Contacts of the helix formed by residues 390 - 407 (chain C) in PDB entry 1C2O
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 390 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C HIS* 3.1 31.1 + - + +
389C GLU* 1.3 75.3 - - - +
391C PRO* 1.3 74.0 - - - +
392C THR* 3.6 14.4 + - - +
393C HIS* 3.0 29.2 + - + +
394C LEU* 3.0 24.6 + - - +
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Residues in contact with PRO 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 3.7 28.9 - - + +
354C ILE 3.2 27.4 + - - +
389C GLU 2.8 10.5 - - - +
390C ASP* 1.3 90.4 - - - +
392C THR* 1.3 68.9 + - - +
393C HIS 3.1 0.3 + - - -
394C LEU* 3.1 2.8 + - + +
395C ARG* 2.7 25.3 + - - +
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Residues in contact with THR 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 3.7 24.0 - - - +
390C ASP* 3.3 12.8 + - - +
391C PRO* 1.3 82.8 - - - +
393C HIS* 1.3 63.4 + - - +
395C ARG* 3.5 13.8 + - - +
396C ASP* 3.2 34.5 + - - +
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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
----------------------------------------------------------
382C TYR 3.3 24.7 + - - -
383C THR* 4.5 0.9 - - - -
384C ASP* 3.8 34.7 + - + +
387C HIS* 5.0 4.5 - - + +
390C ASP* 3.0 29.8 + - + +
391C PRO 3.1 0.8 - - - -
392C THR* 1.3 73.7 - - - +
394C LEU* 1.3 61.3 + - + +
396C ASP* 3.1 9.0 + - + +
397C ALA* 2.7 41.2 + - + +
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Residues in contact with LEU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C ILE* 3.6 31.0 - - + +
355C SER 3.7 15.7 - - - -
356C ARG* 3.7 28.0 - - + +
359C PHE* 3.5 36.3 - - + -
383C THR* 6.1 2.7 - - - -
387C HIS 5.7 0.4 - - - +
388C PRO 4.3 2.5 - - - +
389C GLU* 3.5 22.9 - - - +
390C ASP 3.0 19.1 + - - +
391C PRO 3.2 5.6 - - - +
393C HIS* 1.3 78.5 - - + +
395C ARG* 1.3 64.0 + - - +
397C ALA* 2.8 17.0 + - + +
398C MET* 2.9 13.3 + - - +
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Residues in contact with ARG 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C PHE* 3.8 17.7 - - + -
351C GLU* 3.1 33.3 + - - +
352C SER* 3.2 23.6 - - - +
353C LEU* 3.3 25.4 - - + +
354C ILE* 3.8 9.3 - - + +
391C PRO 2.7 19.9 + - - +
392C THR* 3.5 17.1 + - - +
394C LEU* 1.3 75.2 - - - +
396C ASP* 1.3 104.3 + - - +
398C MET* 3.1 11.3 + - - +
399C SER* 3.2 12.1 + - - -
442C TRP* 3.7 40.7 + - + +
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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
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392C THR* 3.2 18.6 + - - +
393C HIS* 3.1 11.1 + - + +
395C ARG* 1.3 109.2 + - - +
397C ALA* 1.3 61.6 + - - +
399C SER* 3.3 9.2 + - - -
400C ALA* 3.0 21.5 + - - +
442C TRP 4.8 4.0 - - - +
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Residues in contact with ALA 397 (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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359C PHE* 3.5 20.2 - - + -
382C TYR* 3.9 25.4 - - + +
393C HIS* 2.7 25.4 + - + +
394C LEU* 2.8 12.7 + - + +
396C ASP* 1.3 69.8 - - - +
398C MET* 1.3 56.3 + - - +
400C ALA* 2.9 9.2 + - - +
401C VAL* 2.7 37.1 + - - +
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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
----------------------------------------------------------
339C LEU* 4.0 13.7 - - + -
343C VAL* 4.4 4.0 - - + -
346C PHE* 3.4 34.8 - - + -
354C ILE* 4.5 2.9 - - + -
359C PHE* 2.9 47.9 - - + +
362C GLY* 3.4 19.3 - - - +
363C VAL* 3.0 29.8 - - + +
366C GLY* 5.8 0.4 - - - -
394C LEU 2.9 8.7 + - - +
395C ARG 3.4 8.7 - - - +
397C ALA* 1.3 75.5 - - - +
399C SER* 1.3 65.6 + - - +
401C VAL* 3.0 19.2 + - + +
402C VAL* 3.1 21.5 + - - +
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Residues in contact with SER 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ASP* 4.2 12.3 + - - +
335C GLY* 3.4 9.6 + - - -
336C SER* 3.3 26.4 + - - -
339C LEU* 3.5 21.0 - - - +
395C ARG* 3.2 7.9 + - - -
396C ASP* 3.6 11.0 - - - -
398C MET* 1.3 79.7 - - - +
400C ALA* 1.3 56.9 + - - +
