Contacts of the helix formed by residues 385 - 400 (chain C) in PDB entry 1SA0
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 ALA 385 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382C THR 3.2 15.4 + - - +
383C ALA 3.0 1.0 - - - -
384C ILE* 1.3 77.5 - - - +
386C GLU* 1.3 54.5 + - - +
387C ALA 3.0 5.4 - - - -
388C TRP* 3.0 32.8 + - + +
389C ALA* 3.2 12.1 + - - +
429C GLU* 4.6 11.0 - - + +
432C TYR* 3.6 31.2 - - + -
433C GLU 5.6 0.4 - - - +
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Residues in contact with GLU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C CYS* 3.3 29.2 - - + +
306C ASP* 3.6 14.4 + - - +
309C HIS* 2.9 38.1 + - + +
383C ALA* 3.2 18.9 + - - +
384C ILE 3.1 0.6 - - - -
385C ALA* 1.3 76.5 - - - +
387C ALA* 1.3 50.9 + - - +
389C ALA* 3.8 8.9 - - - +
390C ARG* 2.7 40.2 + - - +
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Residues in contact with ALA 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 3.0 31.2 + - + -
203C MET* 3.9 25.4 - - + -
303C VAL* 4.0 9.9 - - + -
304C LYS 5.1 0.4 - - - +
305C CYS* 5.4 1.1 - - + +
384C ILE 3.2 13.2 + - - +
385C ALA 3.0 0.2 - - - -
386C GLU* 1.3 78.4 - - - +
388C TRP* 1.3 63.3 + - + +
389C ALA 3.1 2.0 + - - -
390C ARG* 3.8 21.3 - - - +
391C LEU* 3.4 8.8 + - - +
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Residues in contact with TRP 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PHE* 3.7 27.1 - + - -
172C TYR* 5.2 0.7 - + - -
188C ILE* 5.7 0.7 - - + -
191C THR* 3.8 24.7 - - + -
203C MET* 3.6 31.0 - - + -
267C PHE* 3.7 31.4 - + - -
384C ILE* 4.1 7.8 + - - +
385C ALA* 3.0 31.2 + - + +
387C ALA* 1.3 81.7 - - - +
389C ALA* 1.3 54.7 + - - +
391C LEU* 4.1 15.5 - - + +
392C ASP* 2.6 39.3 + - - +
425C MET* 4.4 12.8 - - - +
428C LEU* 3.6 28.0 - - + +
429C GLU* 4.0 15.5 - - + -
432C TYR* 3.8 18.2 - + - -
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Residues in contact with ALA 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ALA 3.2 8.1 + - - +
386C GLU* 3.8 11.7 - - - +
387C ALA 3.1 0.4 - - - -
388C TRP* 1.3 76.6 - - - +
390C ARG* 1.3 64.3 + - + +
391C LEU 2.9 4.3 - - - -
392C ASP* 2.9 14.1 + - - +
393C HIS* 2.9 16.7 + - - +
429C GLU* 3.5 24.7 + - - +
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Residues in contact with ARG 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 3.4 39.8 + - - +
205C ASP* 3.4 14.6 + - - -
207C GLU* 4.8 10.7 + - - -
303C VAL* 4.9 0.2 - - - +
304C LYS* 2.8 33.5 + - - +
305C CYS* 4.9 0.4 - - - +
386C GLU* 2.7 28.8 + - - +
387C ALA* 3.8 19.4 - - - +
389C ALA* 1.3 76.7 - - + +
391C LEU* 1.3 58.1 + - - +
393C HIS* 4.3 6.0 - - - +
394C LYS* 3.3 31.3 + - + +
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Residues in contact with LEU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PHE* 5.1 1.8 - - + -
172C TYR* 3.6 37.2 - - + +
173C PRO* 4.7 12.8 - - + +
184C PRO* 4.4 17.2 - - + +
187C SER* 3.7 33.4 - - - +
188C ILE* 4.3 17.0 - - + +
387C ALA 3.4 10.1 + - - +
388C TRP* 4.1 17.9 - - + +
389C ALA 2.9 0.8 - - - -
390C ARG* 1.3 79.7 - - - +
392C ASP* 1.3 65.4 + - - +
393C HIS 3.3 0.2 - - - -
394C LYS* 3.3 14.8 + - + +
395C PHE* 3.0 22.9 + - - +
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Residues in contact with ASP 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE* 3.2 21.0 - - - +
388C TRP* 2.6 19.7 - - - +
389C ALA 2.9 5.0 + - - +
391C LEU* 1.3 76.9 - - - +
