Contacts of the helix formed by residues 374 - 395 (chain C) 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 VAL 374 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C ASP* 4.7 0.3 - - - +
373C GLY* 1.3 87.9 - - - +
375C ASP* 1.3 66.4 + - + +
376C TRP 3.2 1.6 - - - +
377C MET* 3.2 14.7 - - - +
378C ARG* 3.0 26.8 - - - +
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Residues in contact with ASP 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C GLY 4.9 0.2 - - - +
374C VAL* 1.3 79.5 - - + +
376C TRP* 1.3 66.6 + - - +
377C MET 3.2 0.4 - - - -
378C ARG* 2.7 48.4 + - - +
379C LYS* 3.3 29.0 + - - +
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Residues in contact with TRP 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C CYS* 5.2 10.8 - - + -
354C GLY* 4.0 22.5 + - - -
355C PHE* 4.9 18.9 - + - -
372C GLY* 3.9 16.3 - - - -
373C GLY* 3.7 26.0 - - - +
374C VAL 3.8 0.2 - - - +
375C ASP* 1.3 79.9 + - - +
377C MET* 1.3 102.2 + - - +
379C LYS* 3.0 39.3 + - + +
380C LEU* 3.2 32.7 + - + +
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Residues in contact with MET 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C VAL* 5.2 11.9 - - + -
339C ASP* 2.8 37.9 - - + +
373C GLY* 3.4 29.6 - - - +
374C VAL* 3.2 11.4 - - - +
376C TRP* 1.3 108.5 - - - +
378C ARG* 1.3 51.5 + - - +
380C LEU* 2.6 36.0 + - + +
381C ALA* 2.7 16.2 + - - +
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Residues in contact with ARG 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ASP* 3.0 38.3 + - - +
340C ASP* 3.8 8.7 - - - +
341C ASN* 4.9 6.3 - - - +
374C VAL* 3.0 29.2 + - - +
375C ASP* 2.7 49.9 + - - +
376C TRP 3.5 0.6 - - - -
377C MET* 1.3 77.4 - - - +
379C LYS* 1.3 57.7 + - - +
381C ALA* 4.0 0.5 - - - +
382C PHE* 2.9 50.1 + - + -
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Residues in contact with LYS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C TYR* 4.0 18.4 - - + +
353C ASP* 2.6 42.6 + - - +
354C GLY* 4.5 10.3 - - - -
355C PHE* 6.3 0.4 - - - -
375C ASP* 3.3 33.3 + - - +
376C TRP* 3.0 24.0 + - + +
377C MET 3.0 0.8 - - - -
378C ARG* 1.3 80.2 - - - +
380C LEU* 1.3 62.4 + - - +
382C PHE* 3.2 22.6 - - + +
383C ARG* 3.3 19.6 + - - +
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LEU* 4.8 5.4 - - + -
328C CYS* 4.1 20.4 - - + -
330C GLN* 4.3 7.0 - - - +
336C VAL* 3.6 35.0 - - + -
376C TRP* 3.2 38.5 + - + +
377C MET* 2.6 24.6 + - + +
379C LYS* 1.3 72.0 - - - +
381C ALA* 1.3 68.3 + - + +
382C PHE 2.9 4.3 - - - -
383C ARG* 2.6 40.0 + - - +
384C TYR* 3.3 19.6 + - + -
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C VAL* 3.2 35.3 - - + +
337C SER* 5.1 1.0 - - - -
339C ASP* 3.0 30.3 - - + +
340C ASP* 4.2 7.6 - - + +
377C MET 2.7 14.0 + - - +
378C ARG 4.0 0.2 - - - +
380C LEU* 1.3 80.0 - - + +
382C PHE* 1.3 55.7 + - - +
384C TYR* 3.6 3.1 + - - +
385C ARG* 3.1 27.0 + - - +
