Contacts of the helix formed by residues 19 - 32 (chain D) in PDB entry 4O46
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 ARG 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ALA 6.2 0.2 - - - -
56B ARG* 4.5 12.9 - - - +
59B SER* 3.8 12.2 + - - +
85B TYR* 3.2 20.3 + - - +
88B LYS* 4.1 9.9 - - - +
89B ILE* 3.6 35.8 - - - +
92B GLU* 2.8 42.2 + - - -
14D ALA* 2.8 19.5 + - - +
17D ALA* 3.5 15.0 - - - +
18D GLU* 1.3 70.3 - - - +
20D TYR* 1.3 59.3 + - - +
21D ASP 3.3 3.4 - - - -
22D ASP* 2.9 37.1 + - + +
23D MET 3.1 21.3 + - - -
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Residues in contact with TYR 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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15D GLU* 3.9 21.3 + - + +
18D GLU* 3.8 41.6 + - + +
19D ARG* 1.3 69.8 - - - +
21D ASP* 1.4 59.2 + - - +
23D MET* 3.6 29.1 - - - +
24D ALA* 2.9 31.2 + - - +
47D VAL* 4.5 4.3 - - + -
48D ALA 4.0 2.4 - - - +
51D ASN* 3.4 56.4 + - + -
52D VAL* 3.4 14.6 - - + +
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Residues in contact with ASP 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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19D ARG 3.3 1.4 - - - -
20D TYR* 1.4 75.7 - - - +
22D ASP* 1.4 61.6 + - - +
24D ALA* 3.4 3.7 + - - +
25D ALA* 3.0 27.9 + - - +
52D VAL* 3.5 28.5 - - - +
56D ARG* 4.1 17.4 + - - -
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Residues in contact with ASP 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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85B TYR* 2.7 35.5 + - + +
88B LYS* 3.5 20.2 + - - -
10D LYS* 5.2 5.7 - - + +
14D ALA* 4.0 4.8 - - + +
19D ARG* 2.9 38.7 + - - +
21D ASP* 1.4 77.4 - - - +
23D MET* 1.4 63.0 + - - +
25D ALA* 3.5 8.2 + - - +
26D ALA* 3.1 23.0 + - - +
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Residues in contact with MET 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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11D ALA* 3.3 21.5 - - + +
14D ALA* 3.6 10.7 - - + +
15D GLU* 3.7 34.1 - - + +
19D ARG 3.1 13.8 + - - +
20D TYR* 3.6 23.8 - - - +
21D ASP 3.3 0.2 - - - -
22D ASP* 1.4 72.4 - - - +
24D ALA* 1.4 64.7 + - - +
26D ALA* 3.3 4.9 + - - +
27D MET* 3.0 24.0 + - + +
44D LEU* 3.3 50.7 - - + +
47D VAL* 4.0 7.0 - - + -
48D ALA* 3.7 19.5 - - + -
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Residues in contact with ALA 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 TYR 2.9 17.2 + - - +
21D ASP* 3.7 4.7 - - - +
23D MET* 1.4 74.3 - - - +
25D ALA* 1.4 52.8 + - - +
27D MET* 3.4 1.9 + - - +
28D LYS* 2.8 35.2 + - - +
48D ALA* 3.5 16.0 - - + +
49D TYR* 3.8 37.5 + - + -
52D VAL* 4.2 11.9 - - + -
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Residues in contact with ALA 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 ASP 3.0 15.0 + - - +
22D ASP* 3.5 12.8 - - - +
24D ALA* 1.4 75.6 - - - +
26D ALA* 1.3 62.2 + - - +
28D LYS* 3.2 9.7 + - - +
29D ASN* 3.0 22.9 + - - +
49D TYR* 5.5 0.2 - - - -
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Residues in contact with ALA 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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7D LEU* 3.3 31.4 - - + +
10D LYS* 4.5 10.1 - - + -
11D ALA* 3.9 14.4 - - + +
