Contacts of the helix formed by residues 335 - 354 (chain G) in PDB entry 1RZK
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 LYS 335 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333G LEU 3.3 5.3 + - - -
334G SER* 1.3 73.0 + - - +
336G THR* 1.3 56.9 + - - +
338G TRP* 4.1 0.5 - - - +
339G GLU* 2.9 38.2 + - + +
389G GLN* 6.0 0.6 + - - -
407G LEU* 2.8 34.9 + - + +
408G ASN* 3.3 20.1 - - + +
409G ASN 4.9 0.4 - - - +
411G GLY* 3.2 39.7 + - - +
412G ARG 3.5 20.3 + - - +
413G ASN 4.3 7.8 + - - -
414G ILE* 3.6 31.5 - - + +
908G NAG 4.0 3.8 - - - +
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Residues in contact with THR 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G SER* 3.4 8.6 + - - -
335G LYS* 1.3 75.9 + - - +
337G GLN* 1.3 70.6 + - + +
339G GLU* 3.0 6.3 + - - +
340G ASN* 2.9 40.5 + - - +
412G ARG 4.6 2.1 + - - -
908G NAG 4.0 28.7 + - - +
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Residues in contact with GLN 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G GLU* 6.0 5.4 - - - +
291G SER 4.1 6.2 - - - +
292G VAL* 3.9 31.8 - - + +
293G VAL* 4.1 11.1 + - - +
334G SER* 3.0 30.0 + - - +
336G THR* 1.3 82.6 - - + +
338G TRP* 1.3 57.6 + - - +
340G ASN* 3.4 9.8 + - - +
341G THR* 2.7 35.0 + - - -
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Residues in contact with TRP 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259G LEU* 4.1 13.9 - - + -
292G VAL* 4.2 12.1 - - + +
333G LEU* 3.6 20.9 - - + -
334G SER 2.9 18.1 + - - +
337G GLN* 1.3 74.7 - - - +
339G GLU* 1.3 66.4 + - - +
341G THR* 4.2 14.4 - - + -
342G LEU* 3.1 53.9 + - + +
389G GLN 4.6 2.0 - - - -
390G LEU* 2.9 54.3 + - + +
391G PHE* 4.5 4.3 - + - -
414G ILE* 3.6 16.8 - - + -
449G ILE* 3.7 30.1 - - + -
452G LEU* 3.9 27.4 - - + -
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Residues in contact with GLU 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G LYS* 2.9 25.1 + - + +
336G THR* 3.4 5.2 - - - +
338G TRP* 1.3 76.3 - - - +
340G ASN* 1.3 71.8 + - - +
342G LEU* 3.4 6.4 + - + +
343G GLU* 2.9 32.1 + - - +
393G TRP* 3.0 30.9 + - + -
397G ARG 4.8 0.5 - - - +
398G LYS* 3.7 32.0 - - + +
407G LEU* 4.7 17.7 - - + +
408G ASN* 6.2 2.2 - - + -
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Residues in contact with ASN 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G GLU* 6.1 0.7 - - - +
336G THR* 2.9 31.8 + - - +
337G GLN* 3.6 9.7 - - - +
339G GLU* 1.3 78.1 - - - +
341G THR* 1.3 54.7 + - - +
343G GLU* 2.6 48.2 + - - +
344G GLN* 2.9 24.5 + - - +
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Residues in contact with THR 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 4.8 1.3 - - + -
288G LEU* 3.4 27.1 - - + -
290G GLU 4.8 3.1 + - - -
292G VAL* 3.2 17.5 - - - +
337G GLN* 2.7 26.8 + - - +
338G TRP* 3.7 20.2 - - + -
340G ASN* 1.3 72.5 - - - +
342G LEU* 1.3 63.1 + - - +
344G GLN* 3.2 11.0 + - - -
345G ILE* 2.9 49.8 + - + +
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Residues in contact with LEU 342 (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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338G TRP* 3.1 61.0 + - + +
339G GLU* 3.8 7.0 - - - +
340G ASN 3.1 0.2 + - - -
341G THR* 1.3 76.1 - - - +
343G GLU* 1.3 52.8 + - - +
345G ILE* 3.6 9.8 - - + +
346G ALA* 2.7 37.2 + - - +
361G PHE* 3.7 29.4 - - + -
389G GLN 5.6 1.1 - - - +
390G LEU 3.6 13.5 - - - +
391G PHE* 5.3 2.0 - - + -
393G TRP* 3.5 40.8 - - + -
407G LEU* 6.3 0.9 - - + -
452G LEU* 5.0 3.6 - - + -
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Residues in contact with GLU 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G GLU* 2.9 43.4 - - - +
340G ASN* 2.6 28.7 + - - +
342G LEU* 1.3 67.9 - - - +
344G GLN* 1.3 55.2 + - + +
345G ILE 2.7 5.6 + - - -
346G ALA* 2.9 6.9 + - - +
347G ILE* 2.7 37.8 + - - +
393G TRP* 4.3 13.3 + - + -
398G LYS* 6.0 0.9 - - - -
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Residues in contact with GLN 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.0 33.3 - - + +
289G ASN* 5.8 0.9 - - - -
290G GLU* 5.2 6.8 + - - +
340G ASN* 2.9 34.7 + - - +
341G THR* 3.2 7.3 + - - +
343G GLU* 1.3 77.0 - - + +
345G ILE* 1.3 55.3 + - - +
347G ILE* 4.1 8.7 - - - -
348G LYS* 3.5 5.5 - - - +
789G NAG 3.2 65.5 + - + +
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Residues in contact with ILE 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270G ILE* 3.9 14.4 - - + -
272G ILE* 5.4 2.1 - - + +
286G VAL* 4.0 14.8 - - + -
288G LEU* 3.8 7.4 - - + -
341G THR* 2.9 42.4 + - + +
342G LEU* 3.6 7.9 - - + +
