Contacts of the helix formed by residues 355 - 367 (chain G) in PDB entry 5U0A
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 SER 355 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327F GLU 3.8 9.4 - - - -
328F VAL* 3.1 18.2 - - - +
330F PRO* 3.8 18.5 - - - +
338G ALA* 4.2 2.9 - - - +
353G TYR* 3.2 2.7 - - - +
354G ASP* 1.3 82.4 - - - +
356G TYR* 1.3 61.7 + - - +
357G PRO* 4.0 2.5 - - - +
358G ALA* 3.1 24.2 + - - +
359G LEU* 3.0 28.2 + - - +
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Residues in contact with TYR 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325F LEU* 6.2 0.2 - - + -
328F VAL* 3.0 34.8 + - + +
329F TRP* 3.5 32.1 - + + -
264G LEU* 4.0 20.0 - - + -
280G LEU* 4.7 9.2 - - + -
281G PRO* 2.5 45.0 + - + -
282G ASP 3.9 10.2 + - - -
283G LEU 4.1 1.6 + - - -
284G VAL* 3.4 33.2 - - + -
338G ALA* 3.6 19.3 + - + -
340G VAL* 4.4 3.8 + - - +
355G SER* 1.3 70.8 - - - +
357G PRO* 1.3 64.7 - - + +
359G LEU* 3.1 5.5 + - - +
360G ILE* 2.9 34.8 + - + +
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Residues in contact with PRO 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328F VAL 4.1 0.7 - - - +
329F TRP* 4.5 8.3 - - + -
330F PRO* 4.1 19.1 - - + +
261G ARG* 4.0 23.6 - - - +
355G SER* 3.7 10.5 - - - +
356G TYR* 1.3 94.5 - - + +
358G ALA* 1.3 56.4 + - - +
360G ILE* 3.9 8.9 - - + +
361G ASP* 2.9 41.2 + - - +
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Residues in contact with ALA 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G TYR* 4.3 13.7 - - + -
354G ASP* 5.0 2.7 - - + +
355G SER* 3.1 27.8 + - - +
356G TYR 3.2 0.8 - - - -
357G PRO* 1.3 78.5 - - - +
359G LEU* 1.3 58.2 + - - +
361G ASP* 3.8 5.0 - - - +
362G ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284G VAL* 3.4 33.4 - - + +
286G ILE* 3.9 20.9 - - + -
336G GLY 3.7 19.5 - - - +
337G TYR* 3.9 16.4 - - - -
338G ALA* 3.9 2.0 - - + +
353G TYR* 3.6 32.9 - - + +
355G SER 3.0 14.0 + - - +
356G TYR* 3.1 8.0 + - - +
358G ALA* 1.3 74.7 - - - +
360G ILE* 1.3 66.3 + - + +
362G ALA* 3.2 1.1 + - - -
363G MET* 2.9 37.3 + - + +
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Residues in contact with ILE 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F TRP* 6.2 1.1 - - + -
257G ALA* 3.9 23.6 - - + +
260G LEU* 3.8 14.4 - - + -
261G ARG* 3.6 36.3 - - + +
264G LEU* 3.9 16.6 - - + -
286G ILE* 3.9 23.8 - - + -
356G TYR* 2.9 24.7 + - + +
357G PRO* 3.9 7.2 - - + +
359G LEU* 1.3 74.8 - - + +
361G ASP* 1.3 62.3 + - - +
364G VAL* 2.9 41.0 + - + +
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Residues in contact with ASP 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ARG* 5.0 1.2 + - - -
257G ALA* 5.1 7.3 - - - +
357G PRO* 2.9 26.1 + - - +
358G ALA* 3.9 5.2 - - - +
360G ILE* 1.3 82.3 - - - +
362G ALA* 1.3 58.5 + - - +
364G VAL* 4.8 3.1 - - - +
365G ALA* 2.9 31.7 + - - +
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Residues in contact with ALA 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353G TYR* 3.6 36.3 - - + +
358G ALA 2.9 19.0 + - - +
359G LEU 3.2 3.1 + - - +
361G ASP* 1.3 79.3 - - - +
363G MET* 1.3 61.8 + - + +
365G ALA* 3.8 4.8 - - - +
366G ALA* 2.9 27.0 + - - +
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Residues in contact with MET 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 5.6 1.5 - - + +
260G LEU* 5.6 0.4 - - + -
286G ILE* 3.7 32.3 - - + +
288G VAL* 3.7 14.8 - - + +
334G ILE* 4.0 26.9 - - + +
335G ARG 3.5 26.2 - - - +
353G TYR* 3.4 42.8 - - + +
359G LEU* 2.9 31.3 + - + +
360G ILE 4.3 1.1 - - - +
362G ALA* 1.3 77.7 - - + +
364G VAL* 1.3 67.5 + - + +
366G ALA* 3.1 5.2 + - - +
367G ALA* 3.1 18.4 + - - +
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Residues in contact with VAL 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G VAL* 5.9 2.7 - - + -
253G ARG* 3.8 47.4 + - + +
256G VAL* 4.0 18.6 - - + -
257G ALA* 4.0 28.9 - - + +
260G LEU* 4.2 9.0 - - + -
360G ILE* 2.9 26.4 + - + +
361G ASP* 4.3 3.1 - - - +
363G MET* 1.3 76.0 - - - +
365G ALA* 1.3 63.0 + - - +
367G ALA* 3.0 22.4 + - - +
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Residues in contact with ALA 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253G ARG* 3.6 24.0 - - - +
361G ASP 2.9 21.0 + - - +
362G ALA* 3.9 4.7 - - - +
364G VAL* 1.3 78.2 - - - +
366G ALA* 1.3 60.8 + - - +
367G ALA 3.4 3.1 + - - -
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Residues in contact with ALA 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288G VAL* 4.7 3.2 - - + +
290G PHE* 5.3 3.1 - - - -
334G ILE* 3.6 46.4 - - + +
362G ALA 2.9 18.6 + - - +
363G MET* 3.4 10.5 - - + +
364G VAL 3.1 0.6 - - - -
365G ALA* 1.3 78.1 - - - +
367G ALA* 1.3 56.7 + - - +
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Residues in contact with ALA 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G THR 6.1 0.2 - - - +
4G VAL* 4.3 6.5 - - + -
239G LEU* 3.7 31.5 - - + +
288G VAL* 3.8 20.0 - - + -
290G PHE* 6.1 2.2 - - + -
363G MET 3.1 11.3 + - - +
364G VAL* 3.0 17.4 + - - +
365G ALA 3.2 3.3 - - - -
366G ALA* 1.3 81.6 - - - +
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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