Contacts of the helix formed by residues 242 - 250 (chain B) in PDB entry 5ZR1
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 THR 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ASP* 1.3 86.4 + - - +
243B PHE* 1.3 71.1 + - + +
244B GLU* 3.6 15.7 - - + -
245B GLY 3.5 4.7 - - - +
246B TYR 3.0 18.2 + - - -
613C TRP* 4.6 1.0 - - - +
614C ARG 3.9 6.9 + - - +
615C GLY* 4.8 6.3 - - - +
616C ILE* 3.5 17.9 - - - +
353E LYS* 3.6 16.5 + - - -
391E GLN* 3.5 15.9 - - - +
413E LEU* 3.6 26.5 - - + -
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B THR* 1.3 85.2 - - + +
244B GLU* 1.3 87.5 + - + +
246B TYR* 3.5 8.8 - - - +
247B PHE* 2.9 53.5 + + + -
616C ILE* 4.2 0.7 - - - -
350E PHE 3.5 18.4 - - - -
351E SER* 4.6 0.2 - - - -
352E ARG* 3.8 22.2 - - + -
388E ALA* 3.2 31.6 - - + +
391E GLN* 3.0 32.2 - - + +
392E ALA* 3.7 16.8 - - + -
413E LEU* 3.6 23.3 - - + -
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B PHE* 3.9 35.6 - - + +
242B THR* 4.0 12.6 - - + +
243B PHE* 1.3 107.4 - - + +
245B GLY* 1.3 58.1 + - - +
247B PHE* 3.5 4.4 + - - +
248B ASP* 3.1 31.2 + - - +
351E SER* 3.4 21.2 + - - -
352E ARG* 3.1 26.4 + - + +
353E LYS* 3.7 29.8 + - + +
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 3.9 18.7 - - - +
240B LEU 4.1 12.8 - - - -
242B THR 3.1 18.8 + - - +
244B GLU* 1.3 76.5 - - - +
246B TYR* 1.3 63.4 + - - +
248B ASP 4.6 0.4 - - - -
249B GLN* 3.3 30.1 + - - +
613C TRP* 3.5 8.0 + - - -
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B THR 3.0 5.5 + - - -
243B PHE* 3.5 8.3 - - - +
244B GLU 3.3 0.2 - - - -
245B GLY* 1.3 78.1 - - - +
247B PHE* 1.3 87.2 + + - +
248B ASP 3.5 0.2 + - - -
250B ARG* 3.3 64.1 + - - +
613C TRP* 3.4 44.4 - + - +
616C ILE* 3.8 17.7 - - + -
382E ALA* 5.2 4.7 - - - +
384E GLU* 3.6 19.2 - - + +
385E ARG* 3.3 43.4 + - + +
388E ALA* 3.6 7.9 - - + -
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B PHE* 2.9 43.0 + + - +
244B GLU 4.1 3.1 - - - +
246B TYR* 1.3 102.3 - + - +
248B ASP* 1.3 60.4 + - - +
250B ARG* 4.1 12.1 + - - +
251B LYS* 4.2 7.3 - - - -
346E ASP* 3.8 33.4 - - + -
347E ALA* 3.8 31.5 - - + +
350E PHE* 3.7 18.6 - + + -
351E SER* 4.3 13.0 - - - +
385E ARG* 5.2 0.7 - - + -
388E ALA* 4.2 9.9 - - + -
389E ILE* 3.6 30.3 - - + -
392E ALA* 4.8 0.4 - - + -
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B SER* 3.3 26.5 - - - -
238B SER* 3.3 11.3 + - - -
239B PHE* 3.8 22.5 + - + +
244B GLU 3.1 19.0 + - - +
245B GLY 4.5 1.1 - - - +
247B PHE* 1.3 78.6 - - - +
249B GLN* 1.3 59.1 + - - +
250B ARG 3.4 0.9 - - - -
251B LYS* 3.3 34.0 + - - +
532C ASN* 5.2 0.2 - - - +
347E ALA* 5.6 0.7 - - - -
355E ARG* 3.0 28.1 + - - +
360E ARG 4.8 0.9 - - - +
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Residues in contact with GLN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B SER* 3.5 28.5 + - - +
239B PHE 3.6 5.8 + - - +
240B LEU* 3.6 17.6 + - - +
245B GLY 3.3 16.9 + - - +
246B TYR 4.6 0.2 - - - +
248B ASP* 1.3 75.0 - - - +
250B ARG* 1.3 58.6 + - - +
251B LYS* 3.3 9.9 + - - +
529C ARG 3.4 20.8 + - - -
530C GLU 4.7 0.6 - - - -
531C ALA 3.0 21.4 + - - +
532C ASN* 3.9 20.8 - - - +
533C MET* 3.4 19.1 + - - +
610C LYS* 3.2 7.3 + - - -
613C TRP* 2.7 37.2 + - + +
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Residues in contact with ARG 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B TYR* 3.3 60.5 + - - +
247B PHE* 4.1 8.4 + - - +
248B ASP 3.4 1.6 - - - -
249B GLN* 1.3 76.9 - - - +
251B LYS* 1.3 65.1 + - - +
252B ILE* 5.5 2.3 - - - +
533C MET* 3.4 39.0 - - + +
598C LYS* 5.8 0.2 - - - +
609C GLU* 3.6 20.4 + - - -
610C LYS 4.6 1.8 + - - -
613C TRP* 3.7 23.7 - - + -
343E PRO* 6.2 4.0 - - - +
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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