Contacts of the helix formed by residues 2 - 20 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A PHE* 1.3 83.9 - - - +
3A LEU* 1.3 62.0 + - - +
4A ILE* 3.2 13.9 - - - +
5A GLU* 3.0 28.4 + - - +
6A LEU* 3.4 15.4 + - - +
1I PHE* 3.6 14.1 - - + -
5I GLU* 3.6 6.7 - - - -
9I VAL* 3.9 2.5 - - - +
20K LEU* 3.4 46.1 + - + +
21K ILE* 3.9 12.8 - - + -
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Residues in contact with LEU 3 (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 THR* 1.3 71.5 - - - +
4A ILE* 1.3 54.5 + - - +
6A LEU* 3.2 13.7 + - + +
7A LEU* 2.7 43.3 + - + +
5I GLU* 2.9 26.2 + - + +
8I ILE* 4.1 15.9 - - + -
9I VAL* 3.6 20.0 - - + +
12I ILE* 5.7 2.5 - - + -
22L PRO* 4.3 18.6 - - + -
23L ASN 5.1 1.8 - - - +
27L ALA* 4.4 24.9 - - + -
45O LYS* 4.0 30.2 - - + +
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Residues in contact with ILE 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A THR* 3.2 17.7 - - - +
3A LEU* 1.3 79.2 - - - +
5A GLU* 1.3 58.1 + - - +
7A LEU* 4.0 9.0 - - + -
8A ILE* 3.0 28.1 + - - +
21K ILE* 4.0 19.1 - - + -
22K PRO* 3.9 15.0 - - + -
24K LEU* 4.0 15.9 - - + -
41O ASN* 5.0 4.0 - - - +
44O VAL* 4.0 14.8 - - + +
45O LYS* 3.8 38.0 - - + +
48O GLU* 3.7 30.5 - - + -
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 3.2 41.9 - - - -
2A THR* 3.0 25.0 + - - +
4A ILE* 1.3 76.0 - - - +
6A LEU* 1.3 59.3 + - - +
8A ILE* 3.5 10.6 - - - +
9A VAL* 3.1 19.8 - - - +
2H THR* 3.6 6.4 - - - -
3H LEU* 2.9 42.6 + - + -
20K LEU 5.1 1.1 - - - +
22K PRO* 4.0 20.4 - - + -
41N ASN* 6.0 0.6 + - - -
45N LYS* 4.5 9.4 - - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A PHE* 3.9 19.1 - - + -
2A THR 3.4 11.1 + - - +
3A LEU* 3.2 14.7 + - + +
5A GLU* 1.3 79.8 - - - +
7A LEU* 1.3 59.0 + - - +
9A VAL* 3.3 6.6 + - + +
10A ILE* 3.0 36.8 + - + +
1H PHE 4.1 13.9 - - - +
9I VAL* 3.8 29.4 - - + +
12I ILE* 3.5 36.3 - - + -
13I ILE* 4.2 10.5 - - + -
16I LEU* 4.3 19.3 - - + -
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Residues in contact with LEU 7 (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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3A LEU* 2.7 26.1 + - + +
4A ILE* 3.4 11.2 + - + +
6A LEU* 1.3 71.5 - - - +
8A ILE* 1.3 60.7 + - - +
10A ILE* 3.4 11.3 + - + +
11A ALA* 3.0 25.1 + - - +
27L ALA* 5.6 7.9 - - + +
30L ARG* 4.3 21.5 - - + -
45O LYS* 3.4 47.8 - - + +
48O GLU* 4.6 7.4 - - + -
49O MET* 4.0 24.2 - - + -
52O ILE* 4.5 5.1 - - + +
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Residues in contact with ILE 8 (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 ILE* 3.0 16.6 + - - +
5A GLU* 3.5 18.2 - - - +
7A LEU* 1.3 72.7 - - - +
9A VAL* 1.3 62.2 + - - +
11A ALA* 3.2 6.1 + - - +
12A ILE* 3.0 34.7 + - + +
3H LEU* 4.1 20.0 - - + -
22K PRO* 5.2 0.4 - - + -
24K LEU* 3.4 49.4 - - + +
27K ALA* 4.2 10.8 - - + -
28K ARG* 3.7 18.8 - - + +
48O GLU* 3.5 23.3 - - + +
