Contacts of the helix formed by residues 24 - 41 (chain D) in PDB entry 6X0A
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 24 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ILE 3.1 9.7 + - - +
21D ALA* 3.3 4.8 + - - -
23D ASP* 1.3 89.6 - - - +
25D PRO* 1.3 71.1 - - - +
26D ARG* 3.2 22.0 + - - +
27D ALA* 3.2 26.4 + - - +
28D ALA 3.2 8.7 + - - -
26F ARG* 4.1 19.6 + - - +
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Residues in contact with PRO 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TRP* 3.8 25.3 - - + -
21D ALA* 3.6 17.4 - - + +
23D ASP 4.6 1.3 - - - +
24D SER* 1.3 83.7 - - - +
26D ARG* 1.3 63.2 + - + +
28D ALA* 3.3 4.3 + - - +
29D ASP* 3.2 26.6 + - - -
26F ARG* 6.0 1.1 - - - +
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASN* 3.7 31.5 + - - +
24D SER* 3.1 10.1 + - - +
25D PRO* 1.3 81.5 - - + +
27D ALA* 1.3 65.5 + - - +
29D ASP* 3.1 16.5 + - - +
30D HIS* 3.1 36.5 + - + +
24F SER* 3.9 13.9 + - - -
26F ARG* 4.4 34.0 - - - +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ILE* 3.9 13.7 - - + +
23D ASP* 5.3 4.7 - - - +
24D SER* 3.2 21.6 + - - +
26D ARG* 1.3 81.2 - - - +
28D ALA* 1.3 63.0 + - - +
30D HIS* 3.2 18.2 + - - +
31D PHE* 3.2 13.7 + - - +
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Residues in contact with ALA 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TRP* 3.3 50.3 - - + +
20D ILE* 3.6 20.4 - - + +
21D ALA* 3.9 2.5 - - - +
24D SER 3.2 10.6 + - - +
25D PRO 3.5 5.2 - - - +
26D ARG 3.2 1.2 - - - -
27D ALA* 1.3 77.5 - - - +
29D ASP* 1.3 62.6 + - - +
31D PHE* 3.4 1.4 + - - +
32D LEU* 3.3 28.6 + - - +
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Residues in contact with ASP 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TRP* 2.8 26.3 + - - +
25D PRO 3.2 11.4 + - - +
26D ARG* 3.1 12.2 + - - +
28D ALA* 1.3 78.5 - - - +
30D HIS* 1.3 60.6 + - + +
32D LEU* 3.5 3.6 + - - +
33D ASP* 2.9 39.0 + - - +
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Residues in contact with HIS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C THR* 6.0 4.7 - - - -
65C GLY* 4.4 16.2 + - - -
66C ASN* 4.8 8.9 + - - -
26D ARG* 3.1 45.2 + - + +
27D ALA* 3.2 10.1 + - - +
29D ASP* 1.3 79.7 - - + +
31D PHE* 1.3 58.2 + - - +
33D ASP* 3.2 14.3 + - + +
34D ALA* 2.8 29.2 + - - +
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Residues in contact with PHE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.9 18.8 - - + -
20D ILE* 3.8 32.5 - - + -
27D ALA 3.2 8.0 + - - +
28D ALA 3.9 3.6 - - - +
29D ASP 3.3 0.4 - - - -
30D HIS* 1.3 78.1 - - - +
32D LEU* 1.3 60.2 + - + +
34D ALA* 3.0 10.2 + - + +
35D ILE* 2.9 63.2 + - + +
64D ILE* 4.4 33.4 - - + -
65D GLY* 5.3 5.6 - - - -
67D TYR* 4.7 19.5 - + + -
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.8 43.1 - - + +
14D VAL* 5.6 0.7 - - + -
16D ILE* 4.5 11.7 - - + -
17D TRP* 3.6 36.8 - - + +
20D ILE* 5.4 0.2 - - + -
28D ALA* 3.3 16.8 + - - +
29D ASP* 4.0 6.3 - - - +
31D PHE* 1.3 81.6 - - + +
33D ASP* 1.3 53.3 + - - +
35D ILE* 3.1 8.7 + - + +
36D ALA* 2.7 36.7 + - - +
