Contacts of the helix formed by residues 231 - 235 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA* 4.5 0.5 - - - +
107B SER* 3.7 20.6 - - - -
108B ARG* 3.2 34.2 + - + +
111B ILE* 4.0 8.3 - - + -
133B VAL* 3.6 16.1 - - - +
230B ALA* 1.3 75.6 - - - +
232B SER* 1.3 65.7 + - - +
233B PHE* 3.3 42.7 - - + -
234B LYS* 2.8 50.8 + - - +
235B PHE* 4.2 3.9 - - - -
287B ASP* 3.4 5.4 - - - -
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.3 4.3 - - - +
103B ARG* 4.0 10.9 + - - -
104B ILE* 5.6 2.8 - - - +
107B SER* 4.8 1.6 + - - -
230B ALA 3.9 0.4 + - - -
231B GLU* 1.3 67.1 - - - +
233B PHE* 1.3 55.3 + - - +
234B LYS 2.7 16.4 + - - -
235B PHE* 2.8 35.3 + - - +
286B THR* 5.3 0.7 - - - -
287B ASP* 2.6 38.8 + - - +
288B LEU* 3.8 22.7 - - - -
303B LEU* 3.9 16.4 - - - +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.8 20.2 - - + -
23B ALA* 3.4 30.1 - - + -
24B VAL* 4.2 10.1 - - + -
27B ILE* 5.5 0.9 - - + -
64B ALA* 4.1 11.0 - - + +
67B SER* 2.8 21.3 + - - -
68B GLY* 3.5 19.5 + - - -
71B LEU* 3.6 16.8 - - + +
100B PHE* 5.4 3.8 - - + -
104B ILE* 4.0 45.3 - - + -
107B SER* 4.9 1.8 - - - -
231B GLU* 3.3 41.7 - - + -
232B SER* 1.3 78.1 + - - +
234B LYS* 1.3 68.2 + - + +
235B PHE 3.3 2.2 - - - -
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 5.5 3.8 - - - +
63B VAL* 5.1 0.5 - - - +
64B ALA* 4.0 15.7 - - + +
67B SER* 4.0 5.3 + - - -
133B VAL* 4.3 1.0 - - - +
197B ALA 3.2 29.2 + - - +
198B GLU* 3.4 20.4 - - - +
199B GLY* 3.2 10.7 - - - -
200B VAL* 3.0 28.4 + - + +
230B ALA* 4.1 10.8 - - + +
231B GLU* 2.8 41.9 + - - +
232B SER 2.7 1.4 + - - -
233B PHE* 1.3 89.4 - - + +
235B PHE* 1.3 62.2 + - - +
236B VAL* 3.2 4.9 + - - +
502B SO4 2.9 31.9 + - - -
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Residues in contact with PHE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.2 6.8 - - - -
71B LEU* 4.8 0.7 - - - +
200B VAL* 3.4 33.0 - - + -
231B GLU 4.2 1.6 - - - -
232B SER* 2.8 30.1 + - - +
233B PHE 4.4 1.0 - - - +
234B LYS* 1.3 75.5 - - - +
236B VAL* 1.3 53.2 + - - +
286B THR* 4.3 13.7 - - + -
288B LEU* 3.8 28.0 - - + -
291B LEU* 4.1 17.3 - - + -
296B VAL* 4.2 14.4 - - + -
299B GLU* 4.0 14.1 - - + -
300B LEU* 3.7 38.6 - - + -
303B LEU* 4.5 8.7 - - + -
304B TYR* 2.7 33.7 + - + -
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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