Contacts of the helix formed by residues 373 - 386 (chain A) in PDB entry 5CTS
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 ASN 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLY* 2.9 31.1 + - - +
318A TYR 3.5 0.8 - - - +
319A GLY 2.6 27.7 + - - +
320A HIS* 4.2 6.5 - - + -
323A LEU* 5.8 0.2 - - + -
327A ASP* 3.6 15.0 - - + +
330A TYR* 3.6 7.9 - - - -
369A ASN* 6.2 0.2 - - - +
372A PRO* 1.3 74.9 - - - +
374A VAL* 1.3 68.2 + - - +
375A ASP* 2.9 25.5 + - - +
376A ALA* 3.0 13.9 + - - +
700A CMC 3.4 41.6 + - - +
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.7 1.8 - - + -
235A HIS* 3.5 29.2 - - + +
327A ASP* 2.9 16.8 + - - +
329A ARG* 3.5 46.7 - - + +
330A TYR* 4.5 2.7 - - - +
333A GLN* 3.1 33.2 + - - +
373A ASN* 1.3 71.0 - - - +
375A ASP* 1.3 77.6 + - - +
377A HIS* 3.2 6.7 + - - -
378A SER* 3.4 5.4 + - - -
397A PHE* 4.7 3.8 - - + -
700A CMC 3.7 12.8 - - + +
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Residues in contact with ASP 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A HIS* 4.8 1.0 + - - -
274A HIS 3.4 1.4 - - - +
275A GLY 4.4 0.7 - - - -
277A ALA* 3.0 34.7 - - + +
278A ASN* 3.4 24.7 - - - +
281A VAL* 3.3 17.5 - - - +
317A GLY* 4.5 1.8 - - - -
373A ASN* 2.9 11.0 + - - +
374A VAL* 1.3 88.5 - - - +
376A ALA* 1.3 63.4 + - - +
377A HIS 3.1 1.1 + - - -
378A SER* 4.0 13.4 + - - -
379A GLY 4.8 1.6 + - - -
397A PHE* 3.5 14.0 - - - -
700A CMC 2.6 28.1 + - - +
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 4.0 22.1 - - + +
316A PRO 4.9 0.2 - - - +
317A GLY* 3.0 30.2 - - - +
318A TYR* 4.1 10.8 - - + -
330A TYR* 3.8 15.3 - - + -
350A VAL* 4.0 18.8 - - + +
372A PRO* 3.9 4.7 - - + -
373A ASN 3.0 9.0 + - - +
375A ASP* 1.3 78.7 - - - +
377A HIS* 1.3 58.5 + - - +
380A VAL* 5.3 1.2 - - - +
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Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A TYR* 3.4 52.6 + + + -
333A GLN* 3.7 30.7 - - + +
334A ARG* 3.5 24.2 + - + +
337A ALA* 4.2 4.0 - - + -
347A PHE* 3.6 35.7 - + - -
350A VAL* 3.9 12.7 - - + +
351A ALA* 6.1 0.2 - - - -
374A VAL 3.2 2.2 + - - -
375A ASP 3.1 0.6 - - - -
376A ALA* 1.3 78.0 - - - +
378A SER* 1.3 63.2 + - - +
379A GLY 3.6 1.8 - - - -
380A VAL* 3.8 11.7 + - + +
381A LEU* 3.5 17.4 + - + +
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 3.8 22.4 + - - -
235A HIS* 4.2 6.4 + - - -
278A ASN* 3.0 25.8 + - - -
333A GLN* 3.1 22.2 + - - -
374A VAL 3.4 11.8 + - - -
375A ASP* 4.0 4.3 + - - -
376A ALA 3.9 0.2 - - - -
377A HIS* 1.3 75.6 - - - +
379A GLY* 1.3 65.4 + - - +
380A VAL 3.2 0.9 + - - -
381A LEU* 3.2 18.9 + - - +
382A LEU* 3.5 12.1 + - - +
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 4.8 3.9 + - - -
281A VAL* 6.1 1.2 - - - +
282A LEU* 3.6 19.7 - - - +
375A ASP 4.8 3.8 + - - -
376A ALA 5.6 0.4 - - - -
377A HIS 3.6 0.6 - - - -
378A SER* 1.3 82.7 + - - +
380A VAL* 1.3 62.0 + - - +
382A LEU* 3.0 15.7 + - - +
