Contacts of the helix formed by residues 9 - 30 (chain A) in PDB entry 1A4I
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 GLY 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU 3.1 7.5 + - - -
8A ASN* 1.3 70.6 - - - +
10A LYS* 1.3 53.1 + - - +
12A ILE* 4.4 0.4 - - - -
13A SER* 2.7 40.9 + - - -
155A LEU* 4.3 5.2 - - - -
273A GLY 3.0 11.2 + - - -
274A GLY 3.3 23.6 - - - -
277A PRO* 3.8 6.3 - - - +
278A MET* 3.9 13.0 - - - +
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Residues in contact with LYS 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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8A ASN* 3.1 13.5 + - - +
9A GLY* 1.3 75.9 - - - +
11A GLU* 1.3 66.1 + - + +
13A SER* 3.0 7.3 + - - -
14A ALA* 3.0 29.1 + - - +
17A ARG* 4.7 1.2 + - - -
273A GLY* 3.3 13.8 + - - +
277A PRO* 3.8 11.6 - - + +
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Residues in contact with GLU 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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8A ASN* 3.2 39.0 + - + +
10A LYS* 1.3 80.3 - - + +
12A ILE* 1.3 66.6 + - + +
14A ALA* 3.3 7.6 + - - +
15A GLN* 3.1 37.3 + - - +
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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
----------------------------------------------------------
7A LEU* 4.4 3.4 - - + -
8A ASN* 2.9 31.6 + - + +
11A GLU* 1.3 76.9 - - + +
13A SER* 1.4 63.7 + - - +
15A GLN* 3.1 17.7 + - - +
16A ILE* 3.0 28.0 + - + +
154A GLU* 4.8 3.1 - - + +
155A LEU* 3.7 22.7 - - + -
158A GLU* 3.8 44.2 - - + +
278A MET* 3.5 28.5 - - + -
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Residues in contact with SER 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 GLY 2.7 25.2 + - - -
10A LYS* 3.0 9.2 + - - -
12A ILE* 1.4 79.1 - - - +
14A ALA* 1.3 55.9 + - - +
16A ILE* 3.1 3.4 + - - +
17A ARG* 2.8 50.9 + - - +
277A PRO* 3.3 32.6 - - - +
278A MET* 3.7 10.5 - - - -
281A ALA* 4.0 9.6 - - - +
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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 LYS 3.0 19.1 + - - +
11A GLU* 3.3 8.3 + - - +
13A SER* 1.3 75.3 + - - +
15A GLN* 1.3 58.5 + - + +
17A ARG* 3.5 24.5 - - - +
18A ALA* 2.9 29.3 + - - +
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Residues in contact with GLN 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 GLU* 3.1 31.7 + - - +
12A ILE* 3.1 21.7 + - - +
14A ALA* 1.3 76.6 - - + +
16A ILE* 1.3 64.1 + - + +
18A ALA* 3.3 7.3 + - - +
19A ARG* 3.1 22.7 + - - +
158A GLU* 5.1 4.7 - - - +
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Residues in contact with ILE 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* 3.0 18.1 + - + +
13A SER* 3.1 6.5 + - - +
15A GLN* 1.3 78.2 - - + +
17A ARG* 1.3 57.9 + - - +
19A ARG* 3.2 40.3 + - - +
20A LEU* 2.9 38.0 + - + +
154A GLU* 4.2 16.4 - - + +
278A MET* 3.8 24.5 - - + -
281A ALA* 4.0 15.3 - - + -
282A MET* 3.6 28.7 - - + -
285A GLN* 4.2 0.4 - - - +
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Residues in contact with ARG 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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10A LYS 4.9 0.8 + - - -
13A SER* 2.8 52.7 + - - +
14A ALA* 3.5 26.4 - - - +
16A ILE* 1.3 74.7 - - - +
18A ALA* 1.3 57.9 - - - +
20A LEU* 3.3 8.1 + - + +
21A LYS* 2.9 29.3 + - - +
59A ALA* 4.2 27.1 - - - +
62A GLU* 4.4 14.7 + - + +
63A ILE* 3.7 20.8 - - + +
277A PRO* 4.8 6.1 + - - +
280A VAL* 5.5 2.0 - - - +
281A ALA* 4.3 18.2 - - + +
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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 2.9 16.9 + - - +
15A GLN* 3.6 7.6 - - - +
16A ILE 3.3 0.2 - - - -
17A ARG* 1.3 78.2 - - - +
19A ARG* 1.3 61.5 + - - +
21A LYS* 3.3 10.2 + - - +
22A ASN* 3.1 29.3 + - - +
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Residues in contact with ARG 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 GLN 3.1 12.6 + - - +
16A ILE* 3.6 38.7 - - - +
18A ALA* 1.3 75.0 - - - +
20A LEU* 1.4 74.6 + - - +
22A ASN* 3.2 8.9 + - - +
23A GLN* 2.9 54.3 + - + +
154A GLU* 5.1 4.8 + - - -
285A GLN* 2.6 34.4 + - - +
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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 ILE* 2.9 29.0 + - + +
