Contacts of the helix formed by residues 281 - 291 (chain F) 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 281 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279F LYS 4.0 2.6 + - - -
280F MET* 1.3 76.6 - - - +
282F THR* 1.3 66.1 + - - +
283F GLU* 3.7 23.7 + - - +
284F GLU* 3.0 36.6 + - + +
285F ILE* 3.2 12.5 + - - +
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Residues in contact with THR 282 (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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280F MET 3.8 1.0 + - - -
281F THR* 1.3 75.4 + - - +
283F GLU* 1.3 58.3 + - - +
284F GLU 3.2 0.2 + - - -
285F ILE* 3.3 12.3 - - - +
286F ILE* 3.0 45.5 + - + +
303F VAL* 3.8 27.7 - - + +
307F ASN* 4.9 7.3 + - - -
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Residues in contact with GLU 283 (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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281F THR* 3.3 19.0 + - - +
282F THR* 1.3 78.6 - - - +
284F GLU* 1.3 55.5 + - - +
286F ILE* 4.5 7.9 - - - +
287F ARG* 3.3 44.7 + - - +
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Residues in contact with GLU 284 (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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280F MET* 3.7 24.7 - - + -
281F THR* 3.0 26.5 + - + +
283F GLU* 1.3 77.0 - - - +
285F ILE* 1.3 60.9 + - - +
286F ILE 3.2 1.8 - - - -
287F ARG* 3.0 26.0 + - - +
288F LEU* 3.0 31.2 + - - +
317F TRP* 3.4 23.4 - - + -
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Residues in contact with ILE 285 (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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280F MET* 3.7 32.1 - - + +
281F THR 3.2 9.4 + - - +
282F THR* 3.3 20.6 - - - +
284F GLU* 1.3 75.3 - - - +
286F ILE* 1.3 60.1 + - - +
288F LEU* 4.0 9.1 + - - +
289F CYS* 3.4 19.1 + - - +
302F ILE* 4.9 12.2 - - + +
303F VAL* 3.7 43.0 - - + +
306F TYR* 4.0 24.0 - - + -
307F ASN* 5.2 1.1 - - - +
320F VAL* 3.8 25.2 - - + +
324F VAL* 5.2 0.7 - - - +
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Residues in contact with ILE 286 (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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282F THR* 3.0 34.9 + - + +
283F GLU* 4.5 6.5 - - - +
285F ILE* 1.3 77.2 - - - +
287F ARG* 1.3 53.7 + - - +
288F LEU 3.2 0.2 - - - -
289F CYS* 3.0 13.2 + - - -
290F ASN* 2.6 48.7 + - + +
299F ALA* 5.2 8.7 - - + +
300F TYR* 5.2 14.6 - - + -
303F VAL* 3.9 19.5 - - + -
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Residues in contact with ARG 287 (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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283F GLU* 3.3 40.8 + - - +
284F GLU* 3.0 30.9 + - - +
286F ILE* 1.3 80.0 - - - +
288F LEU* 1.3 61.6 + - - +
289F CYS 3.4 0.2 + - - -
290F ASN* 3.6 16.6 + - - +
291F ASP* 3.8 13.3 + - - +
353F LEU* 5.5 0.7 - - - +
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Residues in contact with LEU 288 (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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284F GLU* 3.0 18.7 + - - +
285F ILE 4.2 6.1 - - - +
286F ILE 3.2 0.6 - - - -
287F ARG* 1.3 76.5 - - - +
289F CYS* 1.3 57.4 + - - +
291F ASP* 2.9 14.5 - - - +
292F PHE* 3.3 13.5 - - - -
317F TRP* 4.5 9.6 - - + -
320F VAL* 4.0 18.6 - - + +
324F VAL* 3.7 24.7 - - + -
350F MET* 3.7 25.4 - - + -
353F LEU* 3.7 30.1 - - + +
354F MET* 3.7 26.0 - - + -
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Residues in contact with CYS 289 (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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285F ILE 3.4 14.8 - - - -
286F ILE* 3.0 18.8 + - - -
288F LEU* 1.3 76.9 - - - +
290F ASN* 1.3 64.0 + - - +
291F ASP* 3.3 2.2 - - - -
292F PHE* 3.6 9.4 + - - +
293F GLU 3.5 13.2 + - - -
294F LEU* 3.6 27.6 + - + +
299F ALA* 3.8 32.3 - - - -
302F ILE* 4.6 5.4 - - + -
324F VAL* 3.9 21.3 - - + -
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Residues in contact with ASN 290 (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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286F ILE* 2.6 34.3 + - + +
287F ARG* 3.6 14.1 + - - +
289F CYS* 1.3 75.0 - - - +
291F ASP* 1.3 61.2 + - - +
293F GLU* 3.2 23.5 + - - +
294F LEU 5.7 2.1 - - - +
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Residues in contact with ASP 291 (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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287F ARG 4.0 8.4 + - - +
288F LEU 2.9 22.2 - - - +
290F ASN* 1.3 71.3 - - - +
292F PHE* 1.3 71.5 + - - -
293F GLU* 3.1 15.1 + - - +
349F LYS* 3.4 29.6 + - - +
353F LEU* 3.3 25.5 - - - +
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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