Contacts of the helix formed by residues 19 - 33 (chain E) in PDB entry 4Q96
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 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1620C PRO* 3.9 4.3 - - - -
1621C SER* 3.3 18.4 - - - +
1622C TYR 5.9 0.7 - - - -
17E SER* 2.9 10.3 + - - -
18E ASN* 1.3 78.1 - - - +
20E GLN* 1.3 64.1 + - - +
21E HIS* 3.6 8.2 + - - +
22E SER* 3.0 26.9 + - - -
23E VAL* 3.0 25.1 + - - +
1611F BTN 5.5 3.6 - - - -
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Residues in contact with GLN 20 (chain E).
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* 3.3 41.5 - - + +
24A GLN* 5.4 0.6 + - - -
1620C PRO* 3.8 16.1 - - + +
1621C SER 2.9 22.8 + - - +
1623C SER* 3.8 8.5 - - - -
1626C SER* 4.4 1.5 - - - -
19E SER* 1.3 73.6 - - - +
21E HIS* 1.3 56.9 + - - +
23E VAL* 4.1 11.6 - - - +
24E GLN* 2.9 63.7 + - - +
61E TYR* 5.9 1.6 - - - +
65E ASP* 4.0 5.7 + - - -
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Residues in contact with HIS 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623C SER* 3.6 9.2 - - - +
1625C THR* 4.2 5.8 - - - -
19E SER* 3.1 7.2 + - - +
20E GLN* 1.3 79.7 - - - +
22E SER* 1.3 58.4 + - - +
24E GLN* 3.8 4.2 - - + +
25E THR* 2.6 62.7 + - + +
1611F BTN 3.4 72.5 + + + +
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Residues in contact with SER 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU 4.2 1.7 + - - -
16E LEU* 3.4 12.0 - - - +
17E SER* 2.7 42.4 + - - -
19E SER* 3.0 19.8 + - - -
21E HIS* 1.3 80.4 + - - +
23E VAL* 1.3 62.8 + - - +
25E THR* 3.7 4.6 - - - -
26E LEU* 3.2 25.3 + - - +
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1620C PRO* 4.3 13.0 - - + -
16E LEU* 4.0 10.5 - - + -
19E SER 3.0 20.9 + - - +
20E GLN* 3.7 16.4 - - - +
22E SER* 1.3 77.2 - - - +
24E GLN* 1.3 57.6 + - - +
27E SER* 3.0 27.5 + - - -
58E THR* 3.9 27.8 - - + +
61E TYR* 3.9 10.3 - - + +
62E LEU* 3.4 31.9 - - - +
65E ASP* 4.0 13.5 - - + +
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Residues in contact with GLN 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1623C SER* 5.0 2.4 + - - -
1625C THR* 4.7 2.8 + - - +
1626C SER* 3.7 30.3 + - - -
20E GLN* 2.9 51.6 + - - +
21E HIS* 4.1 3.4 - - + +
23E VAL* 1.3 70.1 - - - +
25E THR* 1.3 65.9 + - - +
27E SER* 4.2 2.0 - - - -
28E LEU* 3.0 26.0 + - + +
65E ASP* 3.2 21.0 + - - +
69E ASN* 5.3 3.2 - - - +
206E UNX 3.1 18.8 + - - +
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Residues in contact with THR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E HIS* 2.6 47.4 + - + +
22E SER* 3.7 5.6 - - - -
24E GLN* 1.3 79.1 - - - +
26E LEU* 1.3 64.1 + - - +
28E LEU* 3.2 10.4 + - - +
29E TRP* 3.4 1.4 + - - +
202E UNX 4.2 13.9 - - - +
204E UNX 2.9 36.7 + - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 4.9 1.6 - - + -
12E LYS* 3.8 50.5 - - + +
13E LEU* 3.9 17.3 - - + +
16E LEU* 4.3 10.3 - - + -
22E SER 3.2 14.8 + - - +
23E VAL 3.9 2.7 - - - +
25E THR* 1.3 79.8 - - - +
