Contacts of the helix formed by residues 6 - 24 (chain B) 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 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B ARG* 1.3 80.2 - - - +
7B PRO* 1.3 74.2 - - - +
8B ALA* 3.5 8.1 + - - +
9B ALA* 2.9 17.7 + - - +
10B GLU 3.3 8.7 + - - -
80B ILE 3.2 7.6 + - - -
81B VAL* 2.8 33.1 + - - +
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Residues in contact with PRO 7 (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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5B ARG* 3.7 18.8 - - - +
6B SER* 1.3 85.5 - - - +
8B ALA* 1.3 61.1 + - - +
10B GLU* 3.3 10.3 - - + +
11B GLY* 3.2 17.2 + - - -
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Residues in contact with ALA 8 (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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6B SER* 3.1 9.0 + - - +
7B PRO* 1.3 78.9 - - - +
9B ALA* 1.3 58.5 + - - +
11B GLY* 3.1 4.0 + - - -
12B ASP* 2.9 34.0 + - - +
82B ARG* 4.1 32.3 - - + +
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Residues in contact with ALA 9 (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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5B ARG* 4.2 7.9 - - + -
6B SER* 2.9 15.5 + - - +
8B ALA* 1.3 78.0 - - - +
10B GLU* 1.3 62.7 + - - +
12B ASP* 3.2 13.1 + - - +
13B LEU* 3.2 26.8 + - + +
80B ILE* 3.6 17.3 - - + +
81B VAL 3.4 21.9 + - - +
83B ILE* 3.9 14.9 - - + +
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Residues in contact with GLU 10 (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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5B ARG* 2.9 45.9 + - - +
6B SER 3.3 4.9 + - - -
7B PRO* 3.3 15.1 - - - +
8B ALA 3.3 0.2 - - - -
9B ALA* 1.3 77.4 - - - +
11B GLY* 1.3 68.8 + - - +
13B LEU* 3.0 12.1 + - - +
14B VAL* 2.9 34.4 + - + +
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Residues in contact with GLY 11 (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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7B PRO 3.2 4.7 + - - -
8B ALA* 3.1 8.4 + - - -
10B GLU* 1.3 85.4 - - - +
12B ASP* 1.3 64.3 + - - +
14B VAL* 3.3 7.1 + - - +
15B ASP* 2.9 33.7 + - - +
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Residues in contact with ASP 12 (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 ALA 2.9 13.5 + - - +
9B ALA 3.4 7.4 - - - +
11B GLY* 1.3 78.3 - - - +
13B LEU* 1.3 57.1 + - - +
15B ASP* 3.3 5.9 + - - +
16B ILE* 2.8 35.9 + - - +
82B ARG* 2.7 45.2 + - - +
83B ILE* 2.9 45.9 + - + +
84B VAL* 4.9 0.2 - - - -
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Residues in contact with LEU 13 (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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5B ARG* 6.5 1.3 - - + -
9B ALA* 3.4 15.0 - - + +
10B GLU* 3.0 11.3 + - - +
12B ASP* 1.3 76.1 - - - +
14B VAL* 1.3 59.5 + - + +
16B ILE* 3.7 9.2 - - + +
17B TRP* 2.8 29.8 + - - +
32B LEU* 3.7 26.2 - - + +
35B ILE* 4.3 20.9 - - + -
83B ILE* 4.0 38.6 - - + -
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Residues in contact with VAL 14 (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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10B GLU* 2.9 30.5 + - + +
11B GLY* 3.8 6.7 - - - +
13B LEU* 1.3 74.8 - - + +
15B ASP* 1.3 63.7 + - - +
17B TRP* 3.2 7.4 + - + +
18B LEU* 2.8 52.9 + - + +
32B LEU* 5.5 0.4 - - - -
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Residues in contact with ASP 15 (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 GLY* 2.9 22.6 + - - +
12B ASP* 3.7 5.8 - - - +
14B VAL* 1.3 78.8 - - - +
16B ILE* 1.3 64.6 + - + +
18B LEU* 3.2 15.2 + - - +
19B ALA* 3.0 24.5 + - - +