383A GLN* 3.0 17.0 + - - +
393A TYR* 3.7 22.5 + - - -
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 6.0 0.2 - - + -
282A LEU* 3.8 5.8 - - + +
285A LEU* 3.9 9.6 - - + -
341A LEU* 4.7 4.3 - - + -
344A ASP* 4.2 2.9 - - - +
346A MET* 3.3 25.1 - - + -
347A PHE* 3.5 42.8 - - + +
350A VAL* 3.3 30.1 - - + -
376A ALA 5.3 2.7 - - - +
377A HIS* 3.8 11.3 + - + +
378A SER 3.2 0.8 + - - -
379A GLY* 1.3 74.8 - - - +
381A LEU* 1.3 65.3 + - + +
383A GLN* 3.0 25.3 + - - +
384A TYR* 3.3 7.3 + - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU* 3.9 33.7 - - + -
230A LEU* 5.9 0.7 - - + -
231A TYR* 6.2 1.6 - - + -
333A GLN* 3.6 45.3 - - + +
336A PHE* 4.4 6.7 - - + -
337A ALA* 3.9 28.7 - - + +
341A LEU* 4.2 16.6 - - + -
377A HIS* 3.5 19.7 - - + +
378A SER 3.5 6.3 - - - +
380A VAL* 1.3 81.0 - - + +
382A LEU* 1.3 58.9 + - + +
384A TYR* 3.5 9.9 - - - +
385A TYR* 3.1 27.0 - - - -
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PHE* 4.3 14.8 - - + -
227A LEU* 4.0 19.7 - - + -
228A MET* 5.3 4.5 - - - -
231A TYR* 4.1 25.6 - - + +
378A SER* 3.7 14.8 - - - +
379A GLY* 3.0 8.2 + - - +
381A LEU* 1.3 73.8 - - + +
383A GLN* 1.3 58.5 + - - +
385A TYR* 3.0 20.3 + - - +
386A GLY 3.4 0.2 + - - -
387A MET* 3.2 26.6 + - + +
393A TYR* 3.6 40.2 - - + -
396A LEU* 3.9 27.8 - - + -
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A LEU* 4.1 9.9 - - + -
344A ASP* 3.7 26.2 + - - +
346A MET* 3.7 32.7 - - - +
379A GLY 3.0 14.9 + - - +
380A VAL* 3.0 19.9 + - - +
382A LEU* 1.3 71.3 - - - +
384A TYR* 1.3 66.9 + - - +
386A GLY* 2.9 20.3 + - - -
387A MET 3.5 11.8 + - - -
388A THR* 3.9 16.8 - - + +
393A TYR* 3.7 9.0 - - - +
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Residues in contact with TYR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A HIS 3.7 10.9 + - - -
341A LEU* 3.4 42.2 - - + +
344A ASP* 3.9 22.2 - - + -
380A VAL 3.3 7.5 + - - +
381A LEU 3.5 10.3 - - - +
382A LEU 3.2 0.2 - - - -
383A GLN* 1.3 87.5 - - - +
385A TYR* 1.3 101.8 + + - +
386A GLY 3.3 1.2 + - - -
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Residues in contact with TYR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A TYR* 3.6 15.2 - - - -
221A ASP* 4.0 24.6 - - + +
223A GLN* 3.7 29.7 - - + +
224A PHE* 3.2 30.3 - + + -
227A LEU* 3.7 23.8 - - + -
336A PHE* 3.7 15.6 - + - -
340A HIS* 3.6 26.5 + - - +
341A LEU* 4.0 2.6 - - + +
381A LEU 3.1 23.8 - - - -
382A LEU 3.0 7.2 + - - +
384A TYR* 1.3 106.8 - + - +
386A GLY* 1.3 54.6 + - - +
387A MET 3.4 3.6 - - - -
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Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ARG* 4.9 3.8 + - - -
219A TYR* 3.6 11.3 + - - -
383A GLN 2.9 12.7 + - - -
384A TYR 3.2 2.6 + - - -
385A TYR* 1.3 77.4 - - - +
387A MET* 1.3 59.8 + - - +
388A THR* 3.0 19.6 + - - +
389A GLU* 4.1 2.6 - - - +
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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