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C THR* 5.9 3.1 - - - +
29D ASP* 2.9 26.1 + - - +
30D HIS* 3.2 20.3 + - + +
32D LEU* 1.3 76.8 - - - +
34D ALA* 1.3 62.7 + - - +
36D ALA* 3.2 8.1 + - - +
37D GLU* 3.1 24.4 + - - +
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D HIS 2.8 16.1 + - - +
31D PHE* 3.0 14.3 + - + +
33D ASP* 1.3 72.6 - - - +
35D ILE* 1.3 63.0 + - - +
37D GLU* 3.3 18.2 - - - +
38D ARG* 3.2 22.2 + - - +
64D ILE* 3.9 15.3 - - + +
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 4.0 32.1 - - + -
16D ILE* 5.0 2.0 - - + -
31D PHE* 2.9 47.7 + - + +
32D LEU* 3.5 11.4 - - + +
34D ALA* 1.3 72.7 - - - +
36D ALA* 1.3 62.1 + - - +
38D ARG* 3.2 4.2 + - - +
39D ILE* 2.9 48.0 + - + +
64D ILE* 3.7 26.5 - - + -
67D TYR* 6.3 0.2 - - + -
69D ILE* 4.0 13.2 - - + -
83D ILE* 4.8 9.9 - - + -
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Residues in contact with ALA 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU 2.7 20.9 + - - +
33D ASP* 3.5 9.0 - - - +
35D ILE* 1.3 73.1 - - - +
37D GLU* 1.3 65.8 + - - +
39D ILE* 3.0 9.8 + - - +
40D LEU* 2.9 35.4 + - + +
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 2.5 45.9 + - - -
41C GLN* 5.7 0.4 - - - -
48C SER* 4.1 33.1 - - - +
62C LEU* 4.3 0.2 - - - +
33D ASP 3.1 10.0 + - - +
34D ALA* 3.3 20.1 - - - +
36D ALA* 1.3 79.4 - - - +
38D ARG* 1.3 68.0 + - + +
40D LEU* 3.3 14.1 + - - +
41D GLN* 3.1 34.6 + - - +
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Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA 3.4 14.4 - - - +
35D ILE* 3.2 8.0 + - - +
36D ALA 3.0 0.6 - - - -
37D GLU* 1.3 81.5 - - + +
39D ILE* 1.3 65.9 + - - +
41D GLN* 3.5 35.3 + - - +
42D LEU 4.1 0.7 + - - -
62D LEU* 4.0 34.1 - - + +
63D THR* 3.0 39.1 + - - +
64D ILE* 4.0 19.6 - - + +
69D ILE* 4.1 16.6 - - + -
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Residues in contact with ILE 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 3.6 22.3 - - + +
13D LEU* 5.3 7.6 - - + -
35D ILE* 2.9 38.3 + - + +
36D ALA* 3.6 6.5 - - - +
38D ARG* 1.3 78.6 - - - +
40D LEU* 1.3 62.1 + - + +
42D LEU* 3.1 27.5 + - + +
62D LEU* 5.2 0.2 - - - -
69D ILE* 3.8 30.7 - - + -
80D ILE* 3.8 37.9 - - + -
83D ILE* 5.2 3.4 - - + -
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Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU 5.7 6.1 - - - +
48C SER 5.9 2.7 - - - +
50C PRO* 6.3 4.3 - - + -
3D ILE* 3.9 19.7 - - + -
36D ALA* 2.9 31.1 + - + +
37D GLU* 3.3 10.3 + - - +
39D ILE* 1.3 75.3 - - + +
41D GLN* 1.3 63.6 + - - +
42D LEU 3.1 1.1 + - - -
43D ALA* 3.3 20.6 + - + +
44D ALA* 4.4 1.0 + - - +
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Residues in contact with GLN 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLN* 5.5 4.4 + - - -
45C PHE* 3.1 61.5 - - + +
48C SER* 4.0 12.0 + - - +
37D GLU* 3.1 25.4 + - - +
38D ARG* 3.5 32.8 + - - +
39D ILE 3.2 0.6 - - - -
40D LEU* 1.3 75.4 - - - +
42D LEU* 1.3 59.9 + - + +
43D ALA 3.1 0.2 - - - -
44D ALA* 3.1 10.1 + - - +
45D PHE* 3.0 25.9 + - - +
48D SER* 5.5 2.9 - - - +
62D LEU* 6.3 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