Contacts of the helix formed by residues 5 - 25 (chain A) in PDB entry 4U7Y
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 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A SER* 3.8 4.8 + - - -
4A THR* 1.3 76.4 - - - +
6A PRO* 1.3 63.9 - - - +
7A ASN 3.4 2.6 + - - -
8A LEU* 2.9 27.8 + - - +
9A GLN* 2.7 31.9 + - - +
48A GLU* 2.7 31.2 + - - -
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Residues in contact with PRO 6 (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 THR 4.3 2.2 - - - +
5A SER* 1.3 88.7 - - - +
7A ASN* 1.3 59.7 + - - +
9A GLN* 3.6 7.7 - - + +
10A LYS* 2.9 28.1 + - - +
48A GLU* 5.7 0.7 - - - +
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Residues in contact with ASN 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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5A SER* 3.3 1.4 + - - -
6A PRO* 1.3 81.3 - - - +
8A LEU* 1.3 62.6 + - - +
10A LYS* 3.2 6.7 + - - +
11A ALA* 3.1 18.9 + - - +
40A TYR* 3.5 34.9 - - + +
43A HIS* 4.0 19.5 + - + -
44A VAL* 3.8 11.7 - - + -
48A GLU* 3.0 26.3 + - - +
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Residues in contact with LEU 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 THR* 4.3 14.4 - - + +
5A SER* 2.9 25.6 + - - +
7A ASN* 1.3 77.5 - - - +
9A GLN* 1.3 61.7 + - - +
11A ALA* 3.2 2.4 + - - +
12A ILE* 3.2 39.6 + - + +
41A PHE* 3.6 33.0 - - + -
44A VAL* 3.5 28.0 - - + +
58A ILE* 4.5 14.4 - - + -
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Residues in contact with GLN 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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4A THR* 3.3 24.5 + - + +
5A SER 2.7 15.8 + - - +
6A PRO* 3.6 9.6 - - + +
7A ASN 3.2 0.2 - - - -
8A LEU* 1.3 75.0 - - - +
10A LYS* 1.3 65.0 + - - +
12A ILE* 3.4 18.0 + - - +
13A ASP* 3.0 56.5 + - - +
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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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6A PRO 2.9 12.8 + - - +
7A ASN* 3.3 12.1 - - - +
9A GLN* 1.3 78.1 - - - +
11A ALA* 1.3 60.7 + - - +
13A ASP* 3.9 5.2 - - - +
14A LEU* 3.0 47.7 + - + +
40A TYR* 4.1 24.7 - - + -
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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 ASN 3.1 7.6 + - - +
8A LEU* 3.5 11.9 - - - +
9A GLN 3.2 0.2 - - - -
10A LYS* 1.3 77.9 - - - +
12A ILE* 1.3 57.1 + - - +
15A ALA* 3.0 29.8 + - - +
37A ALA* 3.6 11.8 - - - +
40A TYR* 3.6 26.2 - - + -
41A PHE* 3.6 36.9 - - + +
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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
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4A THR* 4.5 10.5 - - + +
8A LEU* 3.2 37.1 + - + +
9A GLN* 3.9 21.3 - - - +
10A LYS 3.3 0.2 - - - -
11A ALA* 1.3 76.6 - - - +
13A ASP* 1.3 62.0 + - - +
15A ALA* 3.4 3.8 + - - +
16A SER* 2.8 31.0 + - - -
41A PHE* 4.2 17.3 - - + -
61A LYS* 6.4 0.4 - - - +
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Residues in contact with ASP 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 GLN* 3.0 46.8 + - - +
10A LYS* 3.9 6.3 + - - +
12A ILE* 1.3 78.6 - - - +
14A LEU* 1.3 64.2 + - + +
16A SER* 3.1 8.8 + - - -
17A LYS* 2.9 24.2 + - - +
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Residues in contact with LEU 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 33.9 + - + +
11A ALA 3.8 3.4 - - - +
13A ASP* 1.3 76.9 - - + +
15A ALA* 1.3 57.0 + - - +
17A LYS* 3.3 7.2 + - - +
18A ALA* 2.8 28.2 + - - +
33A LEU* 3.8 28.3 - - + +
36A HIS* 3.7 39.9 - - + +
37A ALA* 3.8 10.8 - - + +
40A TYR* 3.9 17.3 - - + -
