Contacts of the helix formed by residues 229 - 234 (chain A) in PDB entry 4ZSL
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 ALA 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A TYR 3.5 4.6 + - - -
228A ARG* 1.3 72.9 - - - +
230A PRO* 1.4 72.2 - - + +
231A GLU* 3.3 29.6 - - + +
232A LEU* 2.9 20.2 + - + +
233A MET 3.2 9.0 + - - -
243A ILE* 4.0 18.8 + - + +
246A TRP* 3.5 22.4 - - + -
247A SER* 5.2 0.2 + - - -
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Residues in contact with PRO 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG 3.8 0.6 - - - +
229A ALA* 1.4 80.5 - - - +
231A GLU* 1.4 55.3 + - - +
233A MET* 3.3 9.8 + - + -
234A LEU* 2.9 44.1 + - + +
236A LEU* 4.3 4.9 - - + -
246A TRP* 3.5 38.4 - - + -
271A LEU* 5.9 1.6 - - + -
274A ILE* 4.9 7.4 - - + -
330A PHE* 4.1 35.7 - - + +
335A ARG* 3.4 21.3 - - - +
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA* 3.3 12.0 - - + +
230A PRO* 1.4 71.8 - - - +
232A LEU* 1.3 57.8 + - - +
235A SER* 3.0 9.9 + - - -
236A LEU* 3.0 44.2 + - + +
238A GLU 3.4 23.7 - - - +
239A TYR* 3.3 12.2 - - + -
240A THR 5.0 0.7 + - - +
242A ALA* 4.4 0.2 - - - +
243A ILE* 3.4 30.9 + - + +
330A PHE 4.3 0.2 - - - +
332A PRO* 3.6 22.4 - - + +
335A ARG* 2.8 43.2 + - - -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ARG* 5.0 8.5 - - + +
219A THR* 2.7 48.0 + - + +
220A GLU* 3.0 11.4 + - - -
222A VAL* 4.0 28.9 - - + +
223A ALA* 5.4 0.2 - - + -
228A ARG* 3.7 20.9 - - + -
229A ALA* 2.9 14.4 + - + +
231A GLU* 1.3 75.4 - - - +
233A MET* 1.3 63.9 + - - +
234A LEU 3.4 0.2 + - - -
235A SER 3.6 0.2 + - - -
239A TYR* 4.0 21.3 - - + -
243A ILE* 3.9 41.1 - - + -
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Residues in contact with MET 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLU* 3.7 10.3 - - - +
225A ARG* 5.3 0.4 - - + -
228A ARG* 3.6 54.3 - - - +
229A ALA 3.2 4.2 + - - +
230A PRO* 3.6 10.1 - - + +
232A LEU* 1.3 76.3 - - - +
234A LEU* 1.3 55.9 + - - +
235A SER* 4.0 0.7 + - - -
267A TYR* 2.7 78.3 + - + +
270A GLN* 3.8 25.6 - - + -
271A LEU* 3.9 25.6 - - + -
274A ILE* 5.1 3.4 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A PRO* 2.9 31.1 + - + +
233A MET* 1.3 76.0 - - - +
235A SER* 1.4 71.4 + - - +
236A LEU* 3.4 19.7 + - + -
267A TYR* 4.1 2.2 - - - +
271A LEU* 3.9 24.2 - - + -
275A MET* 5.8 1.6 - - + -
281A PRO* 5.7 7.0 - - + -
285A VAL* 5.7 2.7 - - + +
289A VAL* 3.6 21.3 - - + +
290A GLY 3.4 16.5 + - - -
291A ALA 5.0 0.5 + - - -
294A VAL* 3.7 19.7 - - + -
298A ILE* 3.7 28.9 - - + -
330A PHE* 5.4 10.1 - - + -
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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