Contacts of the helix formed by residues 39 - 53 (chain B) in PDB entry 3JSP
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 SER 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA* 3.9 5.6 - - - +
37B PHE* 3.3 7.2 - - - +
38B ARG* 1.3 82.1 - - - +
40B PRO* 1.3 67.1 - - - +
41B ASN* 3.3 16.8 + - - +
42B ALA* 3.2 18.2 + - - +
43B ALA 4.1 0.2 + - - -
6D T 3.3 27.4 + - - -
7D G 2.7 35.3 + - - -
8D T 4.4 1.8 - - - +
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Residues in contact with PRO 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.9 20.7 - - + +
29B ALA* 4.4 20.0 - - + +
32B ALA* 4.3 12.3 - - + -
38B ARG 4.2 4.0 - - - +
39B SER* 1.3 84.5 - - - +
41B ASN* 1.3 56.3 + - - +
43B ALA* 3.1 9.5 + - + +
44B GLU* 3.1 22.0 + - - +
15C A 5.8 2.2 - - - +
16C T 4.6 16.8 - - + +
8D T 4.8 14.1 - - + +
9D A 6.0 2.0 - - - +
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER* 3.1 8.4 + - - +
40B PRO* 1.3 76.0 - - - +
42B ALA* 1.3 63.0 + - - +
44B GLU* 3.5 18.1 - - - +
45B GLU* 3.1 40.5 + - - +
16C T 4.8 4.0 + - - +
17C A 4.2 11.5 + - - +
18C C 2.8 26.0 + - - +
19C A 3.0 15.0 - - - +
5D C 4.9 0.4 - - - -
6D T 3.5 5.0 + - - +
7D G 2.5 31.0 + - + +
8D T 4.6 1.9 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.7 24.7 - - + -
39B SER 3.2 14.4 + - - +
40B PRO 3.2 0.2 - - - -
41B ASN* 1.3 77.4 - - - +
43B ALA* 1.3 61.9 + - - +
45B GLU* 4.2 1.3 - - - +
46B HIS* 3.0 31.9 + - - +
5D C 3.8 24.2 - - - -
6D T 3.7 23.1 - - + +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.6 30.7 - - + +
31B ILE* 3.9 24.0 - - + -
32B ALA 4.5 3.8 - - - +
37B PHE* 4.2 7.0 - - + -
39B SER 4.1 0.8 + - - -
40B PRO* 3.1 13.2 + - + +
42B ALA* 1.3 75.8 - - - +
44B GLU* 1.3 54.3 + - - +
46B HIS* 3.1 6.7 + - - +
47B LEU* 2.8 40.9 + - - +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.5 23.8 + - - +
40B PRO 3.1 8.4 + - - +
41B ASN* 3.2 29.4 + - - +
43B ALA* 1.3 73.9 - - - +
45B GLU* 1.3 60.3 + - + +
47B LEU* 3.1 7.8 + - - +
48B LYS* 2.8 63.5 + - + +
58B ILE* 5.3 3.3 - - - +
16C T 3.2 59.9 + - + +
17C A 5.1 1.8 - - + +
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASN* 3.1 35.3 + - - +
42B ALA 4.5 1.3 - - - +
44B GLU* 1.3 77.7 - - + +
46B HIS* 1.3 66.9 - - - +
47B LEU 3.1 1.3 - - - -
48B LYS* 3.9 19.9 + - + +
49B ALA* 3.1 24.9 + - - +
52B ARG* 4.8 1.9 + - - -
18C C 4.5 4.7 + - - -
19C A 4.8 0.7 + - - -
3D T 6.1 0.5 - - - +
4D A 4.8 3.3 - - + +
5D C 2.6 38.8 + - + -
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ARG* 3.3 39.0 - - + +
8B GLN* 4.2 14.7 - - + +
11B VAL* 3.7 31.8 - - + +
37B PHE* 4.9 6.0 - + - -
42B ALA* 3.0 27.8 + - + +
43B ALA* 3.1 7.3 + - - +
45B GLU* 1.3 78.2 - - - +
47B LEU* 1.3 57.8 + - - +
49B ALA* 4.1 5.1 - - - +
50B LEU* 3.1 29.1 + - - +
3D T 6.0 0.2 - - - -
4D A 3.5 41.8 + + + +
5D C 3.6 12.2 - - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 4.2 10.1 - - + -
15B ILE* 3.8 25.1 - - + -
28B ARG* 3.7 45.3 - - + +
31B ILE* 3.9 17.0 - - + -
43B ALA 2.8 15.7 + - - +
44B GLU* 3.3 6.1 - - - +
46B HIS* 1.3 75.6 - - - +
48B LYS* 1.3 66.2 + - - +
49B ALA 3.1 2.0 - - - -
50B LEU* 2.9 17.0 + - + +
51B ALA* 3.0 10.9 + - - +
56B ILE* 3.7 23.3 - - + +
58B ILE* 3.9 11.7 - - + -
66B ILE* 4.0 12.1 - - + -
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLU* 2.8 49.0 + - + +
45B GLU* 3.9 19.4 + - + +
47B LEU* 1.3 73.0 - - - +
49B ALA* 1.3 62.6 + - - +
51B ALA* 3.4 5.1 + - - +
52B ARG* 3.2 39.1 + - - +
58B ILE* 4.1 12.3 - - + +
16C T 5.2 0.7 - - - -
17C A 2.8 32.0 + - - -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 3.6 28.5 - - - +
45B GLU 3.1 17.3 + - - +
46B HIS 4.1 2.9 - - - +
48B LYS* 1.3 75.1 - - - +
50B LEU* 1.3 59.4 + - - +
52B ARG* 3.0 29.3 + - - +
53B LYS* 2.9 34.9 + - - +
3D T 4.4 8.1 - - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 3.6 28.5 - - + -
8B GLN* 3.7 24.0 - - + +
11B VAL* 3.8 25.1 - - + -
12B PHE* 4.2 15.5 - - + +
15B ILE* 4.3 5.8 - - + -
46B HIS 3.1 22.2 + - - +
47B LEU* 2.9 19.5 + - + +
49B ALA* 1.3 77.2 - - - +
51B ALA* 1.3 57.3 + - - +
53B LYS* 3.6 4.1 + - - +
54B GLY 3.1 6.4 + - - -
55B VAL* 3.0 43.0 + - + +
56B ILE* 3.6 12.7 + - + -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU 3.0 10.9 + - - +
48B LYS* 3.4 10.5 - - - +
50B LEU* 1.3 78.9 - - - +
52B ARG* 1.3 57.8 + - + +
54B GLY* 3.2 16.3 + - - -
56B ILE* 3.5 21.4 - - + +
58B ILE* 4.0 24.2 - - + +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 3.6 20.3 + - - +
45B GLU 4.8 2.2 + - - -
48B LYS* 3.2 21.6 + - - +
49B ALA* 3.0 30.0 + - - +
51B ALA* 1.3 74.7 - - + +
53B LYS* 1.3 60.0 + - + +
54B GLY* 3.0 9.9 + - - -
2D A 4.9 12.4 + - - -
3D T 2.6 29.6 + - - -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 4.1 40.9 - - + +
3B ALA 2.8 36.1 + - - +
4B LEU* 4.2 14.4 - - + -
5B THR* 3.8 10.9 - - - +
8B GLN* 2.9 31.8 + - - +
49B ALA* 2.9 18.5 + - - +
50B LEU 4.2 3.8 - - - +
52B ARG* 1.3 76.3 - - + +
54B GLY* 1.3 61.8 + - - +
55B VAL* 3.4 10.4 + - + +
3D T 4.1 16.5 + - - -
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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