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Residues in contact with VAL 9 (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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5A GLU* 3.1 22.0 + - - +
6A LEU* 3.3 10.9 + - + +
7A LEU 3.3 0.6 - - - -
8A ILE* 1.3 73.5 - - - +
10A ILE* 1.3 65.0 + - - +
12A ILE 3.5 0.5 + - - -
13A ILE* 3.1 28.8 + - + +
1H PHE* 3.4 43.5 - - + +
2H THR 3.9 0.7 - - - +
3H LEU* 3.6 40.6 - - + +
6H LEU* 3.8 13.1 - - + +
16I LEU* 5.4 4.3 - - + -
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Residues in contact with ILE 10 (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 LEU* 3.0 27.9 + - + +
7A LEU* 3.6 15.7 - - + +
9A VAL* 1.3 74.9 - - - +
11A ALA* 1.3 61.8 + - - +
13A ILE* 3.5 9.5 + - + +
14A ALA* 3.3 21.2 + - + +
12I ILE* 4.1 24.9 - - + -
16I LEU* 4.1 18.8 - - + -
27L ALA 5.2 3.4 - - - +
30L ARG* 3.5 24.5 - - + +
31L ALA* 4.5 12.6 - - + +
34L THR* 3.2 25.3 + - - +
52O ILE* 5.4 3.4 - - + -
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Residues in contact with ALA 11 (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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7A LEU 3.0 10.1 + - - +
8A ILE* 3.4 12.6 - - - +
10A ILE* 1.3 78.6 - - - +
12A ILE* 1.3 61.1 + - - +
14A ALA* 3.5 6.8 + - - +
15A ILE* 3.3 26.3 + - - +
28K ARG* 4.2 18.6 - - - +
48O GLU* 4.8 3.6 - - + +
52O ILE* 3.2 40.7 - - + +
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Residues in contact with ILE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 3.0 23.9 + - + +
9A VAL 3.5 0.2 + - - -
10A ILE 3.4 0.2 - - - -
11A ALA* 1.3 73.5 - - - +
13A ILE* 1.3 58.9 + - - +
15A ILE* 3.1 17.3 + - + +
16A LEU* 2.8 53.2 + - + +
3H LEU* 5.7 2.9 - - + -
6H LEU* 3.5 31.4 - - + -
10H ILE* 4.1 6.3 - - + -
27K ALA* 4.8 4.9 - - + +
28K ARG* 4.2 24.9 - - + +
31K ALA* 3.3 30.3 - - + -
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Residues in contact with ILE 13 (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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9A VAL* 3.1 36.3 + - + +
10A ILE* 3.8 9.6 - - - +
12A ILE* 1.3 76.2 - - - +
14A ALA* 1.3 57.4 + - - +
16A LEU* 4.1 5.7 - - - +
17A ALA* 2.9 33.7 + - + +
1G PHE 3.9 23.9 + - - +
1H PHE* 4.0 15.7 - - + -
6H LEU* 4.3 14.6 - - + -
16I LEU* 4.9 6.3 - - + -
20I LEU* 4.0 20.2 - - + -
34L THR* 4.3 20.2 - - + -
37L THR* 6.1 3.1 - - + -
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Residues in contact with ALA 14 (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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10A ILE 3.3 10.6 + - - +
11A ALA* 3.6 11.4 - - - +
12A ILE 3.2 0.4 - - - -
13A ILE* 1.3 80.2 - - - +
15A ILE* 1.3 60.6 + - + +
17A ALA* 3.8 4.8 + - - +
18A ALA* 3.5 20.4 + - - +
37L THR* 5.6 7.0 - - + +
52O ILE* 4.9 14.6 - - + -
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Residues in contact with ILE 15 (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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11A ALA 3.4 13.7 - - - +
