Contacts of the helix formed by residues 17 - 29 (chain E) in PDB entry 4H3K
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 17 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLN* 1.3 77.8 - - - +
18E ARG* 1.3 69.1 + - - +
19E SER 3.5 0.9 - - - -
20E MET* 3.3 1.3 + - - +
21E GLU* 3.0 27.4 + - - +
84E MET* 3.1 31.3 - - + +
87E ARG* 3.9 4.7 + - - +
143E ASP* 2.8 18.5 - - - +
144E ASN 3.6 19.8 + - - +
145E HIS* 3.6 10.0 - - - -
148E ALA* 3.5 16.2 - - - +
5F SEP 3.0 22.2 + - - +
6F PRO* 3.6 9.3 - - - +
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Residues in contact with ARG 18 (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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12E SER* 4.2 1.4 - - - +
13E SER* 3.6 15.6 + - - +
17E ASN* 1.3 86.0 - - - +
19E SER* 1.3 61.3 + - - +
21E GLU* 3.6 2.4 + - - +
22E ALA* 3.3 21.8 + - - +
111E CYS* 3.5 34.3 + - + +
112E GLU* 2.7 33.9 + - - +
141E ILE* 3.0 55.0 + - + +
142E GLN 3.8 5.8 - - - +
143E ASP* 3.5 22.0 + - - +
148E ALA* 4.0 15.5 - - + +
152E ALA* 5.1 0.7 + - - +
155E ILE* 5.5 0.3 - - - +
5F SEP 2.6 47.6 + - - +
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Residues in contact with SER 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E VAL* 3.6 37.7 - - - +
12E SER* 2.6 37.2 + - - -
15E ASN* 3.0 27.0 + - - -
18E ARG* 1.3 79.0 - - - +
20E MET* 1.3 58.8 + - - +
22E ALA* 3.6 1.7 + - - +
23E HIS* 2.8 28.5 + - - +
35E SER* 3.9 4.3 - - - -
36E PHE 3.7 0.6 + - - -
111E CYS* 4.1 0.2 - - - -
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Residues in contact with MET 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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15E ASN* 3.5 28.9 - - - +
16E GLN 3.6 8.7 - - - +
17E ASN 3.3 1.0 + - - -
18E ARG 3.3 0.4 - - - -
19E SER* 1.3 75.3 + - - +
21E GLU* 1.3 61.7 + - - +
23E HIS* 3.6 4.7 - - - +
24E ASN* 2.9 30.1 + - - +
35E SER* 3.3 24.2 - - - -
61E TYR* 3.6 17.9 - - + +
87E ARG* 3.6 10.0 - - - +
88E ASN* 3.2 43.5 - - - +
91E ILE* 3.8 40.0 - - + +
92E LYS* 4.1 6.7 - - - -
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Residues in contact with GLU 21 (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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17E ASN* 3.0 19.4 + - - +
18E ARG 3.8 4.5 - - - +
20E MET* 1.3 76.6 - - - +
22E ALA* 1.3 62.1 + - - +
24E ASN* 3.5 6.8 + - - +
25E ILE* 3.2 41.2 + - - +
87E ARG* 2.7 31.2 + - - +
145E HIS* 5.1 3.5 - - - +
148E ALA* 3.6 29.4 - - + +
149E THR* 3.7 28.8 + - - +
152E ALA* 3.7 5.2 - - + -
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Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E VAL* 3.7 28.5 - - + -
18E ARG 3.3 14.8 + - - +
19E SER 3.8 0.2 - - - +
21E GLU* 1.3 77.3 - - - +
23E HIS* 1.3 66.3 + - - +
25E ILE* 3.2 2.0 + - - +
26E LEU* 2.9 31.4 + - - +
152E ALA* 3.6 16.3 - - + +
155E ILE* 4.0 22.9 - - + -
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Residues in contact with HIS 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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10E VAL* 5.0 0.8 - - - +
19E SER 2.8 22.9 + - - +
20E MET* 3.6 9.4 - - - +
21E GLU 3.4 0.2 - - - -
22E ALA* 1.3 71.8 - - - +
24E ASN* 1.3 56.6 + - - +
27E SER* 2.9 35.2 + - - -
33E VAL* 3.8 39.1 + - + +
34E ARG* 4.2 2.0 - - - -
35E SER* 2.7 38.9 + - - +
91E ILE* 3.6 31.5 - - + +
92E LYS* 3.9 14.3 - - + +
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Residues in contact with ASN 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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20E MET 2.9 18.1 + - - +
21E GLU* 3.7 10.2 - - - +
22E ALA 3.2 0.2 - - - -
23E HIS* 1.3 77.9 - - - +
25E ILE* 1.3 72.9 + - + +
27E SER* 3.9 3.5 - - - -
28E LYS* 3.0 61.9 + - - +
87E ARG* 4.5 13.9 + - - +
91E ILE* 3.7 27.1 - - + +
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Residues in contact with ILE 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 GLU* 3.2 29.5 + - - +
22E ALA 4.0 2.0 - - - +
24E ASN* 1.3 86.9 - - - +
26E LEU* 1.3 58.3 + - + +
28E LYS* 3.4 5.4 + - + +
29E ARG* 2.7 52.8 + - - +
152E ALA* 4.1 17.9 - - + +
153E PHE* 3.7 46.4 - - + -
156E CYS* 4.0 17.5 - - + -
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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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8E VAL* 4.2 11.9 - - + -
10E VAL* 3.7 30.1 - - + -
22E ALA* 2.9 19.4 + - - +
25E ILE* 1.3 79.3 - - + +
27E SER* 1.3 61.0 - - - +
29E ARG* 3.2 7.3 + - - -
30E GLY 3.2 0.3 + - - -
31E PHE* 3.0 58.2 + - + +
33E VAL* 3.9 21.3 - - + -
152E ALA 5.6 0.2 - - - +
155E ILE* 3.9 13.9 - - + -
156E CYS* 3.9 26.0 - - + +
159E CYS* 4.1 10.8 - - + -
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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
----------------------------------------------------------
23E HIS* 2.9 28.3 + - - -
24E ASN* 3.9 3.8 - - - -
26E LEU* 1.3 74.7 - - - +
28E LYS* 1.3 70.7 + - - +
30E GLY* 3.1 14.9 + - - -
31E PHE 4.0 6.5 - - - +
33E VAL* 3.6 16.5 - - - +
91E ILE* 6.3 0.2 - - - -
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Residues in contact with LYS 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 ASN* 3.0 47.5 + - - +
25E ILE* 3.7 7.4 - - + +
26E LEU 3.3 0.2 - - - -
27E SER* 1.3 83.1 - - - +
29E ARG* 1.3 65.2 + - + +
30E GLY 3.3 2.4 + - - -
91E ILE* 6.3 0.2 - - - -
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Residues in contact with ARG 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ILE* 2.7 38.5 + - + +
26E LEU 3.2 3.1 + - - +
27E SER 3.2 0.6 - - - -
28E LYS* 1.3 84.0 - - - +
30E GLY* 1.3 59.1 + - - +
31E PHE* 3.5 13.9 + - + -
153E PHE* 3.6 37.4 - - - -
156E CYS* 4.0 16.7 - - - -
160E GLN* 4.2 21.2 + - - +
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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