Contacts of the helix formed by residues 335 - 353 (chain G) in PDB entry 1OPT
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 335 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G ILE 3.1 4.9 + - - -
334G SER* 1.3 71.3 - - - +
336G ALA* 1.3 56.7 + - - +
338G TRP* 4.1 1.6 - - - +
339G ASN* 3.1 31.3 + - + +
410G GLY 3.3 14.5 + - - -
411G SER* 3.0 45.5 + - - +
412G ASP 2.8 23.8 + - - +
413G THR 3.9 17.2 + - - +
414G ILE* 3.5 32.3 - - + +
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Residues in contact with ALA 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G SER* 3.2 2.6 - - - -
335G ARG* 1.3 76.9 - - - +
337G LYS* 1.3 68.2 + - + +
339G ASN* 3.1 8.6 + - - +
340G ASN* 3.0 23.0 + - - +
411G SER 6.2 0.4 - - - +
412G ASP* 4.1 4.2 + - - +
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Residues in contact with LYS 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G SER 5.2 9.4 - - - +
292G VAL* 4.6 19.5 - - + -
293G GLU* 3.9 26.0 + - + +
334G SER* 3.6 28.0 + - - +
336G ALA* 1.3 76.9 - - + +
338G TRP* 1.3 63.6 + - - +
340G ASN* 3.0 10.3 + - - +
341G THR* 3.0 25.9 + - - +
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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 10.3 - - + -
288G LEU* 5.7 2.5 - - + -
292G VAL* 4.3 10.4 - - + +
333G ILE* 3.6 28.0 - - + -
334G SER 3.1 16.4 + - - +
335G ARG 4.3 2.0 - - - +
337G LYS* 1.3 77.5 - - - +
339G ASN* 1.3 58.2 + - - +
341G THR* 2.6 40.4 + - - -
342G LEU* 3.0 38.2 + - + +
345G ILE* 5.3 2.5 - - + -
389G GLN 5.6 0.2 - - - -
390G LEU* 3.0 42.1 + - + +
391G PHE* 3.9 24.7 - + - -
414G ILE* 4.9 7.9 - - + -
449G ILE* 4.1 28.0 - - + -
452G LEU* 3.5 26.9 - - + -
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Residues in contact with ASN 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G ARG* 3.1 23.1 + - + +
336G ALA* 3.1 9.6 + - - +
338G TRP* 1.3 79.4 - - - +
340G ASN* 1.3 59.7 + - - +
342G LEU* 4.7 5.3 - - - +
343G LYS* 3.5 4.5 + - - +
395G TRP* 3.1 40.6 - - - -
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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
----------------------------------------------------------
336G ALA 3.0 11.3 + - - +
337G LYS* 3.0 11.4 + - - +
339G ASN* 1.3 76.8 - - - +
341G THR* 1.3 64.4 + - + +
343G LYS* 3.4 16.7 + - - +
344G GLN* 3.2 33.0 + - - +
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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
----------------------------------------------------------
288G LEU* 5.1 12.6 - - + +
290G THR* 4.9 8.3 - - + +
292G VAL* 3.3 32.8 - - + -
337G LYS 3.0 8.8 + - - +
338G TRP* 2.6 42.6 + - + -
340G ASN* 1.3 73.4 - - + +
342G LEU* 1.3 57.4 + - - +
344G GLN* 3.3 19.0 + - - +
345G ILE* 3.0 40.4 + - - +
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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
----------------------------------------------------------
338G TRP* 3.0 51.9 + - + +
339G ASN* 4.1 3.6 - - - +
340G ASN 3.4 0.2 - - - -
341G THR* 1.3 78.8 + - - +
343G LYS* 1.3 55.5 + - - +
345G ILE* 3.2 10.1 + - + +
346G ALA* 2.7 36.6 + - - +
361G PHE* 3.5 41.6 - - + -
390G LEU 3.9 9.6 - - - +
391G PHE* 5.1 2.0 - - + -
393G SER* 3.7 18.8 - - - +
395G TRP* 3.4 21.8 - - + -
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Residues in contact with LYS 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G ASN 3.5 7.0 + - - +
340G ASN* 3.4 22.1 + - - +
341G THR 3.4 0.4 - - - -
342G LEU* 1.3 76.0 - - - +
344G GLN* 1.3 54.9 + - + +
346G ALA* 3.9 1.4 - - - +
347G SER* 2.8 39.8 + - - -
395G TRP* 3.5 38.2 - - + -
396G PHE* 3.5 34.7 - - + -
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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 VAL* 3.7 21.2 - - + +
288G LEU* 5.8 2.8 - - - +
289G ASN* 3.5 31.5 + - - +
290G THR* 5.3 5.2 + - - -
340G ASN* 3.2 20.7 + - - +
341G THR* 3.4 28.6 + - - +
342G LEU 3.3 0.2 - - - -
