Contacts of the helix formed by residues 371 - 391 (chain B) in PDB entry 3QNF
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 ASP 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B MET* 4.2 15.8 - - + +
368B TRP 3.1 12.4 + - - +
369B TRP 3.0 1.0 - - - -
370B ASN* 1.3 95.4 + - - +
372B LEU* 1.3 63.8 + - - +
373B TRP* 3.1 12.2 + - - +
374B LEU* 3.2 14.2 + - + +
375B ASN* 3.4 10.4 + - - +
420B SER* 4.8 1.2 + - - -
473B THR 4.1 1.9 - - - +
474B LYS* 3.2 14.2 - - - +
475B ASN* 2.7 56.2 + - + +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 4.1 21.3 - - + +
184B PRO* 6.4 0.2 - - + -
366B MET* 3.9 22.2 - - - -
369B TRP* 3.0 35.9 + - + +
371B ASP* 1.3 77.7 - - - +
373B TRP* 1.3 63.2 + - - +
375B ASN* 3.1 11.3 + - - +
376B GLU* 2.9 41.7 + - + +
432B MET 4.4 12.3 - - - +
438B TYR* 4.0 17.9 - - - +
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Residues in contact with TRP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B TRP 4.8 0.2 + - - -
370B ASN 3.2 21.8 + - - -
371B ASP* 3.4 15.8 + - - -
372B LEU* 1.3 79.5 - - - +
374B LEU* 1.3 98.7 + - + +
377B GLY* 2.8 28.2 + - - -
419B VAL* 3.4 33.4 - - + +
420B SER* 3.5 29.2 + - - -
421B THR 5.1 0.4 - - - -
437B SER* 5.3 1.8 - - - +
438B TYR* 4.0 28.0 - - + -
441B GLY* 4.9 10.2 - - - -
444B ILE* 4.9 7.6 - - + -
445B LEU* 6.1 1.1 - - + -
475B ASN* 3.7 26.7 - - + -
479B TRP* 3.9 11.9 - + - -
525B THR* 3.5 30.1 - - + -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PHE* 4.2 13.0 - - + -
371B ASP* 3.2 10.7 + - + +
372B LEU 3.1 0.6 - - - -
373B TRP* 1.3 113.1 - - + +
375B ASN* 1.3 68.3 - - - +
377B GLY* 4.9 0.4 - - - -
378B PHE* 2.9 27.0 + - - +
445B LEU* 4.7 11.9 - - + -
464B TYR* 5.0 5.6 - - - +
473B THR* 5.8 0.7 - - - +
474B LYS 5.4 0.4 - - - +
475B ASN* 3.8 28.5 - - + +
478B LEU* 3.8 38.4 - - + -
479B TRP* 3.9 11.7 - - + -
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Residues in contact with ASN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 5.0 0.6 + - - -
245B TYR* 4.3 3.2 + - - -
320B GLU* 3.8 7.3 + - - -
357B HIS* 3.2 27.0 + - - -
360B PHE* 3.1 36.3 - - + +
361B GLY* 3.2 10.5 - - - -
366B MET* 3.3 34.1 - - + +
371B ASP 3.4 8.4 + - - +
372B LEU* 3.1 13.2 + - + +
374B LEU* 1.3 82.3 - - - +
376B GLU* 1.3 64.4 + - - +
378B PHE* 3.7 3.1 - - - +
379B ALA 3.1 19.2 + - - -
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 4.7 4.5 - - - +
320B GLU* 3.5 8.3 - - - +
353B HIS* 2.8 13.8 + - + -
357B HIS* 3.1 9.2 + - - -
372B LEU* 2.9 34.9 + - + +
375B ASN* 1.3 75.9 + - - +
377B GLY* 1.3 68.6 + - - +
378B PHE 3.1 1.6 - - - -
379B ALA* 3.2 2.4 + - - +
380B LYS* 2.8 30.8 + - + +
432B MET 5.0 4.5 - - - +
433B PHE* 4.7 10.1 - - - +
438B TYR* 3.9 32.5 - - + -
5000B ZN 2.0 37.2 - - - -
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Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TRP* 2.8 24.1 + - - -
374B LEU* 3.8 1.3 - - - -
376B GLU* 1.3 72.9 - - - +
