Contacts of the helix formed by residues 383 - 401 (chain C) in PDB entry 5FLZ
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 383 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C VAL* 5.3 14.4 - - + -
267C PHE* 4.5 17.0 - - + -
269C SER* 5.2 5.4 - - - +
305C LEU 5.9 0.2 - - - +
306C VAL* 3.9 25.8 - - + +
380C MET 3.7 12.7 + - - +
382C THR* 1.4 76.4 - - - +
384C VAL* 1.3 68.4 + - - +
385C ASN 3.1 0.2 - - - -
386C VAL* 3.1 25.9 + - + +
387C PHE* 3.5 30.9 + - + -
434C MET* 3.6 24.0 - - + -
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Residues in contact with VAL 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C SER 3.2 18.8 - - - +
382C THR* 3.1 3.1 - - - +
383C VAL* 1.3 81.0 - - - +
385C ASN* 1.4 69.6 + - + +
387C PHE* 3.0 10.9 + - + -
388C GLU* 3.0 28.1 + - + +
431C GLN* 4.0 21.3 - - + -
434C MET* 3.8 24.9 - - + -
435C GLU* 3.6 33.2 - - - +
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Residues in contact with ASN 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C SER* 3.0 44.4 + - - +
382C THR 3.1 9.7 + - - +
383C VAL 3.1 1.6 - - - -
384C VAL* 1.4 83.9 - - + +
386C VAL* 1.3 57.6 + - - +
388C GLU* 3.5 12.3 + - - +
389C ASN* 3.0 37.1 + - - +
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Residues in contact with VAL 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 3.3 42.0 - - + -
205C ASP* 5.0 1.1 - - - +
305C LEU* 3.6 21.5 - - + +
306C VAL* 3.5 20.4 - - - +
307C SER* 3.7 4.9 - - - +
383C VAL* 3.1 16.6 + - + +
385C ASN* 1.3 71.5 - - - +
387C PHE* 1.4 72.9 + - + +
389C ASN* 3.2 13.1 + - + +
390C ALA* 3.1 21.7 + - + +
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Residues in contact with PHE 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 6.4 0.4 - + - -
191C LEU* 4.5 30.1 - - + -
195C ILE* 6.2 0.2 - - + -
203C VAL* 6.1 3.6 - - + -
267C PHE* 3.9 33.2 - + - -
383C VAL* 3.7 38.4 - - + -
384C VAL* 3.0 17.3 + - + +
386C VAL* 1.4 87.0 - - + +
388C GLU* 1.4 55.6 + - - +
390C ALA* 3.4 7.9 + - - +
391C CYS* 3.0 28.1 + - - +
427C ARG* 4.9 7.5 - - + -
430C VAL* 5.3 5.6 - - + -
431C GLN* 3.5 18.8 + - + +
434C MET* 4.0 28.0 - - + -
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Residues in contact with GLU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C VAL* 3.0 23.9 + - + +
385C ASN* 3.5 16.4 - - - +
387C PHE* 1.4 71.9 - - - +
389C ASN* 1.3 61.2 + - - +
391C CYS* 3.4 9.8 - - - +
392C ASN* 2.9 45.7 + - - +
428C GLU* 4.7 1.2 - - - +
431C GLN* 2.8 37.8 + - - +
435C GLU* 4.4 6.9 - - - +
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Residues in contact with ASN 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C SER* 3.8 5.7 + - - -
385C ASN* 3.0 33.9 + - - +
386C VAL* 3.2 13.0 + - + +
388C GLU* 1.3 78.7 - - - +
390C ALA* 1.4 55.9 + - - +
392C ASN* 3.2 11.1 + - - +
393C THR* 3.1 33.3 + - + +
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Residues in contact with ALA 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C PHE* 6.1 3.1 - - + -
184C SER* 3.8 7.1 - - - -
187C THR* 5.0 12.8 - - + -
188C ILE* 4.7 16.3 - - + +
191C LEU* 6.4 2.2 - - + -
386C VAL* 3.1 13.8 + - + +
387C PHE* 3.5 12.3 - - - +
389C ASN* 1.4 70.8 - - - +
391C CYS* 1.3 59.6 + - - +
393C THR* 3.0 9.8 + - - -
394C PHE* 2.9 29.8 + - - +
427C ARG* 5.7 0.9 - - - -
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Residues in contact with CYS 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C PHE 3.0 15.0 + - - +
388C GLU* 3.4 12.3 - - - +
390C ALA* 1.3 79.4 - - - +
392C ASN* 1.4 56.8 + - - +
394C PHE* 3.2 2.1 + - - +
395C ASP* 2.8 51.9 + - - +
427C ARG* 3.4 27.8 - - - +
428C GLU* 3.2 33.2 - - - -
431C GLN* 3.6 8.3 - - - +
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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
----------------------------------------------------------
388C GLU* 2.9 37.9 + - - +
389C ASN* 3.2 12.3 + - - +
