 1.3 56.9 - - + +
46c GLU* 3.2 19.0 + - - +
47c ARG* 2.9 47.1 + - - +
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Residues in contact with GLU 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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18R TYR* 3.1 29.2 + - - -
19R PHE* 2.7 35.9 - - + -
22R GLN* 4.9 9.0 - - - +
40c ARG 2.9 14.0 + - - +
41c PHE* 3.4 13.3 - - + +
43c LYS* 1.3 75.5 - - - +
45c LEU* 1.3 59.4 + - + +
47c ARG* 3.2 15.7 + - - +
48c GLN* 2.9 41.7 + - - +
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Residues in contact with LEU 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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1811A A 5.4 0.4 - - - +
1812A C 3.2 37.5 + - + +
1813A C 5.0 5.2 - - + +
41c PHE* 2.9 55.6 + - + +
42c GLN* 3.4 15.7 - - + +
44c GLU* 1.3 77.0 - - + +
46c GLU* 1.3 57.9 + - - +
48c GLN* 3.2 20.7 + - - +
49c ARG* 2.9 54.9 + - - +
36i LEU* 4.1 14.4 - - + +
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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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39c PHE* 6.2 0.3 - - - -
42c GLN* 2.9 36.5 + - - +
43c LYS* 3.4 18.4 + - - +
45c LEU* 1.3 76.5 - - - +
47c ARG* 1.3 57.2 + - + +
49c ARG* 3.2 28.9 + - - +
50c LEU* 2.9 38.2 + - + +
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Residues in contact with ARG 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 LYS* 2.9 30.6 + - - +
44c GLU* 3.3 18.0 - - - +
46c GLU* 1.3 76.5 - - + +
48c GLN* 1.3 57.6 + - + +
50c LEU* 3.2 16.0 + - + +
51c LEU* 2.9 39.9 + - + +
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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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1812A C 2.7 33.5 + - - +
1813A C 4.5 14.1 - - - +
18R TYR* 4.7 12.1 + - - -
22R GLN* 5.9 2.2 - - - +
44c GLU* 2.9 24.8 + - + +
45c LEU* 3.2 19.0 + - - +
47c ARG* 1.3 77.0 - - + +
49c ARG* 1.3 57.9 + - - +
51c LEU* 3.2 16.0 + - + +
52c ARG* 2.9 30.4 + - - +
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Residues in contact with ARG 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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1810A A 5.4 2.7 - - - +
1811A A 3.0 54.4 + - + +
1812A C 3.1 27.1 + - - +
42c GLN* 4.2 7.5 + - - +
45c LEU* 2.9 34.5 + - - +
46c GLU* 3.2 41.8 + - - +
48c GLN* 1.3 76.4 - - + +
50c LEU* 1.3 59.5 + - + +
52c ARG* 3.2 11.3 + - - +
53c CYS* 2.9 43.9 + - - -
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Residues in contact with LEU 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 GLU* 2.9 22.4 + - + +
47c ARG* 3.4 17.5 - - + +
49c ARG* 1.3 78.0 - - + +
51c LEU* 1.3 62.6 + - + +
53c CYS 4.7 4.5 - - - +
54c PRO* 3.3 29.3 - - - +
55c PRO* 5.1 15.2 - - + +
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Residues in contact with LEU 51 (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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47c ARG* 2.9 24.4 + - + +
48c GLN* 3.2 19.0 + - + +
50c LEU* 1.3 77.8 - - + +
52c ARG* 1.3 64.4 + - - +
54c PRO* 3.9 6.9 - - - +
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Residues in contact with ARG 52 (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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1671A G 5.5 6.3 + - - -
1811A A 4.2 7.7 + - - -
1812A C 3.4 42.7 + - - -
48c GLN 2.9 13.4 + - - +
49c ARG* 3.5 14.3 - - - +
51c LEU* 1.3 78.6 - - - +
53c CYS* 1.3 66.8 + - + +
54c PRO* 3.2 9.5 - - - +
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Residues in contact with CYS 53 (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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49c ARG* 2.9 31.2 + - - +
50c LEU* 3.7 6.5 - - - +
52c ARG* 1.3 83.2 - - + +
54c PRO* 1.4 66.4 - - - +
55c PRO* 3.9 1.0 - - - +
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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
------------------------------------------------------------
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