12A ILE* 3.1 21.6 + - + +
14A ALA* 1.3 77.4 - - + +
16A LEU* 1.3 71.1 + - + +
18A ALA* 3.3 5.5 + - - +
19A VAL* 3.2 26.2 + - + +
28K ARG* 3.4 28.7 - - - +
31K ALA* 4.8 4.9 - - + +
32K ASN* 5.7 4.7 - - - +
35K VAL* 3.3 33.2 - - + -
51O GLN 6.1 0.4 - - - +
52O ILE* 6.4 2.5 - - + -
55O ASN* 5.7 7.4 - - - +
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Residues in contact with LEU 16 (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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12A ILE* 2.8 43.5 + - + +
13A ILE* 4.1 3.1 - - - +
15A ILE* 1.3 83.3 - - + +
17A ALA* 1.3 61.5 + - - +
19A VAL* 4.1 6.3 - - + -
20A LEU* 3.2 50.2 + - + +
21A ILE* 4.4 0.3 - - - +
1G PHE* 4.4 21.7 - - + -
6H LEU* 4.3 13.7 - - + -
9H VAL* 5.4 1.3 - - + -
10H ILE* 4.1 18.8 - - + -
13H ILE* 4.9 5.6 - - + -
31K ALA* 4.7 6.3 - - + +
34K THR* 4.4 23.1 - - + +
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Residues in contact with ALA 17 (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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13A ILE* 2.9 23.8 + - + +
14A ALA 4.1 3.8 - - - +
16A LEU* 1.3 76.6 - - - +
18A ALA* 1.3 58.3 + - - +
21A ILE* 3.3 31.5 - - + +
1G PHE* 5.9 3.5 - - - +
37L THR* 4.0 28.0 - - + -
41L ASN* 5.8 7.1 - - + +
109L VAL* 4.7 10.7 + - + +
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Residues in contact with ALA 18 (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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14A ALA 3.5 10.5 + - - +
15A ILE* 3.3 9.8 + - - +
16A LEU 3.2 0.4 - - - -
17A ALA* 1.3 81.1 - - - +
19A VAL* 1.3 67.6 + - + +
20A LEU 3.6 0.4 + - - -
21A ILE* 3.8 13.9 - - - +
70K LYS* 4.6 13.7 + - - -
107L LYS 5.6 0.5 - - - +
109L VAL 4.6 13.0 - - - +
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Residues in contact with VAL 19 (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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15A ILE* 3.2 18.6 + - + +
16A LEU* 4.0 3.8 - - + +
18A ALA* 1.3 80.2 - - + +
20A LEU* 1.3 81.9 + - + +
21A ILE 3.5 5.4 + - - +
34K THR* 4.4 3.1 - - + +
35K VAL* 4.0 41.3 - - + +
38K ALA* 3.9 22.6 - - + +
39K TYR 5.7 0.4 - - - +
42K ASP* 3.7 19.8 - - - +
70K LYS* 5.5 2.4 + - - +
73K PRO* 5.8 4.0 - - + -
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Residues in contact with LEU 20 (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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16A LEU* 3.2 34.1 + - + +
19A VAL* 1.3 79.0 - - + +
21A ILE* 1.3 64.2 + - + +
22A PRO* 3.3 8.7 - - - +
1F PHE 4.8 7.2 - - - +
2F THR* 3.4 26.5 + - + +
5F GLU* 5.2 1.4 - - - +
1G PHE* 3.4 34.8 - - + -
13H ILE* 4.0 21.8 - - + -
34K THR* 3.8 22.2 - - + -
38K ALA* 4.0 16.8 - - + -
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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