Contacts of the helix formed by residues 377 - 395 (chain B) in PDB entry 3HB1
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 MET 377 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B VAL* 4.1 11.2 - - + +
339B ASP* 2.8 59.7 - - - +
375B ASP* 3.4 9.0 + - - +
376B TRP* 1.3 110.9 - - + +
378B ARG* 1.3 72.2 + - - +
380B LEU* 3.4 6.7 + - - +
381B ALA* 3.1 22.3 + - - +
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Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER 4.5 1.8 + - - -
339B ASP* 3.0 58.6 + - - +
340B ASP* 4.1 6.4 + - - +
341B ASN* 3.2 29.9 - - - +
375B ASP* 3.0 39.7 + - - +
376B TRP 3.4 0.4 - - - -
377B MET* 1.3 83.5 - - - +
379B LYS* 1.3 60.6 + - + +
380B LEU 3.1 5.5 + - - -
381B ALA 3.8 0.2 + - - -
382B PHE* 3.1 39.0 + - + -
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Residues in contact with LYS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B TYR* 3.9 12.4 + - - +
350B PHE* 5.4 0.7 - - - -
353B ASP* 3.3 26.7 - - - +
354B GLY* 2.9 43.1 + - - +
355B PHE* 3.8 16.5 - - + -
375B ASP 3.6 16.1 + - - +
376B TRP* 3.6 8.0 + - + +
377B MET 3.3 0.6 - - - -
378B ARG* 1.3 77.4 - - + +
380B LEU* 1.3 60.4 + - - +
382B PHE* 4.1 10.1 - - + +
383B ARG* 3.6 28.6 + - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.6 31.2 - - + -
328B CYS* 3.8 14.8 - - + -
330B GLN* 4.4 7.0 - - - +
336B VAL* 3.3 41.1 - - + -
355B PHE* 3.7 18.2 - - + -
376B TRP* 3.4 29.9 + - + +
377B MET* 3.6 9.4 - - - +
378B ARG 3.1 0.6 - - - -
379B LYS* 1.3 77.0 - - - +
381B ALA* 1.3 61.2 + - - +
382B PHE 3.0 5.5 + - - -
383B ARG* 3.2 12.3 + - - +
384B TYR* 3.3 25.2 + - + -
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B VAL* 3.5 37.2 - - + +
337B SER* 5.2 0.9 - - - -
339B ASP 3.3 27.4 - - - +
340B ASP* 3.6 13.7 - - + +
377B MET 3.1 5.9 + - - -
378B ARG 3.8 0.6 + - - +
380B LEU* 1.3 76.5 - - - +
382B PHE* 1.3 57.8 + - - +
384B TYR* 3.9 6.3 - - - +
385B ARG* 3.1 26.9 + - - +
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Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP* 3.0 34.1 - - - -
341B ASN* 3.3 13.9 - - - -
343B GLN* 3.3 36.8 - - + -
345B LEU* 3.7 19.4 - - + +
348B TYR* 3.3 41.5 - + + -
350B PHE* 4.0 9.6 - - + -
378B ARG* 3.1 28.6 + - + +
379B LYS* 4.2 7.9 - - + +
380B LEU 3.0 0.6 - - - -
381B ALA* 1.3 76.4 - - - +
383B ARG* 1.3 61.3 + - - +
385B ARG* 3.2 11.1 + - - +
386B ARG* 2.9 31.2 + - - +
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Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.4 38.5 - - + -
324B ASP* 3.0 28.2 + - - -
325B LEU* 4.1 26.0 - - + -
350B PHE* 3.4 43.8 + - + +
353B ASP* 2.9 28.1 + - - -
355B PHE* 3.1 31.6 - - - +
379B LYS 3.6 12.6 + - - +
380B LEU 3.2 7.4 + - - +
382B PHE* 1.3 78.5 - - - +
384B TYR* 1.3 58.1 + - - +
386B ARG* 3.3 2.1 + - - +
387B VAL* 2.9 34.4 + - - +
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Residues in contact with TYR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 3.3 41.2 - - + +
328B CYS* 3.2 18.3 + - + -
330B GLN* 3.2 41.2 + - + +
333B VAL* 3.9 40.5 - - + +
336B VAL* 5.1 4.7 - - + -
380B LEU* 3.3 26.4 + - + +
381B ALA* 4.0 9.6 - - - +
382B PHE 3.1 0.6 - - - -
383B ARG* 1.3 78.0 - - - +
385B ARG* 1.3 59.8 + - - +
387B VAL* 3.7 7.6 - - + +
388B LYS* 3.0 28.1 + - - +
451B LEU* 3.8 16.2 - - + +
452B ILE* 4.4 14.6 - - + +
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Residues in contact with ARG 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP* 2.6 40.6 + - - +
342B GLY* 3.5 5.8 - - - -
343B GLN* 2.5 45.5 + - - +
345B LEU* 2.8 30.5 - - - +
381B ALA 3.1 19.2 + - - +
382B PHE* 3.2 5.7 + - - +
384B TYR* 1.3 76.7 - - - +
386B ARG* 1.3 58.2 + - - +
388B LYS* 3.5 12.2 + - + +
389B GLU* 2.9 50.0 + - + +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE* 3.9 16.4 - - + -
345B LEU* 3.9 24.0 + - + +
346B SER* 5.5 5.2 - - - +
350B PHE* 3.9 26.0 - - + -
382B PHE 2.9 17.5 + - - +
383B ARG 3.5 5.2 - - - +
