Contacts of the helix formed by residues 354 - 369 (chain X) in PDB entry 5G04
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 ARG 354 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348X HIS* 5.9 1.2 - - - -
349X SER* 3.2 17.0 + - - +
352X SER* 3.4 29.1 + - - +
353X LYS* 1.3 73.6 - - - +
355X TYR* 1.3 62.0 + - - +
356X SER* 3.5 4.3 - - - +
357X ARG* 3.5 62.4 + - + +
358X ALA 3.5 8.5 + - - -
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Residues in contact with TYR 355 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349X SER 5.1 0.2 - - - -
350X PHE* 3.9 32.3 + - + -
353X LYS* 3.3 32.8 + - + +
354X ARG* 1.3 71.1 - - - +
356X SER* 1.3 66.3 + - - +
358X ALA* 3.4 7.4 + - - +
359X LEU* 3.1 24.4 + - - +
382X ALA* 3.5 36.3 - - - +
385X ASN* 2.8 53.7 + - + +
386X MET* 3.5 26.0 - - + -
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Residues in contact with SER 356 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E TYR* 5.3 7.4 - - - -
354X ARG* 3.5 4.0 - - - -
355X TYR* 1.3 77.1 - - - +
357X ARG* 1.3 61.3 + - - +
359X LEU* 3.4 15.0 - - - +
360X TYR* 3.3 32.5 - - - -
386X MET* 5.4 9.2 - - - +
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Residues in contact with ARG 357 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E VAL* 3.5 33.0 - - + +
61E TYR* 4.7 16.1 + - + -
349X SER* 4.4 7.9 - - - +
354X ARG* 3.5 58.3 + - + +
355X TYR 3.3 0.4 - - - -
356X SER* 1.3 75.4 - - - +
358X ALA* 1.3 64.1 + - - +
360X TYR* 3.3 3.8 + - - +
361X LEU* 3.1 46.2 + - + +
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Residues in contact with ALA 358 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346X GLY* 3.9 20.2 - - - +
349X SER* 3.4 28.8 - - - -
350X PHE* 4.4 6.3 - - + -
354X ARG 3.5 3.7 + - - +
355X TYR* 3.4 10.0 + - - +
357X ARG* 1.3 77.1 - - - +
359X LEU* 1.3 63.8 + - - +
361X LEU* 4.2 2.0 - - - +
362X GLY* 3.0 23.4 + - - -
378X LEU* 5.1 2.2 - - + +
379X LYS* 5.2 2.9 - - - -
382X ALA* 3.8 17.9 - - + -
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Residues in contact with LEU 359 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355X TYR 3.1 13.7 + - - +
356X SER* 3.4 14.4 - - - +
358X ALA* 1.3 75.8 - - - +
360X TYR* 1.3 86.7 + - + +
363X ALA 3.1 22.2 + - - -
379X LYS* 3.2 48.0 + - + +
382X ALA* 4.2 6.6 - - + +
383X LEU* 3.7 32.8 - - + +
386X MET* 6.1 4.3 - - + -
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Residues in contact with TYR 360 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E TYR* 3.2 53.4 - + + +
64E ALA* 4.9 8.2 - - + +
65E SER* 4.0 22.7 - - - -
68E LYS* 3.9 30.8 - - - +
356X SER* 3.3 26.0 + - - -
357X ARG 3.3 4.4 + - - +
359X LEU* 1.3 97.4 - - + +
361X LEU* 1.3 64.9 + - - +
363X ALA* 3.3 15.8 + - + +
364X LYS* 3.3 12.1 + - - +
379X LYS* 5.6 1.1 - - - -
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Residues in contact with LEU 361 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E SER* 4.1 20.2 - - - +
58E VAL* 5.0 2.9 - - + +
61E TYR* 4.4 10.3 - - + -
342X TRP* 3.6 52.0 - - + +
345X SER* 3.7 37.2 - - - +
346X GLY* 4.2 2.0 - - - +
349X SER* 4.5 2.2 - - - +
357X ARG* 3.1 42.4 + - + +
358X ALA 4.2 1.8 - - - +
360X TYR* 1.3 75.1 - - - +
362X GLY* 1.3 56.8 + - - +
364X LYS* 3.4 7.0 + - - +
365X ALA 3.2 19.2 + - - -