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Residues in contact with PHE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ASP* 2.9 22.7 - - - -
341C ASN* 3.2 33.2 - - - -
343C GLN* 3.8 12.3 - - - -
345C LEU* 3.1 33.2 - - + +
348C TYR* 3.3 27.4 - + + -
350C PHE* 3.8 12.9 - - + -
378C ARG* 2.9 35.3 + - + +
379C LYS* 3.2 12.1 - - + +
380C LEU 2.9 0.2 - - - -
381C ALA* 1.3 75.1 - - - +
383C ARG* 1.3 59.3 + - - +
385C ARG* 2.9 25.4 - - - -
386C ARG* 2.9 25.8 + - - +
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Residues in contact with ARG 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PHE* 3.5 40.3 - - + -
324C ASP* 3.3 25.4 + - - +
325C LEU* 3.7 20.8 - - + +
348C TYR* 4.2 3.2 + - - -
350C PHE* 2.9 41.1 + - - +
353C ASP 2.9 30.5 + - - -
354C GLY* 3.0 20.6 - - - -
379C LYS 3.3 20.7 + - - +
380C LEU* 2.6 23.1 + - - +
382C PHE* 1.3 68.8 - - - +
384C TYR* 1.3 50.9 + - - +
386C ARG* 3.1 3.3 + - - +
387C VAL* 2.7 40.9 + - - +
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Residues in contact with TYR 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LEU* 3.5 39.7 + - + +
328C CYS* 4.1 3.4 + - - -
329C ASP* 3.5 13.6 + - - -
330C GLN* 3.5 51.7 + - + -
333C VAL* 3.4 42.2 - - + +
336C VAL* 4.3 11.2 - - + -
380C LEU* 3.3 21.7 + - + -
381C ALA 4.1 5.2 - - - +
383C ARG* 1.3 76.0 - - - +
385C ARG* 1.3 65.3 + - - +
387C VAL* 3.8 6.7 - - + +
388C LYS* 3.0 24.1 + - - +
451C LEU* 4.4 9.4 - - + -
452C ILE* 4.2 18.2 - - + -
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Residues in contact with ARG 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ASP* 2.5 27.2 + - - +
342C GLY* 3.9 5.2 - - - -
343C GLN 2.7 45.8 + - - +
345C LEU* 3.1 20.0 - - + +
381C ALA 3.1 17.9 + - - +
382C PHE* 2.9 38.5 - - - +
384C TYR* 1.3 76.6 - - - +
386C ARG* 1.3 52.2 + - - +
388C LYS* 3.3 10.4 - - + +
389C GLU* 2.8 50.9 + - + +
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Residues in contact with ARG 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PHE* 3.7 22.6 - - + -
345C LEU* 4.0 20.1 + - + +
346C SER* 4.4 19.0 + - - +
350C PHE* 3.8 18.6 - - + -
382C PHE 2.9 19.0 + - - +
383C ARG 3.1 4.7 + - - +
385C ARG* 1.3 74.1 - - - +
387C VAL* 1.3 64.4 + - - +
389C GLU* 3.2 30.2 + - - +
390C MET* 3.1 49.8 + - + +
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 3.8 28.0 - - + +
321C PHE* 3.6 22.7 - - + -
325C LEU* 4.1 12.1 - - + -
333C VAL* 5.6 2.5 - - + -
383C ARG 2.7 32.0 + - - +
384C TYR* 3.8 9.9 - - + +
386C ARG* 1.3 70.6 - - - +
388C LYS* 1.3 68.3 + - - +
390C MET* 3.2 9.5 + - - +
391C TYR* 3.0 21.9 + - + +
452C ILE* 4.4 8.5 - - + -
455C LEU* 3.9 26.5 - - + -
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Residues in contact with LYS 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C VAL* 3.8 15.0 - - + +
334C ASP* 2.9 36.9 + - - +
384C TYR 3.0 19.3 + - - +
385C ARG* 3.3 8.3 - - + +
386C ARG 3.2 0.2 - - - -
387C VAL* 1.3 80.6 - - - +
389C GLU* 1.3 64.1 + - - +
391C TYR* 3.1 8.0 + - - +
