Contacts of the helix formed by residues 292 - 305 (chain O) in PDB entry 5MQF
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 VAL 292 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286O GLU 4.6 4.1 + - - -
287O MET* 4.6 8.1 - - - +
289O ASN 3.9 13.5 + - - +
290O ARG 4.8 1.3 - - - +
291O GLN* 1.3 77.9 - - - +
293O ASN* 1.3 58.3 + - - +
294O HIS 3.5 1.7 - - - +
295O ALA* 3.6 18.5 - - + +
296O ARG* 2.9 28.1 + - - +
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Residues in contact with ASN 293 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L ALA* 4.5 21.1 - - + -
291O GLN* 2.8 11.6 + - + +
292O VAL* 1.3 77.0 - - - +
294O HIS* 1.3 60.1 + - - +
296O ARG* 3.3 4.7 + - - +
297O ASN* 2.9 29.5 + - - +
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Residues in contact with HIS 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224L PHE* 6.1 5.8 - - + -
286O GLU* 5.5 1.3 - - - +
291O GLN* 5.0 7.2 - - + +
292O VAL 4.6 0.8 - - - +
293O ASN* 1.3 78.2 - - - +
295O ALA* 1.3 57.5 + - - +
297O ASN* 4.2 7.3 - - - +
298O ILE* 2.9 29.3 + - - +
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Residues in contact with ALA 295 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283O ALA* 4.7 7.0 - - - +
286O GLU* 3.4 41.4 - - + +
287O MET* 3.8 11.0 - - + +
292O VAL* 3.5 17.5 + - + +
293O ASN 3.1 0.8 - - - -
294O HIS* 1.3 77.1 - - - +
296O ARG* 1.3 59.2 + - - +
298O ILE* 3.4 6.2 + - - +
299O TRP* 2.9 27.0 + - - +
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Residues in contact with ARG 296 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292O VAL 2.9 18.9 + - - +
293O ASN* 3.8 4.9 - - - +
295O ALA* 1.3 74.8 - - - +
297O ASN* 1.3 59.9 + - - +
299O TRP* 3.0 9.6 + - - +
300O ASP* 2.9 26.3 + - - +
319O MET* 5.5 10.8 - - + -
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Residues in contact with ASN 297 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L TYR 5.4 0.7 - - - +
226L ASP* 3.6 37.0 - - + +
293O ASN 2.9 17.8 + - - +
294O HIS* 4.2 7.9 - - - +
296O ARG* 1.3 76.3 - - - +
298O ILE* 1.3 57.5 + - - +
300O ASP* 3.3 9.2 + - - +
301O ARG* 2.9 25.5 + - - +
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Residues in contact with ILE 298 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283O ALA* 5.9 8.1 - - + -
286O GLU* 5.8 4.5 - - + -
294O HIS 2.9 22.7 + - - +
295O ALA* 3.6 7.9 - - - +
296O ARG 3.2 0.2 - - - -
297O ASN* 1.3 72.2 - - - +
299O TRP* 1.3 60.5 + - - +
301O ARG* 3.2 10.1 + - - +
302O ALA* 2.9 27.5 + - - +
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Residues in contact with TRP 299 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283O ALA* 5.8 8.0 - - + +
295O ALA 2.9 14.4 + - - +
296O ARG* 3.0 12.8 + - - +
298O ILE* 1.3 76.5 - - - +
300O ASP* 1.3 55.7 + - - +
302O ALA* 3.2 8.7 + - - +
303O ILE* 2.9 25.8 + - - +
315O LYS* 5.1 17.0 - - + +
319O MET* 5.3 12.1 - - + -
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Residues in contact with ASP 300 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 5.6 6.7 - - + +
296O ARG 2.9 11.5 + - - +
297O ASN* 3.6 11.9 - - - +
299O TRP* 1.3 73.7 - - - +
301O ARG* 1.3 61.3 + - - +
303O ILE* 3.1 10.2 + - - +
304O THR* 2.9 27.4 + - - -
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Residues in contact with ARG 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 6.4 0.7 - - - -
297O ASN 2.9 15.3 + - - +
298O ILE* 3.2 13.7 + - + +
300O ASP* 1.3 76.1 - - - +
302O ALA* 1.3 58.6 + - - +
304O THR* 3.5 8.6 + - - +
305O THR* 2.9 25.7 + - - -
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Residues in contact with ALA 302 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O TRP* 5.8 8.3 - - + -
298O ILE 2.9 14.0 + - - +
299O TRP* 3.2 11.6 + - - +
301O ARG* 1.3 73.3 - - - +
303O ILE* 1.3 64.3 + - - +
305O THR* 3.1 27.1 + - - +
306O LEU 3.7 9.7 - - - +
307O PRO* 4.6 1.0 - - - +
311O GLN* 6.5 1.6 - - + -
312O PHE* 5.7 1.9 - - - +
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Residues in contact with ILE 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299O TRP 2.9 12.9 + - - +
300O ASP* 3.1 14.1 + - + +
302O ALA* 1.3 77.2 - - - +
304O THR* 1.3 56.1 + - - +
305O THR 3.0 12.6 - - - +
307O PRO* 4.8 7.2 - - - +
312O PHE* 5.4 13.5 - - + +
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Residues in contact with THR 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 4.3 10.5 - - - -
102C ALA* 3.8 39.5 - - - +
226C PRO 5.5 0.9 - - - +
227C ALA 4.8 0.2 - - - -
228C PRO* 3.7 21.1 - - - +
300O ASP 2.9 11.8 + - - -
301O ARG* 3.7 10.8 - - - -
303O ILE* 1.3 73.8 - - - +
305O THR* 1.3 61.4 + - - +
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Residues in contact with THR 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C PRO* 5.0 18.4 - - - -
227C ALA 4.1 8.5 - - - -
228C PRO* 4.0 6.3 - - - +
301O ARG 2.9 18.0 + - - -
302O ALA* 3.1 14.0 + - - +
303O ILE 3.0 14.4 - - - +
304O THR* 1.3 77.9 - - - +
306O LEU* 1.3 68.4 + - - +
307O PRO* 3.1 6.4 - - - +
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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