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Residues in contact with ALA 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 3.0 19.7 + - - +
12A ILE* 3.7 5.6 - - - +
14A LEU* 1.3 74.6 - - - +
16A SER* 1.3 64.2 + - - +
18A ALA* 3.1 7.7 + - - +
19A ALA* 2.9 24.8 + - - +
34A TYR* 4.7 3.3 - - - -
37A ALA* 3.7 11.4 - - + +
41A PHE* 4.3 2.5 - - + -
65A TYR* 3.6 40.9 + - + +
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Residues in contact with SER 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 21.5 + - - -
13A ASP* 3.1 10.3 + - - -
15A ALA* 1.3 77.9 - - - +
17A LYS* 1.3 57.9 + - - +
19A ALA* 3.4 6.8 + - - +
20A GLN* 3.0 26.4 + - - +
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Residues in contact with LYS 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 ASP 2.9 14.8 + - - +
14A LEU* 3.7 6.1 - - - +
16A SER* 1.3 74.7 + - - +
18A ALA* 1.3 58.1 + - - +
20A GLN* 3.3 7.5 + - - +
21A GLU* 2.8 35.5 + - + +
33A LEU* 3.7 18.4 - - + -
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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 LEU 2.8 14.6 + - - +
15A ALA* 3.1 10.5 + - - +
17A LYS* 1.3 75.9 - - - +
19A ALA* 1.3 52.8 + - - +
21A GLU* 3.3 1.8 + - - +
22A ASP* 2.6 37.9 + - - +
30A ALA* 3.8 4.8 - - - +
33A LEU* 3.5 25.7 - - + +
34A TYR* 3.5 37.0 - - + +
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Residues in contact with ALA 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 ALA 2.9 12.5 + - - +
16A SER* 3.5 11.4 - - - +
18A ALA* 1.3 75.4 - - - +
20A GLN* 1.3 63.9 + - - +
22A ASP* 3.4 2.0 - - - +
23A LYS* 3.0 30.3 + - + +
34A TYR* 3.6 15.4 + - + +
65A TYR* 6.2 2.2 - - + -
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Residues in contact with GLN 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 SER 3.0 14.8 + - - +
17A LYS* 3.5 11.9 - - - +
19A ALA* 1.3 76.9 - - - +
21A GLU* 1.3 66.8 + - + +
23A LYS* 3.3 5.3 + - - +
24A ALA* 3.1 22.4 + - - +
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Residues in contact with GLU 21 (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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17A LYS* 2.8 24.7 + - + +
18A ALA 3.7 2.2 - - - +
20A GLN* 1.3 74.3 - - + +
22A ASP* 1.3 63.9 + - - +
24A ALA* 3.1 12.6 + - - +
25A GLY 3.2 8.5 + - - -
26A ASN* 3.2 39.6 + - - +
29A GLU* 3.3 23.8 - - + +
30A ALA* 4.0 20.0 - - - +
33A LEU* 3.7 15.5 - - + -
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Residues in contact with ASP 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 2.6 21.4 + - - +
19A ALA* 3.4 4.7 - - - +
21A GLU* 1.3 71.0 - - - +
23A LYS* 1.3 60.2 + - + +
25A GLY* 2.9 17.3 + - - -
27A TYR* 3.3 17.3 + - - -
30A ALA* 3.6 9.7 - - - +
34A TYR* 2.6 29.1 + - + +
68A ARG* 2.6 50.4 + - - +
72A LEU* 4.6 3.8 - - - -
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Residues in contact with LYS 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 ALA* 3.0 20.4 + - + +
20A GLN* 3.8 5.4 - - - +
22A ASP* 1.3 80.4 - - + +
24A ALA* 1.3 59.4 + - - +
25A GLY* 3.5 0.7 + - - -
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Residues in contact with ALA 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 GLN 3.1 14.2 + - - +
21A GLU* 3.5 14.8 - - - +
22A ASP 3.1 0.4 - - - -
23A LYS* 1.3 75.8 - - - +
25A GLY* 1.3 61.1 + - - +
26A ASN* 3.3 19.7 - - - +
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Residues in contact with GLY 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 GLU 3.2 0.2 + - - -
22A ASP 2.9 14.9 + - - -
23A LYS 3.2 1.8 - - - -
24A ALA* 1.3 79.9 - - - +
26A ASN* 1.3 61.8 + - - +
27A TYR* 3.1 28.7 + - - +
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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