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Residues in contact with GLY 362 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342X TRP 4.8 1.0 + - - -
358X ALA 3.0 18.2 + - - -
359X LEU 3.9 1.1 - - - -
361X LEU* 1.3 76.0 - - - +
363X ALA* 1.3 62.1 + - - +
365X ALA* 3.3 12.1 - - - +
366X ILE* 3.1 25.3 + - - +
375X ALA 4.2 5.2 - - - +
378X LEU* 4.2 18.6 - - - +
379X LYS* 4.4 8.5 - - - -
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Residues in contact with ALA 363 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359X LEU 3.1 6.0 + - - +
360X TYR* 3.3 14.6 + - + +
362X GLY* 1.3 75.4 - - - +
364X LYS* 1.3 62.0 + - - +
366X ILE* 3.1 27.9 + - + +
367X GLN* 3.1 13.1 + - - +
379X LYS* 3.1 29.6 - - + +
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Residues in contact with LYS 364 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E SER* 4.2 13.8 + - - +
336X ASP* 5.2 4.2 + - - -
337X GLN* 5.5 3.2 + - - +
342X TRP* 3.7 47.9 - - + +
360X TYR 3.3 7.7 + - - +
361X LEU* 3.4 10.8 - - - +
362X GLY 3.3 0.2 - - - -
363X ALA* 1.3 74.9 - - - +
365X ALA* 1.3 59.8 + - - +
367X GLN* 2.9 37.5 + - - +
368X LEU* 2.8 45.5 + - + +
337Y GLN* 6.0 2.4 - - - +
364Y LYS* 5.9 2.0 - - - +
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Residues in contact with ALA 365 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339X ALA* 3.4 20.1 - - - +
342X TRP* 3.9 14.3 - - + +
343X VAL* 3.6 31.2 - - + +
361X LEU 3.2 4.2 + - - +
362X GLY* 3.3 18.2 - - - +
364X LYS* 1.3 79.0 - - - +
366X ILE* 1.3 60.6 + - - +
368X LEU* 4.9 0.2 - - - -
369X ASN 3.2 23.4 + - - +
375X ALA* 3.8 7.4 - - + +
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Residues in contact with ILE 366 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362X GLY 3.1 14.2 + - - +
363X ALA* 3.3 21.5 - - + +
365X ALA* 1.3 74.1 - - - +
367X GLN* 1.3 61.9 + - - +
369X ASN 3.2 23.2 - - - +
370X SER* 3.3 21.8 + - - +
372X SER 5.5 1.1 - - - +
375X ALA* 4.0 14.1 - - + +
376X LEU* 4.3 38.1 - - + +
379X LYS* 4.1 15.7 - - + -
395X HIS* 5.5 2.2 - - + +
402X LEU* 5.7 1.6 - - + -
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Residues in contact with GLN 367 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X LYS* 3.5 36.8 + - + +
363X ALA 3.1 10.9 + - - +
364X LYS* 2.9 44.2 + - - +
366X ILE* 1.3 78.7 - - - +
368X LEU* 1.3 73.6 + - + +
369X ASN* 4.7 0.2 - - - -
370X SER* 4.7 2.8 + - - -
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Residues in contact with LEU 368 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X LYS* 5.9 3.1 - - - +
337X GLN* 3.6 41.3 - - + +
338X HIS 3.5 32.8 - - - +
339X ALA* 4.0 10.8 - - - +
342X TRP* 3.5 25.4 - - + +
364X LYS* 2.8 33.0 + - + +
365X ALA 4.1 1.1 - - - +
367X GLN* 1.3 89.5 - - - +
369X ASN* 1.3 68.7 + - - +
370X SER 4.2 0.5 + - - -
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Residues in contact with ASN 369 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305X ILE* 5.8 0.2 - - - +
337X GLN 5.2 3.6 - - - +
338X HIS* 4.8 7.4 + - - +
339X ALA* 3.5 30.1 - - + +
340X GLU* 3.6 19.4 + - - -
365X ALA 3.2 10.9 + - - +
366X ILE* 3.2 11.3 - - - +
368X LEU* 1.3 86.2 - - - +
370X SER* 1.3 64.6 + - - +
371X ASN* 3.5 20.1 + - - +
372X SER* 3.6 18.6 + - - +
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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