378B PHE* 1.3 56.0 + - - +
380B LYS* 3.4 3.0 + - - +
381B PHE* 2.8 28.9 + - - +
438B TYR* 3.6 23.1 - - - +
441B GLY 4.2 3.8 - - - -
442B ALA* 3.5 9.2 - - - +
445B LEU* 3.9 6.7 - - - -
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Residues in contact with PHE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TYR* 4.8 1.3 - + - -
297B PHE* 3.9 17.5 - + - -
356B ALA* 5.5 0.9 - - + -
360B PHE* 3.2 63.0 - + + -
374B LEU* 2.9 18.2 + - + +
375B ASN 3.7 0.2 - - - +
377B GLY* 1.3 71.9 - - - +
379B ALA* 1.3 58.3 + - - +
381B PHE* 3.6 4.8 - + - +
382B MET* 2.7 75.0 + - + +
445B LEU* 3.5 25.2 - - + +
457B PHE* 4.2 23.6 - + - -
461B ILE* 4.6 12.3 - - + -
478B LEU* 5.1 4.7 - - + -
482B MET* 6.2 0.2 - - + -
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B HIS* 3.3 40.0 - - + +
356B ALA* 4.3 11.4 - - + -
357B HIS* 3.3 29.6 - - + +
360B PHE 6.0 0.4 - - - -
375B ASN 3.1 5.7 + - - -
376B GLU 3.6 3.1 - - - +
378B PHE* 1.3 78.0 - - - +
380B LYS* 1.3 58.0 + - - +
382B MET* 3.1 5.2 + - - +
383B GLU* 2.9 28.2 + - - +
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Residues in contact with LYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B HIS* 3.8 15.9 - - + -
376B GLU* 2.8 18.7 + - - +
377B GLY 3.5 4.3 - - - +
379B ALA* 1.3 77.1 - - - +
381B PHE* 1.3 62.3 + - - +
383B GLU* 3.1 34.7 - - - +
384B PHE* 3.5 5.5 + - - +
400B PHE* 4.4 6.0 - - + -
433B PHE 3.6 23.9 + - - -
434B ASP* 4.1 5.3 - - - +
435B ASP 3.8 16.4 + - - +
438B TYR* 3.9 21.1 - - + -
439B ASP* 2.9 28.7 + - - +
442B ALA* 4.0 11.2 - - + -
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TYR* 5.2 0.2 - - - -
377B GLY 2.8 20.6 + - - +
378B PHE* 3.6 9.6 - + - +
379B ALA 3.2 0.2 - - - -
380B LYS* 1.3 72.9 - - - +
382B MET* 1.3 68.3 + - - +
384B PHE* 3.1 14.0 + + - +
385B VAL* 3.0 47.9 + - + +
400B PHE* 4.5 3.8 - + - -
442B ALA* 3.7 27.3 - - - +
445B LEU* 4.1 15.3 - - + -
446B ASN* 3.4 37.7 - - + -
449B ARG* 3.6 18.6 - - + -
457B PHE* 3.7 33.4 - + - -
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 4.2 5.2 - - + -
293B TYR* 3.6 33.2 - - + +
296B TYR* 3.6 35.7 - - + -
297B PHE* 4.4 1.1 - - + -
356B ALA* 3.9 11.0 - - + -
378B PHE* 2.7 62.8 + - + +
379B ALA 3.5 4.7 - - - +
381B PHE* 1.3 77.1 - - - +
383B GLU* 1.3 54.4 + - - +
385B VAL* 4.0 22.4 - - + -
386B SER* 2.6 43.0 + - - -
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Residues in contact with GLU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 4.3 0.4 + - - -
349B MET* 3.5 56.2 - - + +
352B ALA* 4.4 6.7 - - - -
353B HIS* 2.8 33.7 + - + +
379B ALA 2.9 19.0 + - - +
380B LYS* 3.1 23.1 - - - +
381B PHE 3.2 0.4 - - - -
382B MET* 1.3 74.2 - - - +
384B PHE* 1.3 58.3 + - - +
386B SER* 3.8 4.3 - - - -
387B VAL* 3.0 37.5 + - - +
396B VAL* 4.8 0.2 - - - +
399B TYR* 5.1 4.2 - - - -
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Residues in contact with PHE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B MET* 5.5 1.5 - - - -
