Contacts of the helix formed by residues 6 - 23 (chain B) in PDB entry 5A74
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 ASN 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B PHE* 1.3 75.6 + - + +
8B HIS* 3.3 7.4 - - - +
9B ASP* 2.9 29.8 + - - +
10B GLN* 2.9 37.5 + - - +
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Residues in contact with PHE 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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7A PHE* 4.1 35.0 - + + -
11A LEU* 5.3 0.2 - - - +
6B ASN* 1.3 87.5 - - + +
8B HIS* 1.3 66.2 + - - +
10B GLN* 3.1 15.5 + - + +
11B LEU* 2.9 29.8 + - + +
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Residues in contact with HIS 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 ASN 4.1 3.6 - - - +
7B PHE* 1.3 77.6 - - - +
9B ASP* 1.3 71.0 + - - +
11B LEU* 3.0 26.4 + - + +
12B LYS* 3.0 47.4 + - + +
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Residues in contact with ASP 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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6B ASN* 2.9 35.2 + - - +
8B HIS* 1.3 83.4 + - - +
10B GLN* 1.3 60.3 + - - +
12B LYS* 3.2 10.1 + - - +
13B PHE* 2.9 54.6 + - + -
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.7 12.6 - - + +
6B ASN* 2.9 26.7 + - - +
7B PHE* 3.1 19.0 + - + +
9B ASP* 1.3 78.1 - - - +
11B LEU* 1.3 57.9 + - - +
13B PHE* 3.5 23.2 + - - -
14B ALA* 3.0 28.9 + - - +
94B LYS 5.0 0.7 - - - +
97B PRO* 5.8 1.2 - - - +
98B TYR* 2.4 42.8 + - + +
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Residues in contact with LEU 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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7A PHE 5.2 0.7 - - - +
10A GLN* 3.7 29.4 - - + +
11A LEU* 3.6 23.3 - - + +
14A ALA* 3.7 13.8 - - + +
98A TYR* 4.0 24.7 - - + +
7B PHE* 2.9 20.0 + - + +
8B HIS* 3.0 19.5 + - + +
10B GLN* 1.3 74.7 - - - +
12B LYS* 1.3 64.1 + - - +
14B ALA* 3.4 1.1 + - - -
15B TRP* 3.0 25.1 + - - +
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Residues in contact with LYS 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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100A GLN* 5.4 10.1 + - - +
8B HIS* 3.0 46.0 + - + +
9B ASP* 3.4 11.9 - - - +
11B LEU* 1.3 77.0 - - - +
13B PHE* 1.3 59.1 + - + +
15B TRP* 3.4 11.1 + - + +
16B LEU* 2.9 29.5 + - - +
64B ILE* 3.6 43.5 - - + +
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Residues in contact with PHE 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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9B ASP* 2.9 39.4 + - + +
10B GLN* 3.8 28.3 - - - +
12B LYS* 1.3 74.4 - - + +
14B ALA* 1.3 62.6 + - - +
16B LEU* 3.2 1.3 + - + -
17B ALA* 2.8 31.5 + - - +
64B ILE* 4.0 31.6 - - + -
65B LEU* 4.4 7.6 - - + -
94B LYS* 3.7 63.3 - - + +
95B LEU* 3.7 12.2 - - + +
98B TYR* 3.9 8.7 - - + -
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Residues in contact with ALA 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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11A LEU* 3.6 30.5 - - + +
14A ALA* 4.2 1.8 - - + -
15A TRP* 3.2 15.8 - - + +
10B GLN 3.0 18.5 + - - +
11B LEU 3.8 4.3 - - - +
13B PHE* 1.3 74.9 - - - +
15B TRP* 1.3 63.0 + - - +
17B ALA* 3.3 4.3 + - - +
18B GLY 3.1 17.2 + - - -
98B TYR* 3.7 28.8 - - + -
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Residues in contact with TRP 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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14A ALA* 3.1 21.2 + - + +
17A ALA* 3.9 0.9 - - + -
18A GLY* 3.2 31.5 - - - -
21A ASP* 3.1 22.7 + - - -
98A TYR* 3.3 23.1 + - + -
100A GLN* 3.5 25.1 - - + -
101A LEU* 5.5 0.2 - - + -
11B LEU 3.0 18.1 + - - +
12B LYS* 3.6 10.5 - - + +
14B ALA* 1.3 76.5 - - - +
16B LEU* 1.3 91.2 + - + +
18B GLY 3.1 2.8 + - - -
19B PHE* 2.9 45.1 + + + -
57B ILE* 3.8 27.4 - - + -
60B ASP* 6.3 0.7 - - + -