343G GLU 2.8 0.2 - - - -
344G GLN* 1.3 77.6 - - - +
346G ALA* 1.3 63.3 + - - +
347G ILE 3.0 1.3 - - - -
348G LYS* 3.0 6.9 + - - +
349G LEU* 2.9 32.2 + - + +
361G PHE* 3.7 21.5 - - + -
452G LEU* 3.8 26.2 - - + -
454G LEU* 4.0 17.3 - - + -
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Residues in contact with ALA 346 (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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342G LEU 2.7 20.8 + - - +
343G GLU 2.9 4.0 + - - +
345G ILE* 1.3 79.3 - - - +
347G ILE* 1.3 57.5 + - - +
349G LEU* 3.7 4.4 + - - -
350G LYS* 3.0 24.6 + - - +
359G ILE* 3.4 38.6 - - + +
361G PHE* 4.2 1.8 - - + -
393G TRP* 3.4 24.0 - - + -
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Residues in contact with ILE 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G GLU 2.7 16.7 + - - +
344G GLN* 4.1 10.1 - - - +
346G ALA* 1.3 76.9 - - - +
348G LYS* 1.3 79.4 + - + +
349G LEU 3.2 1.8 - - - -
350G LYS* 3.6 16.4 - - + +
351G GLU* 3.2 24.8 + - - +
789G NAG 4.8 9.4 - - + -
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Residues in contact with LYS 348 (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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232G LYS* 3.4 26.1 - - - +
269G GLU* 3.2 28.0 + - - +
270G ILE* 3.2 33.8 + - + +
271G VAL* 5.5 0.2 - - - -
272G ILE* 3.6 23.5 - - + +
344G GLN 3.5 18.2 - - - +
345G ILE 3.0 8.6 + - - +
347G ILE* 1.3 85.3 - - + +
349G LEU* 1.3 63.6 + - - +
351G GLU* 3.3 47.8 + - - +
352G GLN* 3.9 1.0 - - - +
789G NAG 4.0 11.2 - - - -
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Residues in contact with LEU 349 (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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272G ILE* 3.9 22.0 - - + -
284G ILE* 4.3 6.5 - - + -
345G ILE* 2.9 21.7 + - + +
346G ALA* 3.8 4.9 - - - +
347G ILE 3.2 0.2 - - - -
348G LYS* 1.3 74.8 - - - +
350G LYS* 1.3 53.5 + - - +
351G GLU 2.9 3.8 - - - -
352G GLN* 2.7 28.6 + - - +
353G PHE* 3.0 18.5 + - + -
359G ILE* 4.0 15.9 - - + -
361G PHE* 3.5 32.3 - - + -
454G LEU* 4.4 8.5 - - + -
468G PHE* 3.3 49.6 - - + -
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Residues in contact with LYS 350 (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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346G ALA* 3.0 17.7 + - - +
347G ILE* 3.6 22.0 - - + +
349G LEU* 1.3 69.8 - - - +
351G GLU* 1.3 56.3 + - - +
352G GLN 2.9 6.6 + - - -
353G PHE* 3.8 4.9 - - - +
354G GLY* 2.9 47.2 + - - +
355G ASN* 3.1 30.9 + - - +
357G LYS 2.9 29.8 + - - -
358G THR* 4.5 0.4 - - - +
359G ILE* 3.5 22.8 - - + +
395G ASP* 3.6 20.7 + - - -
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Residues in contact with GLU 351 (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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232G LYS* 4.0 13.2 + - - -
347G ILE* 3.2 19.5 + - - +
348G LYS* 3.3 46.3 + - - +
349G LEU 2.9 1.0 - - - -
350G LYS* 1.3 75.7 - - - +
352G GLN* 1.3 61.6 + - - +
355G ASN* 5.7 1.1 - - - +
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Residues in contact with GLN 352 (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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272G ILE* 4.3 6.7 - - + -
277G PHE* 3.1 60.1 - - + +
348G LYS 3.9 7.4 - - - +
349G LEU 3.2 10.3 - - - +
350G LYS 2.9 1.2 + - - -
351G GLU* 1.3 83.4 - - - +
353G PHE* 1.3 66.4 + - + +
354G GLY 3.6 1.3 - - - +
734G NAG 3.7 23.2 + - - -
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Residues in contact with PHE 353 (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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277G PHE* 3.2 47.1 - + + -
278G THR* 5.2 0.4 - - - -
284G ILE* 3.9 6.1 - - + -
349G LEU* 3.0 31.6 + - + +
350G LYS* 4.8 3.8 - - - -
352G GLN* 1.3 84.1 - - + +
354G GLY* 1.3 59.2 + - - +
357G LYS* 3.1 27.8 + - + +
359G ILE* 5.9 1.3 - - + -
456G ARG* 3.1 49.6 - - - -
466G GLU* 4.3 18.4 - - + +
468G PHE* 3.7 26.9 - + - -
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Residues in contact with GLY 354 (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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350G LYS* 2.9 15.5 + - - +
352G GLN 3.6 1.8 - - - -
353G PHE* 1.3 80.6 - - - +
355G ASN* 1.3 67.8 + - - +
356G ASN 3.3 3.6 - - - -
357G LYS* 2.9 24.8 - - - +
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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
------------------------------------------------------------
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