Contacts of the helix formed by residues 354 - 369 (chain Y) 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 Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E ASP* 5.2 7.9 + - - -
348Y HIS* 5.7 2.4 - - - -
349Y SER* 3.2 16.1 + - - -
352Y SER* 3.4 28.6 + - - +
353Y LYS* 1.3 73.0 - - - +
355Y TYR* 1.3 62.6 + - - +
356Y SER* 3.5 3.4 - - - +
357Y ARG* 3.5 61.8 + - + +
358Y ALA 3.5 8.1 + - - -
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Residues in contact with TYR 355 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350Y PHE* 3.5 41.0 + + + -
353Y LYS* 3.3 36.8 + - + +
354Y ARG* 1.3 70.1 - - - +
356Y SER* 1.3 65.3 + - - +
358Y ALA* 3.4 6.9 + - - +
359Y LEU* 3.1 23.7 + - - +
382Y ALA* 3.7 26.9 - - - +
385Y ASN* 3.2 54.0 + - + -
386Y MET* 4.0 19.1 - - + -
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Residues in contact with SER 356 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354Y ARG* 3.5 2.2 - - - -
355Y TYR* 1.3 77.7 - - - +
357Y ARG* 1.3 62.0 + - - +
359Y LEU* 3.4 15.1 - - - +
360Y TYR* 3.3 31.1 - - - -
386Y MET* 5.1 10.2 - - - +
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Residues in contact with ARG 357 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E THR* 4.0 17.6 + - - +
69E GLN* 4.1 31.3 + - - +
70E VAL* 4.0 17.0 - - + +
73E ASP* 4.2 24.9 + - - +
349Y SER* 4.4 9.9 - - - +
354Y ARG* 3.5 56.8 + - + +
355Y TYR 3.3 0.2 - - - -
356Y SER* 1.3 76.8 - - - +
358Y ALA* 1.3 65.1 + - - +
360Y TYR* 3.3 5.6 + - - +
361Y LEU* 3.1 39.1 + - + +
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Residues in contact with ALA 358 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346Y GLY* 3.9 20.9 - - - +
349Y SER* 3.4 27.9 - - - -
350Y PHE* 4.2 7.6 - - + -
354Y ARG 3.5 3.7 + - - +
355Y TYR* 3.4 9.8 + - - +
357Y ARG* 1.3 77.7 - - - +
359Y LEU* 1.3 64.3 + - - +
361Y LEU* 4.2 1.5 - - - +
362Y GLY* 3.0 24.3 + - - -
378Y LEU* 5.1 2.4 - - + +
379Y LYS* 5.3 2.1 - - - -
382Y ALA* 3.8 16.8 - - + -
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Residues in contact with LEU 359 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355Y TYR 3.1 13.5 + - - +
356Y SER* 3.4 14.6 - - - +
357Y ARG 3.3 0.2 - - - -
358Y ALA* 1.3 77.1 - - - +
360Y TYR* 1.3 86.5 + - + +
363Y ALA* 3.1 28.3 + - + +
379Y LYS* 3.8 26.3 - - + +
382Y ALA* 3.9 10.2 - - + +
383Y LEU* 3.7 36.8 - - + -
386Y MET* 5.4 11.4 - - + -
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Residues in contact with TYR 360 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E PHE* 3.7 30.2 - + + -
62E GLN* 4.6 27.5 - - + -
63E VAL* 4.6 4.3 - - + +
66E THR* 4.8 16.2 - - + +
356Y SER* 3.3 28.6 + - - +
357Y ARG* 3.3 7.3 + - - +
359Y LEU* 1.3 97.1 - - + +
361Y LEU* 1.3 65.4 + - - +
363Y ALA* 3.3 13.3 + - + +
364Y LYS* 3.4 10.4 + - - +
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Residues in contact with LEU 361 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E VAL* 5.1 0.9 - - - -
66E THR* 3.9 19.9 - - + +
67E LEU* 4.9 1.6 - - + +
70E VAL* 3.8 28.7 - - + -
332Y PHE* 5.6 0.4 - - + -
342Y TRP* 3.6 51.7 - - + +
345Y SER* 3.7 38.6 - - - +
346Y GLY* 4.2 2.2 - - - +
349Y SER* 4.5 1.8 - - - +
357Y ARG* 3.1 32.5 + - + +
358Y ALA 4.2 1.6 - - - +
360Y TYR* 1.3 75.0 - - - +
362Y GLY* 1.3 56.3 + - - +
364Y LYS* 3.4 7.9 + - - +
365Y ALA 3.2 19.4 + - - -
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Residues in contact with GLY 362 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342Y TRP 5.0 0.4 - - - -
