Contacts of the helix formed by residues 32 - 37 (chain E) in PDB entry 5CEV
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 VAL 32 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ILE* 4.1 26.0 - - + -
27E MET* 3.3 10.0 + - + +
28E ARG* 3.7 30.6 + - + +
30E ALA 3.8 0.2 - - - -
31E GLY* 1.3 75.3 - - - +
33E ILE* 1.3 71.6 + - + +
35E ARG* 3.5 1.4 + - - +
36E LEU* 3.2 33.1 + - + +
93E LEU* 4.5 1.3 - - + -
95E LEU* 4.5 7.9 - - + -
287E VAL* 3.9 16.8 - - + +
290E MET* 3.8 31.0 - - + -
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Residues in contact with ILE 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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6E ILE* 3.3 30.3 - - + -
28E ARG* 5.7 3.6 - - + +
32E VAL* 1.3 80.7 - - + +
34E GLU* 1.3 69.4 + - + +
36E LEU* 3.1 3.8 + - - +
37E GLU* 2.8 56.1 + - + +
43E ILE* 3.6 20.7 - - + +
45E ASP* 4.2 26.9 - - + +
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Residues in contact with GLU 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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28E ARG 4.4 4.7 - - - +
31E GLY* 3.1 27.4 - - - +
32E VAL 3.9 0.2 + - - -
33E ILE* 1.3 92.3 + - + +
35E ARG* 1.3 62.6 + - - +
37E GLU* 3.8 15.2 - - - +
38E ARG* 3.1 28.3 + - - +
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Residues in contact with ARG 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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30E ALA 5.5 1.4 + - - -
31E GLY 3.0 18.2 + - - +
32E VAL 3.7 4.7 - - - +
33E ILE 3.2 0.2 - - - -
34E GLU* 1.3 77.4 - - - +
36E LEU* 1.3 62.8 + - + +
38E ARG* 3.5 39.2 - - - +
39E LEU* 3.5 17.5 - - - +
252E HIS* 5.5 1.6 - - - -
284E SER 5.7 0.2 + - - -
287E VAL* 3.9 34.2 - - + +
288E ALA* 3.7 31.5 + - - +
291E GLY* 4.2 8.8 - - - +
296E GLU* 2.9 38.9 + - - +
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Residues in contact with LEU 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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4E ILE* 3.9 15.9 - - + -
32E VAL* 3.2 23.1 + - + +
33E ILE 3.1 4.2 + - - +
35E ARG* 1.3 77.3 - - + +
37E GLU* 1.3 64.0 + - - +
38E ARG 3.2 1.6 - - - -
39E LEU* 3.0 19.5 + - + -
41E TYR* 3.3 31.6 + - + -
43E ILE* 4.1 17.9 - - + -
93E LEU* 3.7 29.8 - - + -
290E MET* 4.3 13.0 - - + +
291E GLY* 4.6 2.2 - - - +
294E PHE* 3.6 34.1 - - + -
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Residues in contact with GLU 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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33E ILE* 2.8 32.8 + - - +
34E GLU* 3.8 15.4 - - - +
36E LEU* 1.3 75.9 - - - +
38E ARG* 1.3 54.9 + - - +
40E HIS* 2.7 28.8 + - - -
41E TYR 3.7 11.0 + - - +
43E ILE* 3.2 24.9 - - + +
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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