Contacts of the helix formed by residues 273 - 278 (chain F) in PDB entry 2ZSU
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 PRO 273 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E PHE* 5.0 3.4 - - + -
225E PRO* 5.0 9.9 - - + -
259E GLU 4.3 1.6 - - - +
260E TYR* 3.5 15.5 - - + +
198F VAL* 3.9 9.0 - - + -
199F TYR* 3.7 32.8 - - + +
223F SER* 6.4 0.2 - - - -
232F PRO* 5.7 0.9 - - + -
271F GLN* 4.8 0.9 - - + -
272F MET* 1.3 99.8 - - - +
274F ARG* 1.3 66.6 + - - +
275F TYR* 3.4 17.3 - - + -
276F ILE* 3.1 26.8 + - + +
277F VAL* 3.2 10.0 + - - +
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Residues in contact with ARG 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253E GLY 5.8 1.1 + - - -
254E LYS* 4.7 26.3 + - - +
257E GLY* 3.7 21.3 - - - -
258E LEU* 2.8 33.5 + - - +
259E GLU 3.3 15.0 + - - +
260E TYR 3.0 15.4 + - - +
261E TYR 4.0 15.9 - - - +
262E ASP* 4.1 26.6 + - + +
263E PRO* 4.2 9.0 - - - +
264E ASP* 5.2 4.4 + - - -
272F MET 3.3 2.8 + - - -
273F PRO* 1.3 70.3 - - - +
275F TYR* 1.3 64.6 + - - +
277F VAL* 3.2 9.0 + - + +
278F GLN* 3.0 58.0 + - + +
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Residues in contact with TYR 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E GLU* 2.9 49.1 + - + +
260E TYR* 4.1 21.0 + + - -
199F TYR* 3.8 17.4 + + - -
202F THR* 4.5 8.4 + - + -
273F PRO* 3.7 13.5 - - + -
274F ARG* 1.3 73.3 - - - +
276F ILE* 1.3 84.8 + - + +
278F GLN* 3.4 17.4 + - - +
279F MET* 3.1 51.6 + - + +
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Residues in contact with ILE 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F VAL* 3.4 41.7 - - + +
199F TYR* 4.6 0.4 - - + -
202F THR* 3.8 18.2 - - + -
205F PHE* 4.3 16.6 - - + -
206F LEU* 4.0 8.4 - - + +
272F MET* 3.9 17.3 - - + -
273F PRO* 3.1 23.9 + - + +
275F TYR* 1.3 108.4 - - + +
277F VAL* 1.3 66.8 + - - +
279F MET* 2.9 23.9 + - + +
280F LEU* 3.6 4.6 + - + +
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ASP* 4.7 13.0 - - - +
265E LYS* 5.5 7.0 - - + -
221F TYR* 3.4 26.5 - - - +
272F MET* 3.5 30.1 - - + +
273F PRO 3.5 7.6 - - - +
274F ARG* 3.2 9.6 + - + +
276F ILE* 1.3 77.2 - - - +
278F GLN* 1.3 64.8 + - + +
279F MET 3.2 1.4 + - - -
280F LEU* 3.2 31.1 + - + +
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Residues in contact with GLN 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E LEU 4.6 1.6 + - - -
259E GLU* 5.7 0.2 - - - +
274F ARG* 3.0 55.0 + - + +
275F TYR* 3.7 25.4 - - - +
276F ILE 3.1 0.2 - - - -
277F VAL* 1.3 78.7 - - + +
279F MET* 1.3 61.0 + - + +
280F LEU* 3.3 3.8 + - - +
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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