392C ASN* 3.1 35.1 + - - +
469C ILE* 3.9 17.5 - - + -
470C GLU* 3.7 23.5 + - - +
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Residues in contact with GLU 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C LEU* 4.3 11.4 + - - +
346C SER* 4.7 7.0 + - - -
385C ARG* 2.8 47.4 + - + +
386C ARG* 3.3 40.2 + - - +
388C LYS* 1.3 76.1 - - + +
390C MET* 1.3 59.8 + - + +
392C ASN* 2.9 13.3 + - - +
393C THR* 2.8 30.3 + - + +
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Residues in contact with MET 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C HIS* 2.9 42.2 - - - +
320C LEU* 4.4 5.2 - - + -
321C PHE* 4.8 4.7 - - + -
386C ARG* 3.1 56.7 + - + +
387C VAL* 3.8 11.7 - - - +
389C GLU* 1.3 76.2 - - - +
391C TYR* 1.3 61.4 + - - +
393C THR* 3.0 8.4 + - - +
394C TYR* 2.8 49.5 + - + +
401C LEU* 4.7 11.4 - - + -
459C LEU* 6.0 0.2 - - - -
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Residues in contact with TYR 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 6.1 0.6 - - - +
387C VAL* 3.0 15.3 + - + +
388C LYS 3.3 9.9 - - - +
390C MET* 1.3 75.3 - - - +
392C ASN* 1.3 56.1 - - - +
395C LYS* 2.7 56.1 + - + +
455C LEU* 4.2 17.0 - - + -
458C VAL* 3.6 21.2 - - + +
459C LEU* 3.9 37.9 - - + -
464C GLY* 3.5 16.7 - - - -
467C PHE 2.5 23.8 + - - -
469C ILE* 3.4 55.6 - - + -
472C ILE* 3.7 5.5 - - + +
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Residues in contact with ASN 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C LYS* 3.1 28.1 + - - +
389C GLU* 2.9 10.8 + - - +
391C TYR* 1.3 78.2 - - - +
393C THR* 1.3 60.2 + - + +
395C LYS* 3.3 37.5 + - - +
469C ILE* 3.5 28.3 - - - +
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Residues in contact with THR 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C GLU* 2.8 17.7 + - + +
390C MET* 3.0 16.3 + - - +
392C ASN* 1.3 78.6 - - + +
394C TYR* 1.3 79.1 + - - +
395C LYS* 3.7 0.4 - - - -
396C ASN 5.1 0.9 + - - -
397C ASN* 4.4 7.6 + - - +
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Residues in contact with TYR 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C MET* 2.8 38.9 + - + +
391C TYR* 3.7 0.7 - - - -
393C THR* 1.3 97.3 - - - +
395C LYS* 1.3 61.7 + - - -
396C ASN 2.7 8.2 + - - -
397C ASN* 2.8 47.4 + - - +
398C VAL* 3.2 13.9 + - + +
400C GLY 4.1 2.0 - - - -
401C LEU* 3.4 56.3 - - + -
459C LEU* 4.6 4.0 - - + -
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Residues in contact with LYS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C TYR* 2.7 37.3 + - + +
392C ASN* 3.3 40.2 + - - +
393C THR 3.7 0.2 - - - -
394C TYR* 1.3 72.5 - - - +
396C ASN* 1.3 82.1 + - + +
397C ASN 4.1 0.2 + - - -
398C VAL* 4.1 9.9 - - - +
459C LEU* 3.8 10.8 - - - -
462C GLY* 5.8 2.3 - - - -
464C GLY* 3.8 32.1 + - - +
465C SER* 3.9 12.6 + - - -
468C PRO* 4.1 22.0 - - - +
469C ILE 4.4 0.2 - - - +
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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