Contacts of the helix formed by residues 24 - 34 (chain E) in PDB entry 1RTA
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 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E SER* 3.2 17.0 - - - +
23E SER* 1.3 79.1 + - - +
25E TYR* 1.3 53.0 + - - +
26E CYS 3.2 2.0 - - - -
27E ASN* 2.5 46.1 + - - +
28E GLN* 2.8 36.4 + - - +
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Residues in contact with TYR 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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14E ASP* 3.0 29.2 + - - +
17E THR* 4.3 8.7 - - + -
19E ALA 4.5 0.4 - - - -
20E ALA* 3.9 7.4 - - + -
21E SER* 3.6 26.9 - - - +
22E SER* 3.0 28.9 + - - +
24E ASN* 1.3 71.6 - - - +
26E CYS* 1.3 63.4 + - - +
28E GLN* 3.4 12.3 + - + +
29E MET* 3.1 40.4 + - + +
46E PHE* 4.2 14.0 - + - +
48E HIS* 3.0 25.3 - + - -
82E THR* 3.4 28.9 - - + -
99E THR* 3.6 16.6 - - + -
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Residues in contact with CYS 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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24E ASN 3.0 0.8 + - - -
25E TYR* 1.3 68.1 - - - +
27E ASN* 1.3 59.5 + - - +
29E MET* 3.2 1.7 + - - -
30E MET* 2.9 34.9 + - - +
82E THR* 3.8 3.1 - - - -
84E CYS* 2.0 54.5 - - + -
97E TYR* 3.9 19.5 - - + +
99E THR* 3.0 45.4 + - - +
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Residues in contact with ASN 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 SER 3.8 13.1 + - - -
24E ASN* 2.5 32.5 + - - +
26E CYS* 1.3 76.5 - - - +
28E GLN* 1.3 58.0 + - - +
30E MET* 4.6 2.6 - - - +
31E LYS* 3.2 25.8 + - - +
95E CYS 3.4 9.4 - - - +
96E ALA* 2.9 32.5 - - - +
97E TYR* 2.9 35.1 + - - +
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Residues in contact with GLN 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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21E SER* 3.8 9.9 + - - -
22E SER* 3.7 11.9 + - - -
24E ASN* 2.8 28.2 + - - +
25E TYR* 3.4 29.3 + - + +
27E ASN* 1.3 77.3 - - - +
29E MET* 1.4 55.7 + - + +
31E LYS* 4.2 3.8 - - - +
32E SER* 2.3 37.4 + - - +
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Residues in contact with MET 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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14E ASP* 2.9 35.4 - - + +
17E THR* 5.6 1.6 - - + -
25E TYR* 3.1 36.4 + - + +
28E GLN* 1.4 78.2 - - + +
30E MET* 1.3 65.1 + - - +
31E LYS 3.0 2.0 - - - -
32E SER* 3.4 16.6 - - - -
33E ARG* 2.8 42.6 + - - +
35E LEU* 4.2 0.3 - - - +
46E PHE* 3.9 33.9 - - + -
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Residues in contact with MET 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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26E CYS 2.9 25.8 + - - +
27E ASN 4.6 1.6 - - - +
29E MET* 1.3 73.4 - - - +
31E LYS* 1.3 58.9 + - - +
35E LEU* 2.9 49.1 + - + +
36E THR* 3.4 6.5 + - + -
41E LYS* 4.5 6.7 - - + -
44E ASN* 3.6 46.7 - - + +
46E PHE* 3.8 12.6 - - - -
84E CYS* 4.0 8.7 - - + -
97E TYR* 3.5 55.0 - - + +
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Residues in contact with LYS 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 ASN 3.2 19.2 + - - +
28E GLN* 4.2 2.9 - - - +
29E MET 3.0 0.6 - - - -
30E MET* 1.3 79.7 - - - +
32E SER* 1.4 59.2 - - - +
34E ASN* 3.0 27.9 + - - -
36E THR* 3.1 22.0 + - + +
37E LYS* 4.4 14.3 - - - +
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Residues in contact with SER 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 GLN* 2.3 31.1 + - - +
29E MET* 2.9 24.0 + - - -
31E LYS* 1.4 76.6 - - - +
33E ARG* 1.3 66.7 + - - +
34E ASN* 3.4 9.9 + - - -
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Residues in contact with ARG 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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9E GLU* 2.9 14.5 + - - +
10E ARG* 2.6 66.5 + - + +
13E MET 2.9 31.7 + - - +
14E ASP* 4.5 11.9 + - - +
29E MET* 2.8 32.4 + - - +
32E SER* 1.3 83.8 - - - +
34E ASN* 1.3 71.8 + - - +
35E LEU* 3.1 23.3 - - + +
46E PHE* 4.8 5.9 - - + -
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Residues in contact with ASN 34 (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 ARG* 4.6 16.2 + - - +
30E MET 3.4 0.2 + - - -
31E LYS 3.0 18.5 + - - -
32E SER 4.3 6.4 + - - +
33E ARG* 1.3 82.7 - - - +
35E LEU* 1.3 57.0 + - - +
36E THR* 3.4 4.5 - - - -
37E LYS* 2.8 55.8 + - + +
39E ARG* 5.0 4.2 - - - +
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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