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Residues in contact with ILE 16 (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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12B ASP* 2.8 26.8 + - - +
13B LEU* 3.7 10.5 - - + +
15B ASP* 1.3 73.6 - - + +
17B TRP* 1.3 64.3 + - - +
19B ALA* 3.3 6.6 + - - +
20B ILE* 3.3 25.0 + - + +
31B PHE* 3.7 35.2 - - + -
32B LEU* 4.1 9.0 - - + -
35B ILE* 5.5 0.7 - - + -
67B TYR* 4.2 25.1 - - + -
83B ILE* 3.5 40.6 - - + +
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Residues in contact with TRP 17 (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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13B LEU 2.8 22.6 + - - +
14B VAL* 3.2 8.0 + - + +
16B ILE* 1.3 74.6 - - - +
18B LEU* 1.3 78.9 + - + +
20B ILE* 3.3 1.8 + - - -
21B ALA* 2.9 46.3 + - + +
25B PRO* 3.5 29.2 - - + -
28B ALA* 3.2 45.4 - - + +
29B ASP* 2.9 28.5 + - - +
32B LEU* 3.4 26.0 - - + -
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Residues in contact with LEU 18 (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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14B VAL* 2.8 42.4 + - + +
15B ASP* 3.7 13.0 - - - +
17B TRP* 1.3 94.3 - - + +
19B ALA* 1.3 63.7 + - - +
21B ALA* 2.9 13.1 + - + +
22B ASN* 3.0 17.8 + - - +
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Residues in contact with ALA 19 (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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15B ASP 3.0 12.5 + - - +
16B ILE* 3.6 11.4 - - - +
18B LEU* 1.3 77.1 - - - +
20B ILE* 1.3 63.9 + - + +
22B ASN* 3.3 20.7 + - - +
23B ASP* 4.1 1.7 + - - +
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Residues in contact with ILE 20 (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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16B ILE* 3.3 19.7 + - + +
17B TRP 3.8 0.7 - - - +
19B ALA* 1.3 77.6 - - + +
21B ALA* 1.3 57.6 + - - +
23B ASP* 3.1 11.1 + - + +
24B SER 2.9 23.4 + - - +
27B ALA* 3.8 14.8 - - + +
28B ALA* 3.4 31.6 - - + +
31B PHE* 3.5 43.1 - - + -
32B LEU* 5.1 0.4 - - + -
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Residues in contact with ALA 21 (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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17B TRP* 2.9 50.3 + - + +
18B LEU* 2.9 9.6 + - + +
20B ILE* 1.3 75.3 - - - +
22B ASN* 1.3 65.7 + - - +
23B ASP 3.2 0.4 + - - -
24B SER 3.5 17.3 + - - -
25B PRO* 3.6 16.5 - - + +
28B ALA* 4.2 0.7 - - + -
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Residues in contact with ASN 22 (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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18B LEU* 3.0 15.4 + - - +
19B ALA* 3.4 14.0 - - - +
20B ILE 3.2 0.6 - - - -
21B ALA* 1.3 77.2 - - - +
23B ASP* 1.3 62.0 + - - +
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Residues in contact with ASP 23 (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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19B ALA 4.1 1.2 + - - +
20B ILE* 3.1 13.0 + - + +
21B ALA 3.8 0.7 - - - -
22B ASN* 1.3 82.3 - - - +
24B SER* 1.3 68.6 + - - +
25B PRO* 4.6 1.4 - - - +
27B ALA* 5.3 4.2 - - - +
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Residues in contact with SER 24 (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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20B ILE 2.9 17.8 + - - +
21B ALA* 3.5 1.4 + - - -
23B ASP* 1.3 85.4 - - - +
25B PRO* 1.3 70.7 - - - +
26B ARG* 3.5 9.9 + - - +
27B ALA* 3.2 26.0 + - - +
28B ALA 3.2 16.1 + - - -
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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