Contacts of the helix formed by residues 34 - 39 (chain E) in PDB entry 2RAX
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 THR 34 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E PHE 3.6 9.2 + - - -
28E LEU* 4.0 6.8 - - - +
29E GLU* 3.8 25.1 + - - +
31E CYS* 4.4 6.1 - - - +
32E ALA 3.8 1.8 - - - +
33E CYS* 1.3 77.4 - - - +
35E PRO* 1.4 82.9 - - - +
36E GLU* 3.7 19.4 + - + +
37E ARG* 2.7 37.5 + - + +
38E MET* 2.9 10.3 + - - +
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Residues in contact with PRO 35 (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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19E ILE* 4.3 14.8 - - + -
22E PHE* 4.1 32.2 - - + -
25E TRP* 3.5 20.2 - - + -
27E PHE 3.4 13.7 - - - +
28E LEU* 4.0 16.4 - - + -
34E THR* 1.4 89.8 - - - +
36E GLU* 1.3 58.4 + - - +
38E MET* 3.4 10.0 - - + +
39E ALA* 2.7 38.3 + - - +
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Residues in contact with GLU 36 (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 LYS* 3.5 26.3 + - - +
19E ILE* 4.2 24.0 - - + +
34E THR* 2.9 15.2 + - + +
35E PRO* 1.3 83.6 - - - +
37E ARG* 1.3 63.2 + - + +
39E ALA* 4.8 0.4 - - - -
40E GLU* 3.4 24.4 - - - +
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Residues in contact with ARG 37 (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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32E ALA* 4.2 24.8 + - - +
33E CYS* 4.7 0.7 - - - -
34E THR* 2.7 31.3 + - + +
36E GLU* 1.3 79.5 - - - +
38E MET* 1.3 63.9 + - - +
40E GLU* 3.8 13.4 - - - +
41E ALA* 3.4 21.1 + - - +
73E PRO* 3.8 11.1 - - + +
74E ILE* 4.8 3.5 - - - +
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Residues in contact with MET 38 (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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22E PHE* 3.7 17.5 - - + -
25E TRP* 4.1 23.6 - - + -
33E CYS* 3.9 21.8 - - - +
34E THR 2.9 16.0 + - - +
35E PRO* 3.4 8.5 - - + +
37E ARG* 1.3 76.9 - - - +
39E ALA* 1.3 59.5 + - - +
41E ALA* 3.1 13.7 + - - +
42E GLY 3.3 0.5 + - - -
43E PHE* 3.0 39.1 + - + +
55E ALA* 4.0 27.6 - - + -
67E TRP* 4.3 18.4 - - + -
73E PRO* 3.6 27.4 - - - -
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Residues in contact with ALA 39 (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 LYS* 3.8 17.7 - - + +
18E ARG* 2.6 55.6 + - + +
19E ILE* 3.9 16.8 - - + +
22E PHE* 4.6 0.9 - - + -
35E PRO 2.7 19.9 + - - +
38E MET* 1.3 69.5 - - - +
40E GLU* 1.3 63.9 + - - +
41E ALA 3.1 0.4 - - - -
42E GLY 3.1 3.1 + - - -
43E PHE 3.9 10.5 + - - +
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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