22D ASP 3.1 10.5 + - - +
23D MET 3.6 8.1 - - - +
25D ALA* 1.3 76.4 - - - +
27D MET* 1.4 58.5 + - - +
29D ASN* 3.3 8.4 + - - +
30D VAL* 3.1 32.8 + - - +
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Residues in contact with MET 27 (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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8D VAL* 4.6 4.9 - - + -
11D ALA* 3.7 23.8 - - + -
23D MET* 3.0 20.0 + - + +
24D ALA* 4.0 3.6 - - - +
26D ALA* 1.4 72.2 - - - +
28D LYS* 1.4 59.6 + - - +
30D VAL* 3.4 27.2 + - + +
31D THR* 2.9 32.8 + - - -
37D LEU* 4.7 4.3 - - + -
41D GLU* 3.2 43.7 - - + +
44D LEU* 3.8 17.0 - - - +
45D LEU* 3.7 38.4 - - + +
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Residues in contact with LYS 28 (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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28C LYS* 4.0 12.1 - - - +
32C GLU* 3.4 24.1 + - - -
24D ALA 2.8 18.8 + - - +
25D ALA* 3.5 8.1 - - - +
27D MET* 1.4 75.3 - - - +
29D ASN* 1.4 57.7 + - - +
31D THR* 3.2 4.5 + - - -
32D GLU* 2.9 57.7 + - - +
45D LEU* 4.4 0.8 - - - +
49D TYR* 3.6 13.5 - - - +
99D ASP* 3.2 29.7 + - - +
103D LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 29 (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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98C GLN* 6.4 0.2 - - - +
2D VAL* 5.0 5.1 - - - +
7D LEU* 3.8 32.7 - - + +
25D ALA 3.0 12.3 + - - +
26D ALA* 3.3 10.7 + - - +
28D LYS* 1.4 72.6 - - - +
30D VAL* 1.4 63.5 + - - +
32D GLU* 3.4 24.7 + - - +
33D LEU* 3.4 20.7 + - - +
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Residues in contact with VAL 30 (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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4D ARG* 3.6 44.1 + - + +
7D LEU* 3.7 24.9 - - + -
8D VAL* 3.9 22.7 - - + -
26D ALA 3.1 18.4 + - - +
27D MET* 3.6 17.5 - - + +
28D LYS 3.3 0.4 - - - -
29D ASN* 1.4 72.7 - - - +
31D THR* 1.4 62.6 + - - +
33D LEU* 3.1 28.1 + - - +
34D ASN 4.5 0.2 + - - -
35D GLU 4.7 1.0 - - - +
37D LEU* 3.8 11.1 - - + +
41D GLU* 4.6 0.9 - - - -
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Residues in contact with THR 31 (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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27D MET 2.9 15.1 + - - -
28D LYS* 3.4 9.2 - - - -
30D VAL* 1.4 74.5 - - - +
32D GLU* 1.3 56.3 - - - +
33D LEU 3.0 5.5 + - - -
34D ASN* 3.1 13.7 + - - -
35D GLU 4.6 4.1 + - - +
37D LEU* 3.8 24.8 - - - +
45D LEU* 3.9 9.4 - - - +
103D LEU* 3.8 21.3 - - + -
107D TYR* 3.4 27.3 - - + +
108D LEU* 3.7 29.5 - - + +
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Residues in contact with GLU 32 (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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28C LYS* 3.4 22.9 + - - -
32C GLU* 2.9 25.8 - - - +
99C ASP* 4.5 4.0 - - - +
102C SER* 3.1 30.2 + - - +
103C LEU* 5.6 1.0 - - - +
106C ASN* 4.1 1.6 + - - -
107C TYR* 5.9 0.3 - - - -
28D LYS* 2.9 36.8 + - - +
29D ASN* 3.7 22.0 + - - +
30D VAL 3.3 0.6 - - - -
31D THR* 1.3 72.7 - - - +
33D LEU* 1.3 57.2 + - - +
34D ASN 3.2 4.6 + - - -
103D LEU* 4.3 6.4 - - + +
107D TYR* 3.7 33.5 + - + +
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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