Contacts of the helix formed by residues 231 - 235 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ALA* 4.6 4.5 - - - +
107H SER* 3.8 21.5 - - - +
108H ARG* 4.7 11.2 + - + +
111H ILE* 4.0 6.7 - - + -
133H VAL* 3.4 27.5 - - + +
230H ALA* 1.3 79.6 - - - +
232H SER* 1.3 63.8 + - - +
233H PHE* 3.2 40.8 - - + -
234H LYS* 2.8 47.5 + - - +
235H PHE* 4.0 4.7 - - - -
287H ASP* 3.2 7.9 - - - +
508H SO4 3.9 5.0 + - - -
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Residues in contact with SER 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H LEU* 5.3 0.9 - - - +
104H ILE* 5.4 5.2 - - - +
231H GLU* 1.3 65.3 - - - +
233H PHE* 1.3 57.6 + - - +
234H LYS 2.9 10.8 + - - -
235H PHE* 3.1 35.7 + - - +
286H THR* 5.2 0.2 - - - -
287H ASP* 2.4 46.1 + - - -
288H LEU* 4.0 27.8 - - - +
303H LEU* 3.9 18.1 - - - +
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Residues in contact with PHE 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA* 4.5 5.4 - - + -
23H ALA* 3.1 36.1 - - + -
24H VAL* 4.5 18.4 - - + -
27H ILE* 6.2 0.7 - - + -
64H ALA 4.9 0.4 - - - -
67H SER* 2.7 25.5 + - - +
68H GLY* 3.4 20.5 + - - -
71H LEU* 4.8 10.5 - - + +
100H PHE* 5.1 8.7 - - + -
104H ILE* 4.1 40.8 - - + -
107H SER* 5.1 1.8 - - - -
231H GLU* 3.2 50.3 - - + -
232H SER* 1.3 80.4 + - - +
234H LYS* 1.3 68.5 + - + +
235H PHE 3.3 2.1 + - - +
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Residues in contact with LYS 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA* 5.7 1.6 - - - -
23H ALA* 5.6 0.4 - - - -
64H ALA* 4.4 10.5 - - + -
67H SER* 3.4 8.8 + - - -
133H VAL* 4.2 0.6 - - - +
197H ALA 3.1 30.3 + - - +
198H GLU* 3.8 18.2 - - - +
199H GLY* 3.5 8.3 - - - -
200H VAL* 2.9 29.4 + - + +
229H VAL 5.3 0.2 + - - -
230H ALA* 4.2 6.5 - - + +
231H GLU* 2.8 44.2 + - - +
232H SER 2.9 1.4 - - - -
233H PHE* 1.3 101.1 - - + +
235H PHE* 1.3 59.1 + - - +
236H VAL* 3.0 6.2 + - - +
508H SO4 3.2 35.0 + - - -
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Residues in contact with PHE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H SER* 3.6 8.9 - - - -
71H LEU* 4.3 14.8 - - + +
200H VAL* 3.5 21.1 - - + -
231H GLU 4.0 4.0 - - - -
232H SER* 3.1 41.7 + - - +
234H LYS* 1.3 75.7 - - - +
236H VAL* 1.3 59.3 + - - +
237H ARG 4.2 0.5 + - - -
284H LEU* 5.5 0.2 - - + -
286H THR* 3.6 30.5 - - + -
288H LEU* 4.8 5.6 - - + -
291H LEU* 4.0 12.8 - - + -
296H VAL* 3.7 33.2 - - + -
299H GLU* 4.0 17.7 - - + -
300H LEU* 4.0 34.7 - - + +
303H LEU* 4.4 10.8 - - + -
304H TYR* 4.8 1.2 + - - -
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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