402C VAL 3.5 0.2 + - - -
403C GLY* 2.9 25.5 + - - -
442C TRP* 5.3 4.0 - - - -
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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
----------------------------------------------------------
382C TYR* 3.6 18.2 - - + -
396C ASP 3.0 11.9 + - - +
397C ALA* 2.9 10.7 + - - +
399C SER* 1.3 74.6 - - - +
401C VAL* 1.3 59.5 + - - +
403C GLY* 4.9 0.4 - - - -
404C ASP* 2.6 49.0 + - - +
525C ARG* 5.1 9.9 - - - +
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Residues in contact with VAL 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C PHE* 4.7 1.1 - - + -
363C VAL* 4.5 16.2 - - + -
366C GLY* 5.4 1.1 - - - -
367C VAL* 3.7 30.3 - - + -
378C VAL* 3.8 17.3 - - + -
382C TYR* 3.6 37.7 - - + -
397C ALA 2.7 27.0 + - - +
398C MET* 3.0 11.6 + - - +
400C ALA* 1.3 70.7 - - - +
402C VAL* 1.3 62.5 + - + +
405C HIS* 2.9 35.0 + - - +
532C TRP* 4.0 6.4 - - + -
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Residues in contact with VAL 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ILE* 3.8 14.8 - - + -
295C PHE* 4.0 15.7 - - + -
335C GLY* 3.9 18.2 - - - +
338C PHE* 4.3 8.3 - - + -
339C LEU* 3.6 27.4 - - + -
366C GLY* 4.4 15.3 - - - +
398C MET* 3.1 10.8 + - - +
399C SER 3.9 4.7 - - - +
401C VAL* 1.3 79.7 - - + +
403C GLY* 1.3 62.8 + - - +
405C HIS* 4.6 1.1 - - - -
406C ASN* 2.9 49.3 + - - +
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Residues in contact with GLY 403 (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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334C GLU* 3.8 8.7 - - - -
335C GLY* 3.3 24.1 - - - -
399C SER 2.9 16.8 + - - -
400C ALA* 3.8 0.7 - - - -
402C VAL* 1.3 74.3 - - - +
404C ASP* 1.4 63.6 + - - +
407C VAL* 3.0 11.7 + - - +
408C VAL* 3.0 27.5 + - - +
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Residues in contact with ASP 404 (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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382C TYR* 2.6 35.6 + - - +
400C ALA* 2.6 29.1 + - - +
403C GLY* 1.4 74.5 - - - +
405C HIS* 1.3 63.0 + - - +
408C VAL* 4.1 11.2 - - - +
409C CYS* 3.0 37.4 + - - +
410C PRO* 3.3 4.0 - - - +
525C ARG* 3.3 35.7 + - - -
528C THR* 3.4 10.7 - - - +
532C TRP* 3.7 7.0 - - - +
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Residues in contact with HIS 405 (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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235C PRO* 3.7 20.6 - - + +
296C ARG* 3.9 12.5 + - - -
366C GLY 3.9 21.1 - - - -
367C VAL* 4.3 5.5 - - + +
369C GLN* 2.9 34.9 + - - -
401C VAL* 2.9 20.9 + - + +
402C VAL* 3.9 2.7 - - - +
404C ASP* 1.3 80.6 - - - +
406C ASN* 1.3 59.3 + - - +
409C CYS* 5.4 0.3 - - - +
410C PRO* 3.5 13.9 - - - +
532C TRP* 3.3 44.3 - + + +
536C LEU* 5.4 2.2 - - + -
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Residues in contact with ASN 406 (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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230C GLY* 5.8 0.2 - - - -
231C THR* 5.2 2.4 + - - -
234C GLY* 5.1 0.3 - - - -
235C PRO* 3.5 5.8 - - - +
236C TRP* 3.2 36.4 + - + +
295C PHE* 3.2 46.0 - - + +
296C ARG* 3.0 27.9 + - - +
366C GLY 4.8 2.8 + - - -
402C VAL* 2.9 34.2 + - - +
405C HIS* 1.3 83.5 - - - +
407C VAL* 1.3 59.6 + - - +
410C PRO* 3.2 16.7 - - - +
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Residues in contact with VAL 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER* 3.3 34.1 - - - +
230C GLY* 4.0 3.6 - - - +
231C THR* 5.0 0.2 - - - +
236C TRP* 5.0 1.1 - - + +
295C PHE* 3.7 31.2 - - + -
330C VAL* 4.2 0.4 - - + -
334C GLU* 3.2 47.6 - - + +
403C GLY* 3.0 7.5 + - - +
405C HIS 3.8 0.2 - - - -
406C ASN* 1.3 82.2 - - + +
408C VAL* 1.3 59.0 + - - +
410C PRO* 3.0 5.4 - - - +
411C VAL* 2.9 36.9 + - + +
447C HIS* 4.3 2.0 - - - +
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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
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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