393C HIS* 1.3 54.1 + - - +
395C PHE* 3.1 6.0 + - - +
396C ASP* 2.6 39.8 + - - +
422C ARG* 3.3 32.3 + - - +
425C MET* 3.5 18.9 - - - +
429C GLU* 2.4 32.6 - - - +
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Residues in contact with HIS 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ALA 2.9 15.9 + - - +
390C ARG* 4.3 6.5 - - - +
392C ASP* 1.3 74.9 - - - +
394C LYS* 1.3 67.4 + - + +
396C ASP* 3.7 7.7 - - + +
397C LEU* 2.9 55.8 + - + +
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Residues in contact with LYS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C TYR* 5.8 1.8 + - - -
173C PRO 5.1 3.8 + - - -
175C PRO* 3.7 30.2 - - - +
184C PRO* 3.7 24.6 - - + +
390C ARG* 3.3 23.2 + - + +
391C LEU* 3.3 18.5 + - + +
392C ASP 3.3 0.6 - - - -
393C HIS* 1.3 82.7 + - + +
395C PHE* 1.3 64.8 + - - +
397C LEU* 3.2 12.9 + - + +
398C MET* 3.1 22.1 + - - +
348D PRO* 3.6 25.8 - - + -
349D ASN* 4.1 17.3 + - - +
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Residues in contact with PHE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C PRO* 3.9 10.4 - - - +
185C TYR* 3.6 34.8 - + - -
188C ILE* 3.5 40.8 - - + -
189C LEU* 5.4 2.5 - - + -
391C LEU 3.0 10.5 + - - +
392C ASP* 3.4 7.0 - - - +
394C LYS* 1.3 79.3 - - - +
396C ASP* 1.3 65.4 + - - +
398C MET* 3.1 3.5 + - - +
399C TYR* 2.8 52.9 + + + +
418C PHE* 3.8 33.2 - + - -
421C ALA* 6.0 0.4 - - + -
422C ARG* 3.6 33.9 - - + -
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Residues in contact with ASP 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C ASP* 2.6 19.5 + - - +
393C HIS* 3.7 8.2 + - + +
395C PHE* 1.3 78.5 - - - +
397C LEU* 1.3 56.4 + - + +
399C TYR* 3.6 3.0 + - - +
400C ALA* 3.1 27.7 + - - +
422C ARG* 2.7 54.9 + - - +
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Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C HIS* 2.9 40.6 + - + +
394C LYS* 3.5 17.0 - - + +
396C ASP* 1.3 74.2 - - - +
398C MET* 1.3 62.2 + - - +
400C ALA* 3.3 16.7 - - - +
401C LYS* 4.6 1.0 - - - +
345D GLU 3.9 15.9 - - - +
346D TRP* 3.5 33.3 - - + +
348D PRO* 3.6 26.2 - - + -
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Residues in contact with MET 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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181C VAL* 3.2 30.1 - - - +
182C VAL* 4.6 3.6 - - - -
184C PRO* 3.9 28.0 - - + -
185C TYR* 3.4 25.6 - - + +
394C LYS 3.1 6.9 + - - +
395C PHE 3.1 6.5 + - - +
397C LEU* 1.3 73.0 - - - +
399C TYR* 1.3 63.1 + - - +
400C ALA 3.0 3.8 - - - -
401C LYS* 2.9 14.6 + - - +
403C ALA* 3.3 32.7 + - + +
404C PHE* 4.2 17.5 - - - -
346D TRP* 3.7 10.5 - - - +
347D ILE* 4.2 2.9 - - + -
348D PRO* 3.5 32.3 - - + -
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 3.3 15.1 + - + +
395C PHE* 2.8 35.5 + + + +
396C ASP* 3.9 4.5 - - - +
398C MET* 1.3 70.5 - - - +
400C ALA* 1.3 54.5 + - - +
401C LYS 2.7 16.3 + - - -
402C ARG* 2.9 63.1 + - - +
405C VAL* 4.2 5.8 - - + -
415C GLU* 3.5 25.1 + - - -
418C PHE* 3.5 41.5 - + + -
419C SER* 3.7 17.8 + - - -
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Residues in contact with ALA 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C ASP 3.1 14.2 + - - +
397C LEU* 3.3 20.2 - - - +
398C MET 3.0 0.4 - - - -
399C TYR* 1.3 75.2 - - - +
401C LYS* 1.3 80.3 + - - +
402C ARG* 5.5 3.1 - - - +
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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