17A ARG* 3.6 5.2 - - - +
18A ALA 3.3 0.2 - - - -
19A ARG* 1.4 95.5 - - - +
21A LYS* 1.3 55.6 + - - +
23A GLN* 3.1 21.9 + - - +
24A VAL* 2.8 34.8 + - - +
63A ILE* 4.0 18.4 - - + -
281A ALA* 3.8 8.3 - - - +
284A MET* 3.8 16.4 - - + -
285A GLN* 3.5 39.0 - - + +
288A VAL* 4.1 14.6 - - + -
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG 2.9 17.2 + - - +
18A ALA* 3.5 9.0 - - - +
20A LEU* 1.3 74.8 - - - +
22A ASN* 1.3 67.0 + - - +
24A VAL* 3.2 2.4 + - - +
25A THR* 2.9 40.0 + - - +
62A GLU 3.4 24.3 + - - +
63A ILE* 3.6 22.8 - - + +
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Residues in contact with ASN 22 (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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18A ALA* 3.1 17.0 + - - +
19A ARG* 3.6 9.7 - - - +
21A LYS* 1.3 86.5 + - - +
23A GLN* 1.3 62.0 + - + +
25A THR* 3.3 9.3 + - - +
26A GLN* 3.0 39.4 + - + +
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Residues in contact with GLN 23 (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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19A ARG* 2.9 52.8 + - + +
20A LEU* 3.1 23.4 + - - +
22A ASN* 1.3 75.3 - - + +
24A VAL* 1.4 64.3 + - - +
26A GLN* 3.3 12.1 + - - +
27A LEU* 3.0 23.6 + - - +
288A VAL* 4.3 15.0 - - + +
292A LYS* 6.3 0.7 - - - +
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Residues in contact with VAL 24 (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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20A LEU 2.8 21.5 + - - +
23A GLN* 1.4 71.5 - - - +
25A THR* 1.3 65.3 + - - +
27A LEU* 3.6 7.6 - - + +
28A LYS* 2.9 36.8 + - + +
36A PRO* 4.2 19.1 - - + -
63A ILE* 3.5 30.1 - - + +
64A GLY* 3.7 21.5 - - - +
65A ILE* 4.5 2.0 - - + -
288A VAL* 3.6 33.4 - - + -
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Residues in contact with THR 25 (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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21A LYS* 2.9 28.9 + - - +
22A ASN* 3.7 11.0 + - - +
24A VAL* 1.3 76.2 - - - +
26A GLN* 1.3 60.1 + - + +
28A LYS* 3.2 10.4 + - + +
29A GLU* 2.9 45.4 + - + +
63A ILE 5.3 0.7 + - - -
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Residues in contact with GLN 26 (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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22A ASN* 3.0 33.7 + - + +
23A GLN* 3.7 10.6 - - - +
25A THR* 1.3 78.4 - - + +
27A LEU* 1.3 56.6 + - - +
29A GLU* 3.0 31.1 + - - +
30A GLN* 3.0 35.4 + - - +
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Residues in contact with LEU 27 (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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23A GLN 3.0 16.4 + - - +
24A VAL* 3.3 7.4 + - + +
26A GLN* 1.3 74.1 - - - +
28A LYS* 1.3 59.2 + - + +
30A GLN* 3.2 19.8 + - - +
31A VAL* 3.0 31.9 + - + +
34A PHE* 3.8 27.0 - - + -
36A PRO* 4.4 13.2 - - + -
288A VAL* 5.4 8.3 - - + +
291A ALA* 4.8 1.1 - - + -
292A LYS* 4.8 35.7 - - + +
295A LEU* 3.6 26.7 - - + -
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Residues in contact with LYS 28 (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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24A VAL* 2.9 26.8 + - + +
25A THR* 3.5 12.1 - - + +
27A LEU* 1.3 79.7 - - + +
29A GLU* 1.3 57.3 + - - +
31A VAL 4.2 4.9 - - - -
32A PRO* 3.1 31.7 - - + +
33A GLY 5.7 1.1 - - - +
34A PHE* 3.5 24.0 - - + +
35A THR* 4.1 16.3 - - + +
36A PRO* 4.1 6.5 - - + -
64A GLY* 2.9 37.5 + - - -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 2.9 31.7 + - + +
26A GLN* 3.0 20.7 + - - +
28A LYS* 1.3 79.0 - - + +
30A GLN* 1.3 62.4 + - + +
32A PRO* 3.8 12.3 - - - +
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Residues in contact with GLN 30 (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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26A GLN* 3.0 35.7 + - - +
27A LEU* 3.2 23.4 + - - +
29A GLU* 1.3 82.0 - - + +
31A VAL* 1.3 67.6 + - + +
32A PRO* 3.5 5.4 - - - +
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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
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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