Contacts of the helix formed by residues 12 - 27 (chain A) in PDB entry 4H7Y
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 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA 3.0 15.2 + - - +
11A ASN* 1.3 77.5 - - - +
13A PRO* 1.3 75.2 - - + +
14A GLU* 3.1 16.6 + - - +
15A ASP* 2.8 51.8 + - - +
16A TRP* 3.1 21.2 + - - -
49A LEU* 3.7 5.4 - - - -
54A TYR* 4.0 4.9 - - + +
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Residues in contact with PRO 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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12A ASN* 1.3 89.7 - - + +
14A GLU* 1.3 63.1 + - - +
17A LEU* 2.8 32.6 + - - +
49A LEU* 3.9 15.9 - - + -
54A TYR* 3.4 48.5 - - + -
57A ASN* 3.5 23.1 - - - +
59A SER* 3.8 2.5 - - - -
60A PHE* 3.6 22.0 - - + +
63A ILE* 3.5 4.4 - - + +
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Residues in contact with GLU 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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12A ASN* 3.1 14.5 + - - +
13A PRO* 1.3 84.8 - - - +
15A ASP* 1.3 64.7 + - - +
17A LEU* 3.5 3.0 + - - +
18A SER* 3.1 27.0 + - - -
57A ASN* 3.0 26.8 + - - +
59A SER* 3.6 20.8 + - - +
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Residues in contact with ASP 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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10A ALA* 3.7 27.4 + - + +
12A ASN* 2.8 34.8 + - - +
14A GLU* 1.3 74.0 - - - +
16A TRP* 1.3 63.9 + - - +
18A SER* 3.4 7.8 + - - -
19A LEU* 3.1 23.1 + - - +
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Residues in contact with TRP 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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10A ALA 4.1 11.8 + - - -
11A ASN* 3.2 20.0 + - - +
12A ASN 3.1 25.7 + - - +
13A PRO 3.8 3.6 - - - +
15A ASP* 1.3 77.2 - - - +
17A LEU* 1.3 57.2 + - - +
19A LEU* 3.2 23.0 + - + +
20A LEU* 2.9 37.1 + - + +
41A ARG* 3.6 32.3 - - - -
44A GLN 4.1 0.2 - - - -
45A ALA* 3.4 36.6 - - + -
48A ALA* 4.0 18.3 - - + +
49A LEU* 3.8 18.4 - - + -
63A ILE* 3.8 14.6 - - + -
47D GLU* 3.3 29.2 - - - -
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Residues in contact with LEU 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 PRO 2.8 21.7 + - - +
14A GLU* 3.9 4.0 - - - +
15A ASP 3.4 0.2 - - - -
16A TRP* 1.3 72.2 - - - +
18A SER* 1.3 57.9 + - - +
20A LEU* 3.3 3.4 + - + +
21A LEU* 2.8 56.6 + - + +
42A TYR* 4.7 9.9 - - - +
59A SER* 3.9 15.7 - - - +
62A ARG* 3.6 55.4 - - + +
63A ILE* 3.9 22.8 - - + +
66A ARG* 5.2 2.9 - - + -
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Residues in contact with SER 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 GLU 3.1 18.0 + - - -
15A ASP* 3.7 8.9 + - - -
16A TRP 3.3 0.2 - - - -
17A LEU* 1.3 77.9 - - - +
19A LEU* 1.3 55.5 + - - +
21A LEU* 3.5 7.1 + - - +
22A LYS* 3.0 30.7 + - - +
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Residues in contact with LEU 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 ASP 3.1 14.1 + - - +
16A TRP* 3.2 22.2 + - + +
18A SER* 1.3 75.4 - - - +
20A LEU* 1.3 68.0 + - + +
22A LYS* 3.4 8.4 + - - +
