Contacts of the helix formed by residues 8 - 26 (chain B) in PDB entry 3AFF
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 ASP 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ARG* 1.3 78.0 - - - +
9B ALA* 1.3 66.7 + - - +
10B GLN* 3.2 22.7 - - - +
11B SER* 3.0 25.6 + - - -
12B VAL* 3.0 23.7 + - - +
61B LEU* 3.9 13.0 - - + -
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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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8B ASP* 1.3 74.2 - - - +
10B GLN* 1.3 63.1 + - - +
12B VAL* 3.0 5.7 + - - +
13B LEU* 3.0 31.8 + - - +
52B LEU* 4.1 15.7 - - + +
61B LEU* 3.9 7.3 - - + +
63B CYS* 4.1 20.0 - - + -
67B LEU* 3.4 30.7 - - + -
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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
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8B ASP* 3.2 23.9 - - - +
9B ALA* 1.3 82.4 + - - +
11B SER* 1.3 56.4 + - - +
13B LEU* 3.3 13.5 + - + +
14B ALA* 3.0 26.3 + - - +
67B LEU* 4.0 22.0 - - + +
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Residues in contact with SER 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 ARG* 3.3 28.8 - - - +
8B ASP* 3.0 21.6 + - - -
10B GLN* 1.3 73.4 - - - +
12B VAL* 1.3 61.7 + - - +
14B ALA* 3.4 8.0 + - - +
15B ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 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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7B ARG* 3.7 22.2 - - - -
8B ASP 3.0 18.7 + - - +
9B ALA 3.5 6.5 - - - +
11B SER* 1.3 75.1 - - - +
13B LEU* 1.3 64.9 + - - +
15B ALA* 3.1 4.1 + - - +
16B ILE* 2.8 30.4 + - + +
47B VAL* 3.6 20.4 - - + +
48B GLY 3.8 22.4 - - - +
49B PHE* 3.9 7.6 - - - +
52B LEU* 3.7 25.4 - - + -
61B LEU* 3.9 13.7 - - + -
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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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9B ALA 3.0 11.9 + - - +
10B GLN* 3.4 14.1 - - + +
11B SER 3.3 0.2 - - - -
12B VAL* 1.3 78.3 - - + +
14B ALA* 1.3 57.4 + - - +
16B ILE* 3.2 7.8 + - + +
17B ASP 2.9 23.7 + - - -
52B LEU* 5.9 2.7 - - + -
67B LEU* 4.0 36.1 - - + +
70B GLU* 4.2 11.0 - - + -
71B ALA* 3.6 42.8 - - + +
74B ARG* 3.4 40.1 + - - +
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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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10B GLN 3.0 13.4 + - - +
11B SER* 3.7 11.0 - - - +
12B VAL 3.2 0.2 - - - -
13B LEU* 1.3 73.4 - - - +
15B ALA* 1.3 66.6 + - - +
17B ASP* 3.2 10.4 + - - +
18B ASN* 3.0 22.2 + - - +
74B ARG* 4.8 1.6 - - - +
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Residues in contact with ALA 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 SER 2.9 17.9 + - - +
12B VAL* 3.4 6.5 - - - +
14B ALA* 1.3 75.2 - - - +
16B ILE* 1.3 61.5 + - - +
18B ASN* 3.4 10.9 + - - +
19B LEU* 3.3 24.8 + - - +
47B VAL* 3.5 32.2 - - + +
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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 VAL* 2.8 28.1 + - + +
13B LEU* 3.5 9.2 - - - +
14B ALA 3.2 0.2 - - - -
15B ALA* 1.3 72.4 - - - +
17B ASP* 1.3 58.0 + - - +
19B LEU* 2.7 33.0 + - - +
20B LEU* 3.3 13.8 + - + +
44B LEU* 4.5 11.4 - - + -
47B VAL* 3.8 13.7 - - + -
49B PHE* 3.6 35.7 - - + -
52B LEU* 4.7 0.2 - - + -
71B ALA* 3.8 23.1 - - + +
74B ARG* 4.5 9.9 - - + -
75B LEU* 4.1 26.9 - - + -
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Residues in contact with ASP 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 2.9 12.1 + - - +
14B ALA* 3.2 13.0 + - - +
16B ILE* 1.3 76.9 - - - +
18B ASN* 1.3 62.9 + - - +
19B LEU 3.0 1.4 + - - -
