Contacts of the helix formed by residues 12 - 26 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ALA* 3.1 20.2 + - - +
11D ASN* 1.3 74.5 + - - +
13D PRO* 1.4 74.6 - - + +
14D GLU* 3.2 14.9 + - - +
15D ASP* 2.8 51.9 + - - +
16D TRP* 3.1 23.6 + - - -
49D LEU* 3.7 6.3 - - - -
54D TYR* 4.1 5.2 - - + +
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Residues in contact with PRO 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 1.4 89.8 - - + +
14D GLU* 1.3 59.6 + - - +
17D LEU* 2.7 36.7 + - - +
49D LEU* 3.9 15.7 - - + -
54D TYR* 3.4 49.4 - - + -
57D ASN* 3.6 13.5 - - - +
59D SER* 3.9 2.0 - - - -
60D PHE* 3.6 31.2 - - + +
63D ILE* 3.6 3.1 - - + +
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 3.2 14.0 + - - +
13D PRO* 1.3 84.1 - - - +
15D ASP* 1.3 66.0 + - - +
17D LEU* 3.3 3.3 + - - +
18D SER* 3.0 27.0 + - - -
57D ASN* 3.0 27.1 + - - +
59D SER* 3.6 21.1 + - - +
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Residues in contact with ASP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA* 3.8 30.1 + - - +
12D ASN* 2.8 36.6 + - - +
14D GLU* 1.3 74.9 - - - +
16D TRP* 1.3 62.9 + - - +
18D SER* 3.4 7.5 + - - -
19D LEU* 3.2 22.0 + - - +
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Residues in contact with TRP 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ALA 4.7 3.0 + - - -
11D ASN* 2.9 31.3 + - - +
12D ASN 3.1 28.8 + - - +
13D PRO 3.7 3.1 - - - +
15D ASP* 1.3 77.0 - - - +
17D LEU* 1.3 62.6 + - - +
19D LEU* 3.3 21.7 + - + +
20D LEU* 3.0 30.7 + - + +
41D ARG* 3.8 39.3 - - - -
44D GLN* 4.1 6.3 - - + -
45D ALA* 3.5 37.5 - - + -
48D ALA* 4.0 17.6 - - + +
49D LEU* 3.8 12.1 - - + -
63D ILE* 3.9 13.7 - - + -
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PRO 2.7 22.4 + - - +
14D GLU* 3.3 4.9 + - - +
16D TRP* 1.3 72.6 - - - +
18D SER* 1.3 57.3 + - - +
20D LEU* 3.2 3.0 + - + +
21D LEU* 2.9 58.8 + - + +
42D TYR* 4.8 9.0 - - - +
59D SER* 3.6 28.9 - - - +
62D ARG* 3.8 46.4 - - + +
63D ILE* 4.0 22.8 - - + +
66D ARG* 6.3 0.2 - - + -
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Residues in contact with SER 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU 3.0 17.1 + - - -
15D ASP* 3.7 8.0 - - - -
16D TRP 3.2 0.2 - - - -
17D LEU* 1.3 77.7 - - - +
19D LEU* 1.3 62.5 + - - +
21D LEU* 3.4 7.6 + - - +
22D LYS* 3.0 25.1 + - - +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ASP 3.2 11.1 + - - +
16D TRP* 3.6 20.9 - - + +
18D SER* 1.3 79.0 - - - +
20D LEU* 1.3 67.2 + - + +
22D LYS* 3.7 9.0 - - - +
23D LEU* 3.0 31.7 + - + +
41D ARG* 3.8 53.4 - - + +
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D TRP* 3.0 26.1 + - + +
17D LEU* 3.2 4.7 + - + +
19D LEU* 1.3 76.6 - - + +
21D LEU* 1.3 60.2 + - - +
23D LEU* 3.5 4.3 + - - +
24D GLU* 3.0 27.7 + - - +
38D LEU* 4.0 6.2 - - + +
41D ARG* 3.7 44.0 - - + +
42D TYR* 3.7 53.3 + - + +
45D ALA* 3.8 22.7 - - + -
63D ILE* 4.2 10.5 - - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 2.9 48.3 + - + +
18D SER* 3.8 6.5 - - - +
20D LEU* 1.3 73.7 - - - +
22D LYS* 1.3 61.8 + - - +
24D GLU* 3.2 13.6 + - + +
25D LYS* 2.9 29.6 + - - +
42D TYR* 4.7 8.5 - - - +
62D ARG* 4.1 23.8 - - - +
66D ARG* 6.1 1.3 - - + -
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Residues in contact with LYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D SER 3.0 19.0 + - - +
19D LEU* 3.7 8.1 - - - +
21D LEU* 1.3 77.6 - - - +
23D LEU* 1.3 57.2 + - - +
25D LYS* 3.2 10.4 + - + +
26D ASN* 2.9 47.1 + - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.0 21.1 + - + +
20D LEU* 3.8 6.1 - - + +
21D LEU 3.3 0.2 - - - -
22D LYS* 1.3 78.3 - - - +
24D GLU* 1.3 57.2 + - - +
26D ASN* 3.4 7.5 + - + +
27D SER* 2.4 43.9 + - - +
37D LYS* 4.5 4.3 - - + +
38D LEU* 3.8 27.6 - - + +
41D ARG* 3.9 32.5 - - + +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU 3.0 17.0 + - - +
21D LEU* 3.2 13.2 + - + +
23D LEU* 1.3 74.6 - - - +
25D LYS* 1.3 65.8 + - - +
27D SER* 3.3 18.3 + - - +
28D VAL* 4.1 5.4 - - - +
30D LEU* 4.6 9.5 - - + +
38D LEU* 3.8 30.0 - - + +
42D TYR* 4.3 6.4 + - - -
66D ARG* 2.8 49.3 + - - +
70D LEU* 4.1 3.3 - - - +
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LEU 2.9 17.1 + - - +
22D LYS* 3.6 11.0 - - + +
24D GLU* 1.3 76.5 - - - +
26D ASN* 1.3 69.9 + - - +
27D SER 3.3 0.4 - - - -
28D VAL* 3.4 26.9 - - - +
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Residues in contact with ASN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LYS* 2.9 41.6 + - - +
23D LEU* 4.1 7.2 - - + +
24D GLU 3.2 0.2 - - - -
25D LYS* 1.3 90.3 - - - +
27D SER* 1.3 61.8 + - - +
28D VAL* 3.5 6.9 + - - -
34D LEU* 5.5 0.7 - - - +
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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