61B ILE* 4.2 20.0 - - + -
64B ILE* 4.6 13.5 - - + -
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Residues in contact with LEU 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 LYS 2.9 18.0 + - - +
13B PHE* 3.7 5.4 - - + +
15B TRP* 1.3 88.0 - - + +
17B ALA* 1.3 52.4 + - - +
19B PHE* 3.2 4.5 + - + +
20B VAL* 2.7 48.6 + - + +
46B LEU* 6.1 0.7 - - + -
48B VAL* 4.7 1.6 - - + -
61B ILE* 3.8 40.8 - - + -
64B ILE* 4.6 10.3 - - + -
65B LEU* 3.8 43.3 - - + -
95B LEU* 3.8 15.9 - - + -
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Residues in contact with ALA 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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15A TRP* 4.0 2.0 - - - -
13B PHE 2.8 17.6 + - - +
14B ALA 3.4 5.8 - - - +
16B LEU* 1.3 76.9 - - - +
18B GLY* 1.3 51.5 + - - +
20B VAL* 3.1 3.4 + - - +
21B ASP* 2.5 40.1 + - - +
95B LEU* 4.1 10.0 - - + +
98B TYR* 3.7 34.5 - - + +
99B LEU* 3.8 16.8 - - + +
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Residues in contact with GLY 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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15A TRP* 3.3 39.4 - - - -
19A PHE* 3.5 15.1 - - - -
14B ALA 3.1 7.7 + - - -
15B TRP 3.1 5.7 + - - -
17B ALA* 1.3 72.1 - - - +
19B PHE* 1.3 57.5 + - - +
21B ASP* 3.0 5.1 + - - +
22B ALA* 2.9 26.5 + - - +
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Residues in contact with PHE 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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18A GLY 3.5 20.1 - - - +
21A ASP* 3.8 8.5 - - + -
22A ALA* 3.7 15.0 - - + -
101A LEU* 3.6 28.5 - - + -
15B TRP* 2.9 39.1 + + + +
16B LEU* 3.5 13.2 - - + +
18B GLY* 1.3 74.6 - - - +
20B VAL* 1.3 57.9 + - - +
23B ASP* 2.8 35.3 + - + -
48B VAL* 3.5 31.4 - - + -
49B PHE 4.3 0.2 - - - -
50B GLN* 3.5 28.0 - - + -
57B ILE* 4.7 8.1 - - + -
61B ILE* 4.5 9.0 - - + -
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Residues in contact with VAL 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 LEU* 2.7 36.8 + - + +
17B ALA* 3.6 6.3 - - - +
19B PHE* 1.3 69.8 - - - +
21B ASP* 1.3 65.7 + - - +
22B ALA 3.0 1.6 - - - -
24B GLY* 3.0 30.2 + - - -
26B ILE* 4.2 15.5 - - + -
46B LEU* 4.1 32.3 - - + -
48B VAL* 3.9 23.6 - - + -
95B LEU* 4.4 2.9 - - + -
99B LEU* 4.2 12.3 - - + -
102B LYS* 3.1 14.4 + - + -
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Residues in contact with ASP 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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15A TRP* 3.0 17.7 + - - +
19A PHE* 3.7 21.3 - - + -
50A GLN* 4.5 4.3 + - - -
17B ALA 2.5 17.8 + - - +
18B GLY* 3.5 5.6 - - - +
20B VAL* 1.3 73.0 - - - +
22B ALA* 1.3 61.0 + - - +
99B LEU* 3.5 9.4 - - - +
100B GLN* 2.7 24.9 + - - +
101B LEU* 2.9 39.3 + - + +
102B LYS* 3.0 32.6 + - - +
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Residues in contact with ALA 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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19A PHE* 3.8 15.9 - - + +
22A ALA* 3.4 24.0 - - + -
23A ASP* 3.0 27.3 - - + +
18B GLY 2.9 12.4 + - - +
20B VAL 3.0 1.4 - - - -
21B ASP* 1.3 79.8 - - - +
23B ASP* 1.3 59.9 + - - +
24B GLY 3.5 0.7 - - - -
102B LYS* 4.4 0.9 + - - -
615F G 3.1 6.4 + - - +
1625F MN 2.2 30.2 + - - -
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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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22A ALA* 3.3 16.5 - - + +
23A ASP* 2.7 7.4 - - - +
19B PHE* 2.8 17.6 + - + +
22B ALA* 1.3 71.4 - - - +
24B GLY* 1.3 58.1 + - - +
48B VAL* 3.7 3.2 - - - +
49B PHE* 3.1 36.7 + - - +
50B GLN* 3.2 7.3 - - - +
614D C 2.9 12.5 + - - +
1525E MN 2.2 32.3 + - - -
615F G 3.7 10.8 - - - -
1626F MN 2.2 32.1 + - - -
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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