380B LYS 3.5 0.6 + - - +
381B PHE* 3.1 21.0 + + - +
383B GLU* 1.3 80.7 - - - +
385B VAL* 1.3 58.3 + - + +
388B SER* 2.6 46.5 + - - -
396B VAL* 3.7 19.4 - - + +
397B GLY* 4.2 18.2 - - - -
400B PHE* 3.7 50.9 - + + -
401B PHE* 4.1 20.6 - + - -
446B ASN* 3.6 23.6 - - - -
449B ARG* 5.2 4.0 - - - -
605B ASN* 5.2 1.8 - - - -
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 4.0 10.5 - - + -
296B TYR* 4.6 10.5 - - + +
381B PHE* 3.0 55.8 + - + +
382B MET* 3.3 23.8 + - + +
384B PHE* 1.3 79.1 - - + +
386B SER* 1.3 62.2 + - - +
388B SER* 3.0 16.4 + - - -
389B VAL* 3.3 16.3 - - + +
449B ARG* 4.0 28.7 - - - +
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Residues in contact with SER 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 3.7 13.7 - - - -
292B PHE* 3.6 27.8 - - - -
293B TYR* 3.2 19.5 + - - -
352B ALA* 3.5 12.0 - - - +
382B MET 2.6 27.2 + - - -
383B GLU 3.2 4.0 + - - -
385B VAL* 1.3 73.2 - - - +
387B VAL* 1.3 64.2 + - - +
389B VAL* 2.9 20.6 + - - +
390B THR* 2.9 17.5 + - - +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU* 4.5 1.3 - - + -
345B LEU* 4.8 0.7 - - + -
348B THR* 3.5 38.4 - - + +
349B MET* 4.3 6.7 - - + -
352B ALA* 3.8 13.0 - - + -
383B GLU 3.0 19.0 + - - +
386B SER* 1.3 86.1 + - - +
388B SER* 1.3 60.8 + - - +
389B VAL 3.0 0.2 - - - -
390B THR* 3.4 6.7 - - - -
391B HIS* 2.8 43.5 + - + +
394B LEU* 4.4 5.4 - - + -
396B VAL* 3.0 26.9 - - + -
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Residues in contact with SER 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B PHE* 2.6 35.8 + - - -
385B VAL* 3.0 15.6 + - - -
387B VAL* 1.3 76.1 - - - +
389B VAL* 1.3 60.5 + - - +
391B HIS 5.0 0.2 - - - -
392B PRO* 3.8 22.3 - - - +
396B VAL* 3.5 18.6 - - - +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B PHE* 3.8 28.0 - - + -
385B VAL* 3.3 17.7 - - + +
386B SER 2.9 7.2 + - - +
388B SER* 1.3 83.5 - - - +
390B THR* 1.3 64.1 + - + +
392B PRO* 3.9 8.5 - - - +
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Residues in contact with THR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B THR* 3.3 35.3 - - + +
289B LEU* 3.6 16.0 - - + +
292B PHE* 3.8 29.2 - - + -
386B SER 2.9 17.2 + - - +
387B VAL* 3.4 7.6 - - - -
389B VAL* 1.3 80.4 - - + +
391B HIS* 1.3 81.3 + - - +
392B PRO* 3.3 8.3 - - - +
393B GLU* 4.8 0.7 - - - +
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Residues in contact with HIS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B TYR* 3.2 32.4 + + - -
284B ASP 5.4 0.4 - - - -
285B ALA* 4.0 30.0 + - - +
288B THR* 4.7 7.0 - - + -
289B LEU* 5.0 1.1 - - + -
348B THR* 3.5 21.9 + - + +
387B VAL* 2.8 29.2 + - + +
388B SER* 5.0 0.3 - - - -
390B THR* 1.3 95.3 + - - +
392B PRO* 1.3 67.0 - - - +
393B GLU* 3.1 19.7 - - - +
394B LEU* 3.0 24.8 + - + +
395B LYS 4.2 1.0 + - - -
396B VAL 5.4 0.3 + - - -
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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