23A LEU* 2.9 31.7 + - + +
41A ARG* 3.9 48.9 - - + +
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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 TRP* 2.9 27.2 + - + +
17A LEU* 3.7 4.5 - - + +
19A LEU* 1.3 80.0 - - + +
21A LEU* 1.3 64.5 + - - +
23A LEU* 3.3 5.1 + - + +
24A GLU* 3.1 22.7 + - - +
38A LEU* 3.9 6.9 - - + +
41A ARG* 3.7 35.0 - - + +
42A TYR* 3.6 62.6 + - + +
45A ALA* 3.8 22.4 - - + -
63A ILE* 4.3 10.3 - - + -
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Residues in contact with LEU 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 LEU* 2.8 50.1 + - + +
18A SER* 4.0 5.8 - - - +
20A LEU* 1.3 71.3 - - - +
22A LYS* 1.3 57.8 + - - +
24A GLU* 3.5 6.5 + - - +
25A LYS* 3.0 27.9 + - - +
42A TYR* 4.4 11.2 - - - +
62A ARG* 5.5 4.0 - - - +
66A ARG* 4.9 2.9 - - - -
28B VAL* 4.7 7.5 - - + +
29B PRO* 4.4 30.7 - - + -
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Residues in contact with LYS 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 SER 3.0 18.7 + - - +
19A LEU* 3.6 8.3 - - - +
20A LEU 3.2 0.2 - - - -
21A LEU* 1.3 76.6 - - - +
23A LEU* 1.3 59.3 + - - +
25A LYS* 3.3 11.4 + - + +
26A ASN* 2.9 48.7 + - - +
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Residues in contact with LEU 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 LEU* 2.9 20.5 + - + +
20A LEU* 3.3 7.2 + - + +
22A LYS* 1.3 76.7 - - - +
24A GLU* 1.3 58.1 + - - +
26A ASN* 3.2 9.5 + - + +
27A SER* 2.7 35.7 + - - +
37A LYS* 3.9 34.1 - - + +
38A LEU* 3.9 22.2 - - + -
41A ARG* 3.8 39.9 - - + +
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Residues in contact with GLU 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 3.1 16.0 + - - +
21A LEU* 3.8 7.0 - - - +
23A LEU* 1.3 74.6 - - - +
25A LYS* 1.3 67.0 + - - +
27A SER* 3.0 15.9 + - - -
28A VAL* 3.5 11.6 + - - +
30A LEU* 4.3 10.8 - - + +
38A LEU* 3.7 31.1 - - + +
42A TYR* 4.6 8.7 + - - -
66A ARG* 4.7 4.3 + - - -
70A LEU* 5.0 0.8 - - - +
28B VAL* 3.7 16.3 - - + +
29B PRO* 3.2 22.7 - - - +
30B LEU* 2.5 40.5 + - - +
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Residues in contact with LYS 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 LEU 3.0 18.7 + - - +
22A LYS* 3.3 10.1 + - + +
24A GLU* 1.3 77.3 - - - +
26A ASN* 1.3 75.3 + - - +
27A SER 3.3 0.9 + - - -
28A VAL* 3.5 15.9 + - - +
25B LYS* 4.6 17.2 + - + +
28B VAL* 4.3 17.9 - - + +
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Residues in contact with ASN 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 LYS* 2.9 44.5 + - - +
23A LEU* 3.6 10.4 - - + +
24A GLU 3.2 0.2 - - - -
25A LYS* 1.3 93.8 + - - +
27A SER* 1.3 60.0 + - - +
28A VAL 3.5 4.6 + - - +
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Residues in contact with SER 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.7 24.6 + - - +
24A GLU* 3.0 9.4 + - - -
26A ASN* 1.3 79.2 - - - +
28A VAL* 1.3 60.0 + - - +
29A PRO 2.9 20.6 - - - +
30A LEU* 3.5 21.7 + - - -
34A LEU* 3.2 28.1 + - - +
37A LYS* 4.0 18.7 + - - -
38A LEU* 5.7 2.3 - - - +
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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