385B ARG* 1.3 75.9 - - - +
387B VAL* 1.3 65.6 + - - +
389B GLU* 3.2 29.2 + - - +
390B MET* 3.1 54.9 + - + +
394B TYR* 6.2 0.6 - - - -
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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
----------------------------------------------------------
320B LEU* 4.1 34.0 - - + +
321B PHE* 3.9 18.6 - - + -
325B LEU* 4.8 0.9 - - + -
333B VAL* 5.3 3.1 - - + -
383B ARG 2.9 21.6 + - - +
384B TYR* 3.7 9.2 - - + +
386B ARG* 1.3 76.0 - - - +
388B LYS* 1.3 67.5 + - - +
390B MET* 3.0 12.8 + - + +
391B TYR* 2.9 22.8 + - + +
452B ILE* 4.5 11.7 - - + -
455B LEU* 3.7 31.4 - - + -
469B ILE* 4.8 1.8 - - + -
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B VAL* 4.1 11.9 - - + -
334B ASP* 2.6 41.2 + - - +
384B TYR 3.0 17.9 + - - +
385B ARG* 3.6 13.0 - - + +
387B VAL* 1.3 77.0 - - - +
389B GLU* 1.3 58.7 + - + +
391B TYR* 3.4 1.4 + - - +
392B ASN* 2.6 45.3 + - - +
469B ILE* 3.7 34.3 - - + -
470B GLU* 4.0 15.0 - - - +
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Residues in contact with GLU 389 (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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343B GLN 5.4 0.2 - - - +
345B LEU* 3.6 19.7 - - - +
346B SER* 5.6 3.1 + - - -
385B ARG* 2.9 42.2 + - + +
386B ARG* 3.3 33.5 + - - +
387B VAL 3.1 0.4 - - - -
388B LYS* 1.3 78.1 - - + +
390B MET* 1.3 58.0 + - + +
392B ASN* 3.5 5.3 + - - +
393B THR* 2.9 37.2 + - + +
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Residues in contact with MET 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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319B HIS* 3.1 38.6 - - - +
320B LEU* 4.3 7.4 - - + -
321B PHE* 4.3 3.8 - - + -
386B ARG* 3.3 55.9 - - + +
387B VAL* 3.0 21.0 + - + +
389B GLU* 1.3 75.1 - - + +
391B TYR* 1.3 68.0 + - - +
393B THR* 3.3 8.1 - - - +
394B TYR* 2.8 44.8 + - + +
401B LEU* 4.8 14.1 - - + -
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Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 2.9 13.7 + - + +
388B LYS 3.6 8.3 - - - +
390B MET* 1.3 75.9 - - - +
392B ASN* 1.3 68.0 + - - +
395B LYS* 2.7 55.7 + - + +
455B LEU* 4.0 29.2 - - + -
458B VAL* 3.4 20.2 - - + +
459B LEU* 3.8 36.1 - - + -
464B GLY* 3.3 17.5 - - - -
467B PHE 2.6 29.8 + - - -
469B ILE* 3.7 31.2 - - + -
472B ILE* 3.7 5.0 - - + +
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Residues in contact with ASN 392 (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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388B LYS* 2.6 40.0 + - - +
389B GLU* 3.9 5.7 - - - +
391B TYR* 1.3 88.3 - - - +
393B THR* 1.3 62.0 + - + +
394B TYR 3.1 3.1 + - - -
395B LYS* 3.5 40.1 + - - +
469B ILE* 4.2 9.8 + - - +
470B GLU* 4.8 3.7 + - - +
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Residues in contact with THR 393 (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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389B GLU* 2.9 22.8 + - + +
390B MET* 3.2 4.2 + - - +
392B ASN* 1.3 79.6 - - + +
394B TYR* 1.3 90.8 + - - +
397B ASN* 4.4 8.1 + - - +
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Residues in contact with TYR 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG* 6.2 0.7 - - - -
390B MET* 2.8 39.4 + - + +
391B TYR* 5.2 0.4 - - - -
393B THR* 1.3 97.2 - - - +
395B LYS* 1.3 53.9 + - - +
396B ASN 2.7 18.7 + - - +
397B ASN* 2.7 51.2 + - - +
398B VAL* 3.1 13.4 + - - +
400B GLY* 3.6 20.9 + - - -
401B LEU* 3.6 37.7 - - + -
459B LEU* 4.7 4.3 - - + -
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B TYR* 2.7 34.9 + - + +
392B ASN* 3.5 37.7 + - - +
394B TYR* 1.3 71.0 - - - +
396B ASN* 1.3 79.8 + - + +
398B VAL* 4.8 6.7 - - - +
459B LEU* 3.8 15.2 - - + +
462B GLY* 5.7 2.4 - - - +
464B GLY* 3.7 34.8 + - - +
465B SER* 3.8 11.4 + - - +
468B PRO* 5.0 11.3 - - - +
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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