Contacts of the helix formed by residues 2 - 20 (chain D) in PDB entry 6XXD
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 THR 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D PHE* 1.3 86.7 - - - +
3D LEU* 1.3 63.0 + - - +
4D ILE* 3.2 13.6 - - - +
5D GLU* 3.0 28.9 + - - +
6D LEU* 3.4 14.7 + - - +
1E PHE* 3.6 14.6 - - + -
5E GLU* 3.6 6.3 - - - -
9E VAL* 3.9 2.3 - - - +
20G LEU* 3.3 46.1 + - + +
21G ILE* 3.8 13.0 - - + -
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Residues in contact with LEU 3 (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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2D THR* 1.3 72.4 - - - +
4D ILE* 1.3 55.0 + - - +
6D LEU* 3.2 14.1 + - + +
7D LEU* 2.7 42.0 + - + +
5E GLU* 2.9 26.0 + - + +
8E ILE* 4.2 15.7 - - + -
9E VAL* 3.6 20.0 - - + -
12E ILE* 5.8 2.5 - - + -
22H PRO* 4.3 17.9 - - + -
23H ASN 5.2 1.6 - - - +
27H ALA* 4.4 25.1 - - + -
45J LYS* 4.0 31.2 - - + +
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Residues in contact with ILE 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D THR* 3.2 17.5 - - - +
3D LEU* 1.3 79.8 - - - +
5D GLU* 1.3 58.4 + - - +
7D LEU* 4.0 9.4 - - + -
8D ILE* 3.0 28.5 + - - +
21G ILE* 4.0 19.7 - - + -
22G PRO* 3.9 14.8 - - + -
24G LEU* 4.0 15.9 - - + -
41J ASN* 5.0 4.0 - - - +
44J VAL* 4.0 15.3 - - + +
45J LYS* 3.8 38.6 - - + +
48J GLU* 3.7 30.1 - - + -
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Residues in contact with GLU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C PHE 4.3 0.2 - - - +
2C THR* 3.6 6.7 - - - +
3C LEU* 2.9 42.2 + - + +
1D PHE* 3.2 40.7 - - - -
2D THR* 3.0 24.4 + - - +
4D ILE* 1.3 76.0 - - - +
6D LEU* 1.3 60.0 + - - +
8D ILE* 3.4 10.8 - - - +
9D VAL* 3.1 18.9 - - - +
20G LEU 5.1 1.3 - - - +
22G PRO* 3.9 20.9 - - + -
41I ASN* 5.9 0.6 + - - -
45I LYS* 4.5 9.2 - - - +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C PHE 4.0 14.4 - - - +
1D PHE* 3.9 18.6 - - + -
2D THR 3.4 11.3 + - - +
3D LEU* 3.2 14.2 + - + +
5D GLU* 1.3 80.1 - - - +
7D LEU* 1.3 58.4 + - - +
9D VAL* 3.3 6.6 + - + +
10D ILE* 3.0 36.6 + - + +
9E VAL* 3.8 29.4 - - + +
12E ILE* 3.5 35.9 - - + -
13E ILE* 4.3 10.8 - - + -
16E LEU* 4.3 19.1 - - + -
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Residues in contact with LEU 7 (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 LEU* 2.7 26.3 + - + +
4D ILE* 3.7 9.4 - - + +
6D LEU* 1.3 71.9 - - - +
8D ILE* 1.3 59.9 + - - +
10D ILE* 3.4 12.6 + - + +
11D ALA* 3.0 25.1 + - - +
27H ALA* 5.6 7.9 - - + +
30H ARG* 4.3 20.6 - - + -
45J LYS* 3.4 49.1 - - + +
48J GLU* 4.5 7.6 - - + -
49J MET* 4.0 24.7 - - + -
52J ILE* 4.5 5.6 - - + +
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Residues in contact with ILE 8 (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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3C LEU* 4.1 19.1 - - + -
4D ILE* 3.0 16.9 + - - +
5D GLU* 3.4 18.6 - - - +
7D LEU* 1.3 73.3 - - - +
9D VAL* 1.3 62.7 + - - +
11D ALA* 3.2 5.6 + - - +
12D ILE* 3.0 35.3 + - + +
22G PRO* 5.2 0.9 - - + -
24G LEU* 3.4 49.6 - - + +
27G ALA* 4.2 9.2 - - + -
28G ARG* 3.7 19.1 - - + +
48J GLU* 3.5 24.2 - - + +
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Residues in contact with VAL 9 (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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1C PHE* 3.4 44.4 - - + +
2C THR 3.9 0.7 - - - +
3C LEU* 3.5 40.8 - - + +
6C LEU* 3.8 12.9 - - + +
5D GLU* 3.1 20.2 - - - +
6D LEU* 3.3 10.5 + - + +
7D LEU 3.3 0.4 - - - -
8D ILE* 1.3 74.1 - - - +
10D ILE* 1.3 65.8 + - - +
12D ILE 3.5 0.5 + - - -
13D ILE* 3.1 28.9 + - + +
16E LEU* 5.4 3.8 - - + -
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Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 3.0 28.1 + - + +
7D LEU* 3.6 14.8 - - + +
8D ILE 3.3 0.2 - - - -
9D VAL* 1.3 76.5 - - - +
11D ALA* 1.3 62.6 + - - +
13D ILE* 3.5 9.5 + - + +
14D ALA* 3.3 21.1 + - - +
12E ILE* 4.1 23.8 - - + -
16E LEU* 4.1 19.1 - - + -
27H ALA 5.3 2.9 - - - +
30H ARG* 3.5 25.6 - - + +
31H ALA* 4.6 13.0 - - + +
34H THR* 3.3 25.0 + - - +
52J ILE* 5.4 2.2 - - + -
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU 3.0 11.3 + - - +
8D ILE* 3.2 13.4 + - - +
10D ILE* 1.3 77.7 - - - +
12D ILE* 1.3 61.4 + - - +
14D ALA* 3.5 7.1 + - - +
15D ILE* 3.3 26.0 + - - +
28G ARG* 4.1 17.9 - - - +
48J GLU* 4.8 3.6 - - + +
