Contacts of the helix formed by residues 153 - 158 (chain E) in PDB entry 5EJK
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 GLN 153 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E GLN* 3.5 9.6 - - + -
63E THR 5.6 0.8 + - - -
64E ASP* 6.0 1.6 - - + -
119E LYS* 3.0 29.1 + - - +
120E THR* 2.7 39.2 + - - +
121E ASP* 3.4 17.1 - - + +
145E GLY* 4.4 11.1 - - - -
146E ILE* 5.7 0.7 - - - +
149E ASN 4.7 2.9 - - - +
150E SER* 2.9 31.8 + - - +
152E GLY* 1.3 76.1 - - - +
154E ALA* 1.3 65.5 + - - +
155E MSE 3.3 2.0 - - - -
156E VAL* 2.9 33.9 + - + +
157E GLU* 3.3 6.7 + - + +
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Residues in contact with ALA 154 (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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51E ASN* 3.3 11.7 - - - +
150E SER 3.3 4.4 + - - -
151E GLN* 2.9 21.4 + - - +
152E GLY 3.1 2.4 + - - -
153E GLN* 1.3 74.9 - - - +
155E MSE 1.3 53.7 + - - +
156E VAL 2.9 2.6 + - - -
157E GLU* 2.9 6.4 + - - +
158E ARG* 2.7 36.4 + - - +
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Residues in contact with MSE 155 (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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51E ASN* 3.1 25.7 + - - +
52E PRO 4.0 1.6 - - - +
53E ARG* 3.7 32.1 - - + +
62E GLN* 3.6 13.9 - - - +
81E VAL* 3.2 20.3 - - + +
82E ASP 5.0 1.3 - - - +
83E THR* 3.4 46.4 - - + +
86E SER* 5.8 2.2 - - - -
153E GLN 3.1 0.6 + - - -
154E ALA* 1.3 77.0 - - - +
156E VAL* 1.3 56.8 + - - +
158E ARG* 4.0 43.9 + - - +
159E ALA* 4.4 2.4 + - - +
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Residues in contact with VAL 156 (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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62E GLN* 3.2 45.8 + - + +
63E THR* 4.0 4.7 - - - +
64E ASP* 4.2 18.4 - - + +
79E VAL* 3.8 22.9 - - + +
81E VAL* 3.7 10.8 - - + -
119E LYS 5.8 0.2 - - - +
153E GLN* 2.9 32.4 + - + +
155E MSE 1.3 78.1 - - - +
157E GLU* 1.3 64.2 + - + +
158E ARG 3.2 0.7 - - - -
159E ALA* 2.9 24.6 + - - +
160E ASN* 3.2 9.8 + - - +
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Residues in contact with GLU 157 (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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64E ASP* 2.9 26.2 - - - +
66E THR* 5.5 0.2 - - - -
150E SER* 3.7 31.8 + - - +
153E GLN* 3.7 15.4 - - + +
154E ALA* 2.9 7.4 + - - +
156E VAL* 1.3 77.0 - - + +
158E ARG* 1.3 60.9 + - - +
160E ASN* 2.5 56.8 + - + +
161E ARG* 3.4 7.4 + - - +
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Residues in contact with ARG 158 (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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81E VAL* 5.1 4.3 - - - +
86E SER* 4.3 17.4 + - - +
88E ILE* 5.5 1.2 - - - +
154E ALA 2.7 20.5 + - - +
155E MSE 4.0 42.9 + - - +
157E GLU* 1.3 72.1 - - - +
159E ALA* 1.3 66.7 + - - +
161E ARG* 2.9 68.2 + - - +
162E MSE 3.8 13.5 + - - +
201E ARG* 3.5 26.9 - - - +
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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