343G LYS* 1.3 74.5 - - + +
345G ILE* 1.3 58.8 + - - +
347G SER* 3.2 8.0 + - - -
348G LYS* 2.8 34.8 + - - +
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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 VAL* 4.7 6.2 - - + +
272G ILE* 5.2 1.7 - - + +
286G VAL* 4.0 22.9 - - + -
288G LEU* 4.5 15.9 - - + -
338G TRP* 5.3 2.0 - - + -
341G THR* 3.0 29.2 + - - +
342G LEU* 3.5 15.9 - - + +
344G GLN* 1.3 73.4 - - + +
346G ALA* 1.3 52.3 + - - +
348G LYS* 3.1 8.5 + - - +
349G LEU* 2.7 50.1 + - + +
361G PHE* 3.7 20.4 - - + -
452G LEU* 4.0 26.5 - - + -
454G LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G LEU 2.7 19.7 + - - +
343G LYS 3.9 2.7 - - - +
345G ILE* 1.3 73.1 - - - +
347G SER* 1.3 57.0 + - - +
349G LEU* 3.1 3.1 + - - +
350G ARG* 2.9 34.9 + - - +
359G ILE* 3.5 36.6 - - + +
361G PHE* 4.0 2.4 - - + -
395G TRP* 3.9 19.3 - - + -
396G PHE* 3.9 7.6 - - + -
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Residues in contact with SER 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G LYS* 2.8 26.8 + - - -
344G GLN* 3.3 8.7 - - - -
346G ALA* 1.3 71.0 - - - +
348G LYS* 1.3 59.4 + - - +
350G ARG* 2.9 53.3 + - - +
351G GLU* 3.3 11.5 + - - +
396G PHE* 4.0 3.0 - - - -
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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
----------------------------------------------------------
269G GLU* 2.9 40.6 + - - +
270G VAL* 2.9 42.2 + - + +
271G VAL* 5.1 2.1 - - - +
272G ILE* 4.1 22.8 - - + +
344G GLN 2.8 18.2 + - - +
345G ILE* 3.4 8.1 - - - +
347G SER* 1.3 73.0 - - - +
349G LEU* 1.3 64.4 + - - +
351G GLU* 3.1 34.1 + - - +
352G GLN* 3.0 22.0 + - - +
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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
----------------------------------------------------------
272G ILE* 4.2 24.0 - - + -
284G ILE* 4.9 8.5 - - + -
345G ILE* 2.7 40.8 + - + +
346G ALA 3.1 6.0 + - - +
348G LYS* 1.3 70.2 - - - +
350G ARG* 1.3 57.9 + - - +
352G GLN 2.9 18.2 + - - -
353G PHE* 2.9 25.3 + - + -
359G ILE* 3.7 31.2 - - + -
361G PHE* 4.1 3.6 - - + -
454G LEU* 4.8 2.9 - - + -
468G PHE* 3.4 49.1 - - + -
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Residues in contact with ARG 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G LYS* 5.5 0.2 - - - +
346G ALA 2.9 13.9 + - - +
347G SER* 2.9 50.7 + - - +
349G LEU* 1.3 72.5 - - - +
351G GLU* 1.3 58.4 + - - +
353G PHE* 3.7 1.1 - - - -
354G GLY 2.8 46.5 + - - +
355G ASN* 3.3 23.0 + - - +
357G LYS 4.6 0.2 - - - +
359G ILE* 3.4 19.7 - - + +
396G PHE* 3.4 48.7 - - - -
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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
----------------------------------------------------------
269G GLU* 5.5 0.7 - - - +
347G SER 3.3 11.6 + - - +
348G LYS* 3.1 49.7 + - - +
349G LEU 3.0 0.6 - - - -
350G ARG* 1.3 80.7 - - - +
352G GLN* 1.3 58.5 + - - +
353G PHE 5.0 0.7 - - - +
355G ASN* 4.7 7.9 + - - +
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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
----------------------------------------------------------
272G ILE* 3.5 35.2 - - + -
277G PHE* 3.2 48.8 - - + +
348G LYS 3.0 4.6 + - - +
349G LEU 2.9 5.9 + - - +
351G GLU* 1.3 76.6 - - - +
353G PHE* 1.3 71.4 + - + +
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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
----------------------------------------------------------
277G PHE* 3.7 39.9 - + + -
278G THR* 5.6 0.9 - - - -
284G ILE* 4.5 0.9 - - + -
349G LEU* 2.9 26.9 + - + +
350G ARG* 3.7 2.4 - - - +
351G GLU 5.0 0.9 - - - +
352G GLN* 1.3 87.3 - - + +
354G GLY* 1.3 59.8 + - - +
355G ASN* 5.0 1.9 + - - -
357G LYS* 5.3 4.9 - - + +
456G ARG* 3.1 53.8 - - - -
466G GLU* 4.4 22.4 - - + +
468G PHE* 3.9 22.7 - + - -
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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