52J ILE* 3.2 39.7 - - + +
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Residues in contact with ILE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 5.7 2.9 - - + -
6C LEU* 3.5 28.7 - - + -
10C ILE* 4.1 6.5 - - + -
8D ILE* 3.0 25.3 + - + +
10D ILE 3.4 0.2 - - - -
11D ALA* 1.3 73.9 - - - +
13D ILE* 1.3 60.0 + - - +
15D ILE* 3.1 17.9 + - + +
16D LEU* 2.8 52.8 + - + +
27G ALA* 4.7 4.0 - - + +
28G ARG* 4.2 25.6 - - + +
31G ALA* 3.2 31.9 - - + -
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Residues in contact with ILE 13 (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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1B PHE 3.9 23.5 + - - +
1C PHE* 4.0 15.9 - - + -
6C LEU* 4.2 16.4 - - + -
9D VAL* 3.1 37.3 + - + +
10D ILE* 3.8 9.2 - - - +
12D ILE* 1.3 75.4 - - - +
14D ALA* 1.3 57.4 + - - +
16D LEU* 4.1 5.0 - - - +
17D ALA* 2.9 34.7 + - + +
16E LEU* 4.9 5.8 - - + -
20E LEU* 4.1 20.2 - - + -
34H THR* 4.3 21.1 - - + -
37H THR* 6.1 2.9 - - + -
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Residues in contact with ALA 14 (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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10D ILE* 3.3 10.4 + - + +
11D ALA* 3.6 11.9 - - - +
12D ILE 3.2 0.4 - - - -
13D ILE* 1.3 79.6 - - - +
15D ILE* 1.3 60.3 + - + +
17D ALA* 3.8 5.0 + - - +
18D ALA* 3.5 20.4 + - - +
37H THR* 5.6 7.0 - - - +
52J ILE* 4.9 14.4 - - + -
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Residues in contact with ILE 15 (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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11D ALA 3.4 14.1 - - - +
12D ILE* 3.1 20.3 + - + +
14D ALA* 1.3 75.9 - - + +
16D LEU* 1.3 71.9 + - + +
18D ALA* 3.3 5.4 + - - +
19D VAL* 3.2 26.4 + - + +
28G ARG* 3.4 28.9 - - - +
31G ALA* 4.8 4.9 - - + +
32G ASN* 5.7 5.2 - - - +
35G VAL* 3.3 33.2 - - + -
51J GLN 6.1 0.4 - - - +
52J ILE* 6.5 2.5 - - - -
55J ASN* 5.7 7.9 - - - +
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Residues in contact with LEU 16 (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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1B PHE* 4.4 21.0 - - + -
6C LEU* 4.3 13.5 - - + -
9C VAL* 5.4 1.8 - - + -
10C ILE* 4.0 19.1 - - + -
13C ILE* 4.9 6.3 - - + -
12D ILE* 2.8 44.3 + - + +
13D ILE* 4.1 3.4 - - - +
15D ILE* 1.3 83.0 - - + +
17D ALA* 1.3 61.2 + - - +
19D VAL* 4.1 6.3 - - + -
20D LEU* 3.2 51.0 + - + +
21D ILE* 4.4 0.3 - - - +
31G ALA* 4.6 7.0 - - + +
34G THR* 4.3 21.5 - - + +
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Residues in contact with ALA 17 (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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1B PHE* 5.9 3.0 - - - +
13D ILE* 2.9 24.4 + - + +
14D ALA 4.1 4.0 - - - +
16D LEU* 1.3 76.4 - - - +
18D ALA* 1.3 59.9 + - - +
21D ILE* 3.3 32.0 - - + +
37H THR* 4.0 26.7 - - + -
41H ASN* 5.8 7.4 - - + +
109H VAL* 4.7 10.3 + - + +
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Residues in contact with ALA 18 (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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14D ALA 3.5 11.4 + - - +
15D ILE* 3.3 9.5 + - - +
16D LEU 3.2 0.6 - - - -
17D ALA* 1.3 80.4 - - - +
19D VAL* 1.3 68.7 + - + +
20D LEU 3.6 0.2 - - - -
21D ILE* 3.8 13.7 - - - +
70G LYS* 4.6 13.7 + - - -
109H VAL 4.6 12.3 - - - +
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 3.5 18.6 - - + +
16D LEU* 4.0 4.3 - - + +
18D ALA* 1.3 79.8 - - + +
20D LEU* 1.3 78.5 + - + +
21D ILE 3.5 4.7 + - - +
34G THR* 4.4 3.4 - - + +
35G VAL* 4.0 41.1 - - + +
38G ALA* 3.9 25.6 - - + +
39G TYR 5.7 0.2 - - - +
42G ASP* 3.7 19.6 - - - +
70G LYS* 5.5 3.2 + - - +
73G PRO* 5.7 4.9 - - + -
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Residues in contact with LEU 20 (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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1B PHE* 3.4 39.9 - - + -
13C ILE* 4.0 22.2 - - + -
16D LEU* 3.2 35.6 + - + +
19D VAL* 1.3 78.1 - - + +
21D ILE* 1.3 69.1 + - + +
22D PRO* 3.3 10.1 - - - +
34G THR* 3.8 22.0 - - + -
38G ALA* 4.0 17.9 - - + -
42G ASP* 5.8 0.4 - - - +
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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
------------------------------------------------------------
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