391C CYS* 1.4 78.7 - - - +
393C THR* 1.4 66.7 + - + +
395C ASP* 3.4 12.2 + - - +
396C LYS* 3.2 22.9 + - - +
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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
----------------------------------------------------------
178C SER* 5.6 6.1 - - - +
184C SER* 3.2 21.3 - - - -
389C ASN* 3.1 14.4 + - + +
390C ALA* 3.0 18.9 + - - -
392C ASN* 1.4 71.1 - - + +
394C PHE* 1.4 62.5 + - - +
396C LYS* 3.4 8.0 + - - +
397C VAL* 3.1 27.9 + - - +
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Residues in contact with PHE 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C SER* 3.5 8.7 + - - +
185C TYR* 3.9 35.9 - + - -
188C ILE* 2.6 33.0 - - + -
390C ALA 2.9 19.0 + - - +
391C CYS 3.2 5.4 + - - +
393C THR* 1.4 76.4 + - - +
395C ASP* 1.3 62.6 + - - +
397C VAL* 3.4 5.2 + - + +
398C PHE* 3.2 33.5 + + + +
404C LEU* 6.3 0.7 - - + -
420C GLN* 3.9 34.8 - - + -
421C ASP* 5.3 2.0 - - - -
424C ALA* 3.8 17.5 - - + -
427C ARG* 3.3 29.2 - - - +
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Residues in contact with ASP 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C CYS* 2.8 41.0 + - - +
392C ASN* 3.4 13.6 + - - +
394C PHE* 1.3 73.1 - - - +
396C LYS* 1.3 56.7 + - - +
398C PHE* 3.3 9.0 + - - +
399C ALA* 3.0 29.3 + - - +
424C ALA* 4.8 2.9 - - - +
427C ARG* 3.4 15.2 + - - -
428C GLU* 5.0 1.6 - - - +
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Residues in contact with LYS 396 (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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392C ASN 3.2 11.4 + - - +
393C THR* 3.6 10.5 - - - +
394C PHE 3.3 0.4 - - - -
395C ASP* 1.3 77.3 - - - +
397C VAL* 1.4 63.6 + - + +
398C PHE 3.3 0.2 + - - -
399C ALA* 3.3 10.8 + - + +
400C LYS* 3.1 45.4 + - + +
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Residues in contact with VAL 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C VAL* 4.3 16.8 - - + +
182C VAL* 5.7 7.0 - - + -
184C SER* 4.2 12.1 - - - +
185C TYR* 5.1 12.1 - - + -
393C THR* 3.1 16.6 + - - +
394C PHE* 3.4 7.8 + - + +
396C LYS* 1.4 73.2 - - + +
398C PHE* 1.4 62.0 + - - +
400C LYS* 3.4 18.9 + - - +
401C GLY 3.4 14.7 + - - -
402C ALA 3.6 21.6 - - - +
403C PHE* 4.7 13.2 - - + +
404C LEU* 3.6 15.1 - - + +
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Residues in contact with PHE 398 (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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394C PHE* 3.2 26.5 + + + +
395C ASP* 3.4 12.6 - - - +
396C LYS 3.2 0.2 - - - -
397C VAL* 1.4 75.1 - - - +
399C ALA* 1.3 66.0 + - - +
401C GLY* 3.2 14.7 + - - -
404C LEU* 4.0 19.6 - - + +
417C GLN* 4.7 16.2 - - - -
420C GLN* 3.6 24.0 - - + -
421C ASP* 3.2 30.1 - - - -
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Residues in contact with ALA 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ASP 3.0 16.5 + - - +
396C LYS* 3.5 14.8 - - + +
398C PHE* 1.3 77.4 - - - +
400C LYS* 1.4 67.4 + - + +
401C GLY* 3.4 0.9 + - - -
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Residues in contact with LYS 400 (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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181C VAL* 5.9 6.7 - - - +
396C LYS* 3.1 42.1 + - + +
397C VAL* 3.9 23.4 - - - +
398C PHE 3.3 0.2 - - - -
399C ALA* 1.4 81.3 - - + +
401C GLY* 1.4 62.2 + - - +
402C ALA* 3.4 20.9 + - + +
403C PHE* 4.7 16.1 - - + -
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Residues in contact with GLY 401 (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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397C VAL 3.4 2.8 + - - -
398C PHE 3.2 13.3 + - - -
399C ALA 3.2 3.4 - - - -
400C LYS* 1.4 78.9 - - - +
402C ALA* 1.3 56.7 + - - +
403C PHE 4.4 0.2 + - - -
404C LEU* 4.0 23.8 - - - +
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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