Contacts of the helix formed by residues 231 - 235 (chain C) in PDB entry 3ECS
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 GLU 231 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 4.2 3.3 - - - +
107C SER* 3.8 18.4 - - - -
108C ARG* 4.2 21.9 + - + +
111C ILE* 3.9 6.1 - - + -
133C VAL* 3.1 32.2 - - - +
230C ALA* 1.3 77.3 - - - +
232C SER* 1.3 64.5 + - - +
233C PHE* 3.2 44.2 - - + -
234C LYS* 3.1 41.4 + - + +
235C PHE* 4.0 4.9 - - - -
287C ASP* 3.3 9.9 - - - +
503C SO4 4.3 0.5 + - - -
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Residues in contact with SER 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 4.1 0.6 - - - +
107C SER* 4.7 1.6 + - - -
230C ALA 3.8 0.4 + - - -
231C GLU* 1.3 67.8 - - - +
233C PHE* 1.3 57.8 + - - +
234C LYS 3.0 9.9 + - - -
235C PHE* 3.1 21.3 + - - +
286C THR* 4.9 1.1 - - - -
287C ASP* 2.6 35.8 + - - +
288C LEU* 3.7 34.5 - - - +
303C LEU* 3.3 27.6 - - - +
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.9 17.9 - - + -
23C ALA* 3.3 32.1 - - + -
24C VAL* 4.6 3.4 - - + -
64C ALA* 4.3 1.8 - - + -
67C SER* 2.7 26.0 + - - -
68C GLY* 3.4 18.5 + - - -
71C LEU* 3.9 14.4 - - + -
100C PHE* 5.3 4.0 - - + -
104C ILE* 4.1 48.2 - - + -
107C SER* 4.8 2.9 - - - -
231C GLU* 3.4 41.7 - - + -
232C SER* 1.3 79.6 + - - +
234C LYS* 1.3 72.0 + - + +
235C PHE 3.3 0.7 - - - -
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 5.9 1.1 - - - -
64C ALA* 3.9 15.3 - - + -
67C SER* 3.6 6.2 + - - -
133C VAL* 4.5 1.4 - - - +
197C ALA 3.0 30.5 + - - +
198C GLU* 3.5 18.4 - - - +
199C GLY* 3.4 8.9 - - - -
200C VAL* 2.9 29.4 + - + +
230C ALA* 4.3 4.6 - - + +
231C GLU* 3.1 48.6 + - - +
232C SER 3.0 1.0 - - - -
233C PHE* 1.3 91.9 - - + +
235C PHE* 1.3 61.2 + - - +
236C VAL* 3.0 9.5 + - - +
503C SO4 2.8 33.9 + - - -
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Residues in contact with PHE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C SER* 3.4 5.6 - - - -
71C LEU* 4.5 2.8 - - - +
200C VAL* 3.4 26.9 - - + -
231C GLU 4.0 4.0 - - - -
232C SER* 3.1 31.9 + - - +
234C LYS* 1.3 76.6 - - - +
236C VAL* 1.3 53.1 + - - +
284C LEU* 6.0 0.2 - - + -
286C THR* 3.9 27.6 - - + -
288C LEU* 3.8 21.1 - - + -
291C LEU* 4.3 7.6 - - + -
296C VAL* 3.9 23.1 - - + -
299C GLU* 4.5 4.5 - - + -
300C LEU* 3.9 36.6 - - + -
303C LEU* 3.5 17.5 - - + -
304C TYR* 2.5 29.7 + - - -
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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