346Y GLY* 5.4 0.2 - - - -
358Y ALA 3.0 18.4 + - - -
359Y LEU 3.9 1.1 - - - -
361Y LEU* 1.3 74.9 - - - +
363Y ALA* 1.3 62.7 + - - +
365Y ALA* 3.3 11.7 - - - +
366Y ILE* 3.1 26.1 + - - +
375Y ALA 4.1 4.6 - - - +
378Y LEU* 4.1 19.0 - - - +
379Y LYS* 4.6 9.0 - - - -
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Residues in contact with ALA 363 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E PHE* 3.6 20.2 - - + -
359Y LEU* 3.1 13.9 + - + +
360Y TYR* 3.4 11.7 - - + +
362Y GLY* 1.3 75.0 - - - +
364Y LYS* 1.3 61.6 + - - +
366Y ILE* 3.1 27.2 + - + +
367Y GLN* 3.1 12.6 + - - +
379Y LYS* 3.4 24.8 - - - +
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Residues in contact with LYS 364 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PHE* 3.3 13.7 - - + -
60E SER* 4.2 11.9 + - - +
63E VAL* 3.3 50.3 - - + +
364X LYS* 5.9 1.6 - - - +
336Y ASP* 5.7 2.0 - - - -
337Y GLN* 5.5 3.7 + - - -
342Y TRP* 3.7 32.3 - - + +
360Y TYR 3.4 1.6 + - - +
361Y LEU 3.4 9.6 - - - +
362Y GLY 3.3 0.2 - - - -
363Y ALA* 1.3 75.1 - - - +
365Y ALA* 1.3 60.8 + - - +
367Y GLN* 2.9 32.1 + - - +
368Y LEU* 2.8 48.2 + - + +
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Residues in contact with ALA 365 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339Y ALA* 3.4 19.3 - - - +
342Y TRP* 3.9 9.4 - - + +
343Y VAL* 3.6 32.1 - - + +
361Y LEU 3.2 8.3 + - - +
362Y GLY* 3.3 17.7 - - - +
364Y LYS* 1.3 79.8 - - - +
366Y ILE* 1.3 60.6 + - - +
368Y LEU* 3.5 0.4 + - - -
369Y ASN 3.2 23.0 + - - +
375Y ALA* 3.8 7.3 - - + +
378Y LEU* 5.2 0.2 - - + -
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Residues in contact with ILE 366 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362Y GLY 3.1 14.2 + - - +
363Y ALA* 3.1 12.7 + - + +
365Y ALA* 1.3 76.0 - - - +
367Y GLN* 1.3 62.8 + - - +
369Y ASN 3.2 23.4 - - - +
370Y SER* 3.3 20.9 + - - +
372Y SER 5.6 0.7 - - - +
375Y ALA* 4.0 13.4 - - + +
376Y LEU* 4.3 38.6 - - + +
379Y LYS* 3.6 35.2 - - + +
395Y HIS* 5.3 1.6 - - + +
402Y LEU* 5.9 0.4 - - + -
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Residues in contact with GLN 367 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLU* 2.8 29.0 + - - +
59E PHE* 3.2 26.3 - - + -
60E SER* 5.7 3.0 - - - -
150Y LYS* 6.1 0.9 - - - -
363Y ALA 3.1 12.1 + - - +
364Y LYS* 2.9 34.3 + - - +
366Y ILE* 1.3 79.7 - - - +
368Y LEU* 1.3 73.2 + - - +
370Y SER* 4.8 2.6 + - - -
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Residues in contact with LEU 368 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336Y ASP* 5.3 0.2 - - - +
337Y GLN* 3.6 41.6 - - + +
338Y HIS 3.5 32.5 - - - +
339Y ALA* 4.0 11.2 - - - +
342Y TRP* 3.5 24.7 - - + +
364Y LYS* 2.8 30.2 + - + +
365Y ALA 4.1 1.6 - - - +
367Y GLN* 1.3 93.5 - - - +
369Y ASN* 1.3 69.1 + - - +
370Y SER 4.1 0.7 + - - -
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Residues in contact with ASN 369 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Y ILE* 5.7 0.4 - - - +
337Y GLN 5.4 2.4 - - - +
338Y HIS* 4.8 7.4 + - - +
339Y ALA* 3.5 30.6 - - + +
340Y GLU* 3.6 18.8 + - - -
365Y ALA 3.2 10.9 + - - +
366Y ILE* 3.2 11.6 - - - +
368Y LEU* 1.3 87.1 - - - +
370Y SER* 1.3 64.1 + - - +
371Y ASN* 3.3 21.1 + - - +
372Y SER* 3.7 19.0 + - - +
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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
------------------------------------------------------------
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