27E SER* 1.3 64.5 + - - +
29E TRP* 3.2 14.7 + - + +
30E LEU* 3.0 30.1 + - + +
62E LEU* 3.6 30.3 - - + -
202E UNX 3.9 9.6 - - - +
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Residues in contact with SER 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E VAL 3.0 18.5 + - - -
24E GLN 3.7 3.4 - - - -
26E LEU* 1.3 75.5 - - - +
28E LEU* 1.3 55.4 + - - +
30E LEU* 3.3 3.3 + - - +
31E ILE* 2.9 34.7 + - - +
62E LEU* 3.8 3.5 - - - +
65E ASP* 2.6 34.7 + - - -
66E VAL* 3.5 34.9 + - - +
206E UNX 3.6 2.5 + - - -
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 3.0 22.9 + - + +
25E THR* 3.4 8.7 - - - +
26E LEU 3.2 0.2 - - - -
27E SER* 1.3 75.5 + - - +
29E TRP* 1.3 53.2 + - - +
31E ILE* 3.1 12.0 + - + +
32E HIS* 2.8 35.3 + - - +
204E UNX 3.7 13.5 - - - +
206E UNX 3.6 14.4 - - - +
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Residues in contact with TRP 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E SER 3.9 20.0 + - - +
4E PHE* 3.7 24.9 - + - -
5E SER 4.2 1.1 - - - -
8E ALA* 4.1 7.2 - - + -
9E LEU* 4.0 27.1 - - + -
12E LYS* 3.3 46.1 - - + +
25E THR 3.4 7.4 + - - +
26E LEU* 3.2 13.4 + - + +
28E LEU* 1.3 78.5 - - - +
30E LEU* 1.3 86.6 + - + +
32E HIS* 3.3 10.8 - + - +
33E HIS* 3.0 65.4 + + - -
204E UNX 3.8 7.9 + - - +
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 3.6 30.5 - - + -
13E LEU* 5.8 0.7 - - + -
26E LEU* 3.0 31.1 + - + +
27E SER 3.7 5.4 - - - +
29E TRP* 1.3 87.6 - - + +
31E ILE* 1.3 65.9 + - - +
33E HIS* 3.1 15.2 + - - +
34E ARG* 3.1 13.7 + - - -
40E ILE* 3.6 30.0 - - + +
44E TRP* 6.0 2.9 - - + -
62E LEU* 4.4 12.3 - - + -
66E VAL* 3.8 25.4 - - + -
77E PHE* 3.6 16.3 - - + -
81E PHE* 6.2 2.0 - - + -
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Residues in contact with ILE 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E SER* 2.9 32.2 + - - +
28E LEU* 3.6 13.5 - - + +
30E LEU* 1.3 73.7 - - - +
32E HIS* 1.3 64.4 + - - +
34E ARG* 2.8 47.8 + - - +
66E VAL* 4.2 10.5 - - + +
69E ASN* 3.4 38.6 - - + +
70E SER* 4.1 17.0 - - - +
72E ARG* 6.2 0.2 - - - +
73E LYS* 4.1 26.7 - - + +
77E PHE* 4.4 1.1 - - + -
207E SO4 4.8 1.3 - - - +
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Residues in contact with HIS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU 2.8 13.8 + - - +
29E TRP* 3.3 16.2 - + - +
31E ILE* 1.3 77.9 - - - +
33E HIS* 1.3 83.0 + + - +
34E ARG* 3.5 8.0 + - - +
35E LYS* 6.0 0.3 - - - +
207E SO4 2.8 37.8 + - - +
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Residues in contact with HIS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E SER* 3.8 11.2 + - - -
4E PHE* 3.4 44.8 + + + +
29E TRP* 3.0 65.5 + + - +
30E LEU* 3.1 6.9 + - - +
32E HIS* 1.3 96.7 - + - +
34E ARG* 1.3 56.8 + - - +
35E LYS 3.1 3.4 - - - -
36E HIS* 2.9 23.1 + - + +
40E ILE* 3.3 12.6 - - + +
203E UNX 3.1 23.0 + - - -
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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