20B LEU* 3.2 32.5 + - - +
21B PRO* 3.8 4.0 - - - +
74B ARG* 3.4 34.9 + - - +
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Residues in contact with ASN 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 ALA 3.0 10.5 + - - +
15B ALA* 3.5 14.5 - - - +
16B ILE 3.2 0.2 - - - -
17B ASP* 1.3 75.5 - - - +
19B LEU* 1.3 60.7 + - - +
20B LEU 3.4 0.2 - - - -
21B PRO* 3.5 7.5 - - - +
22B GLU* 3.0 21.3 - - - +
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Residues in contact with LEU 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 ALA 3.3 10.6 + - - +
16B ILE* 2.7 20.3 + - + +
18B ASN* 1.3 77.4 - - - +
20B LEU* 1.3 63.3 + - - +
22B GLU* 3.1 33.2 + - + +
23B ILE* 3.4 26.5 + - + +
43B ALA* 3.9 38.8 - - + +
44B LEU* 4.0 26.2 - - + -
47B VAL* 4.2 24.0 - - + -
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Residues in contact with LEU 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 17.7 + - + +
17B ASP* 3.5 30.7 - - - +
19B LEU* 1.3 74.4 - - - +
21B PRO* 1.4 65.6 - - + +
23B ILE* 3.2 2.5 + - + -
24B ARG* 2.9 30.5 + - - +
74B ARG* 3.6 41.1 - - + +
75B LEU* 4.0 22.0 - - + +
77B SER* 4.7 2.9 - - - +
78B VAL* 3.4 29.2 - - + +
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Residues in contact with PRO 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 ASP 3.8 5.4 - - - +
18B ASN* 3.5 16.8 - - - +
19B LEU 3.5 1.3 - - - -
20B LEU* 1.4 90.8 - - + +
22B GLU* 1.3 65.9 + - - +
23B ILE 3.2 0.2 + - - -
24B ARG* 3.3 28.1 + - - +
25B ASP* 3.0 32.8 + - - +
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Residues in contact with GLU 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 ASN* 3.0 29.4 - - - +
19B LEU* 3.1 25.0 + - + +
21B PRO* 1.3 80.1 - - - +
23B ILE* 1.3 61.8 + - + +
25B ASP* 3.4 8.5 + - - +
26B ARG* 3.0 40.9 + - - +
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Residues in contact with ILE 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 LEU* 3.4 35.0 - - + +
20B LEU* 3.2 8.7 + - + +
21B PRO 3.2 0.6 - - - -
22B GLU* 1.3 76.1 - - + +
24B ARG* 1.3 64.9 + - - +
26B ARG* 3.2 14.8 + - + +
27B ALA* 3.1 20.6 + - - +
30B THR* 6.0 0.7 - - - +
40B THR* 4.4 23.8 - - + +
43B ALA* 6.3 0.2 - - + -
44B LEU* 5.0 0.7 - - + -
75B LEU* 3.7 29.4 - - + +
78B VAL* 3.7 15.0 - - + -
79B CYS* 3.8 18.1 - - + -
82B THR* 4.0 16.8 - - + +
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Residues in contact with ARG 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 LEU* 2.9 17.6 + - - +
21B PRO* 3.6 34.3 + - - +
23B ILE* 1.3 76.0 - - - +
25B ASP* 1.3 70.7 + - - +
27B ALA* 3.2 20.1 + - + +
77B SER 5.9 0.4 - - - -
78B VAL* 3.3 43.3 - - + +
357B ARG* 5.0 3.2 + - - +
358B PHE* 6.0 1.8 - - + -
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Residues in contact with ASP 25 (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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21B PRO* 3.0 21.7 + - - +
22B GLU* 4.0 6.7 - - - +
23B ILE 3.3 0.2 - - - -
24B ARG* 1.3 87.1 + - - +
26B ARG* 1.3 58.5 + - - +
27B ALA 3.4 0.4 + - - -
28B GLN* 4.8 3.3 + - - +
29B ALA* 5.3 0.9 + - - +
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Residues in contact with ARG 26 (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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22B GLU* 3.0 35.4 + - - +
23B ILE* 3.2 16.8 + - + +
25B ASP* 1.3 73.4 - - - +
27B ALA* 1.3 66.5 + - - +
28B GLN 3.2 3.1 - - - -
29B ALA* 3.0 17.3 + - + +
30B THR* 2.8 28.2 + - - +
37B PRO* 4.2 16.6 - - - +
39B GLU* 2.4 50.9 + - - +
40B THR* 3.4 28.0 + - - +
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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