Contacts of the helix formed by residues 387 - 406 (chain C) in PDB entry 2YVX
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 LEU 387 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C VAL* 3.8 25.8 - - + +
378C VAL* 3.0 47.6 - - + +
379C TYR* 3.5 29.4 - - + -
383C HIS 3.6 11.4 - - - +
384C PRO* 3.8 13.0 + - + +
385C LEU 2.6 5.5 + - - +
386C LEU* 1.3 72.3 - - - +
388C PRO* 1.4 66.1 - - + +
389C VAL 3.5 1.1 - - - -
390C VAL* 3.7 6.3 - - + +
391C GLY* 3.6 13.5 + - - -
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Residues in contact with PRO 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C LEU* 3.2 11.0 - - + -
387C LEU* 1.4 88.8 - - + +
389C VAL* 1.3 66.7 + - - +
390C VAL 3.0 2.6 + - - -
391C GLY* 3.2 1.1 + - - +
392C VAL* 2.7 49.4 + - + +
446C LEU* 3.2 32.1 - - + -
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Residues in contact with VAL 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 4.8 14.1 - - + -
386C LEU* 3.0 38.8 - - + +
388C PRO* 1.3 77.4 - - - +
390C VAL* 1.3 58.4 - - + +
393C SER* 2.3 36.9 + - - -
439C TYR* 4.5 12.3 - - + +
442C VAL* 3.2 29.0 - - + +
443C ALA* 3.6 24.9 - - + +
446C LEU* 4.1 17.0 - - + -
447C LEU* 5.1 1.3 - - + -
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Residues in contact with VAL 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 5.4 0.9 - - + -
319C TYR* 4.8 15.7 - - + -
323C LEU* 4.1 5.7 - - + +
374C LEU* 3.2 22.1 - - + +
375C VAL* 4.0 3.8 - - + -
378C VAL* 3.2 51.6 - - + -
386C LEU 4.2 1.8 - - - +
387C LEU* 3.7 17.3 - - + +
388C PRO 3.0 0.6 - - - -
389C VAL* 1.3 87.3 - - + +
391C GLY* 1.3 59.6 + - - +
393C SER* 3.0 4.0 + - - -
394C LEU* 2.9 33.6 + - - +
439C TYR* 4.9 3.8 - - - +
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Residues in contact with GLY 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C SER* 3.5 9.9 - - - -
375C VAL* 3.2 25.3 - - - +
387C LEU 3.6 3.7 + - - -
388C PRO* 3.2 3.9 + - - -
390C VAL* 1.3 77.9 - - - +
392C VAL* 1.3 63.8 + - - +
393C SER 3.1 1.0 + - - -
394C LEU* 4.8 0.9 - - - -
395C VAL* 3.0 30.0 + - - +
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Residues in contact with VAL 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C PRO* 2.7 37.5 + - + +
389C VAL* 4.9 0.2 - - - -
391C GLY* 1.3 70.6 - - - -
393C SER* 1.3 50.5 + - - +
395C VAL* 4.5 1.5 - - - +
396C LEU* 2.6 46.1 + - + +
442C VAL* 3.7 27.6 - - + -
446C LEU* 5.4 10.1 - - + -
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Residues in contact with SER 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 3.4 14.7 - - - +
389C VAL 2.3 27.9 + - - -
390C VAL 3.0 9.9 + - - -
392C VAL* 1.3 76.0 - - - +
394C LEU* 1.3 68.0 + - - +
395C VAL 3.1 1.6 - - - -
396C LEU* 3.0 4.8 + - - -
397C ILE* 2.6 31.5 + - - +
438C ILE* 4.2 11.2 - - - -
439C TYR* 3.7 13.4 - - - -
442C VAL* 3.2 17.9 - - - -
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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
----------------------------------------------------------
323C LEU* 3.9 16.3 - - + +
326C THR* 4.3 18.6 - - + +
327C GLY 5.7 0.4 - - - +
370C LEU* 3.6 10.8 - - + -
371C SER* 3.2 39.7 - - - +
374C LEU* 3.2 37.7 - - + -
375C VAL* 5.3 0.2 - - + -
390C VAL 2.9 21.0 + - - +
391C GLY 4.0 1.3 - - - +
393C SER* 1.3 72.2 + - - +
395C VAL* 1.3 54.3 + - - +
397C ILE* 3.4 4.4 - - - +
398C VAL* 2.7 61.2 + - + +
293D ILE* 6.0 2.2 - - + -
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU* 4.6 12.1 - - + -
367C GLY* 3.0 31.6 - - - +
368C LEU* 3.7 20.0 - - + +
371C SER* 2.9 39.0 - - - +
391C GLY 3.0 15.0 - - - +
392C VAL* 4.5 1.8 - - - +
393C SER 3.1 0.4 - - - -
394C LEU* 1.3 71.5 - - - +
396C LEU* 1.3 59.6 + - - +
397C ILE 2.7 11.1 + - - -
398C VAL* 4.1 0.2 - - - +
399C PHE* 3.3 22.9 + - - +
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Residues in contact with LEU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C VAL* 2.6 31.1 + - + +
393C SER* 3.0 3.8 + - - +
395C VAL* 1.3 72.7 - - - +
397C ILE* 1.3 55.7 + - - +
399C PHE* 4.3 3.8 - - - +
400C PHE* 3.1 48.9 + - + +
438C ILE* 4.1 11.9 - - + -
442C VAL* 3.3 32.5 - - + -
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Residues in contact with ILE 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C LEU* 3.7 24.2 - - + +
324C LEU* 5.2 0.9 - - + -
327C GLY* 4.1 21.1 - - - -
393C SER* 2.6 22.9 + - - +
394C LEU* 3.4 4.5 - - - +
395C VAL 2.7 1.2 + - - -
396C LEU* 1.3 72.9 - - - +
398C VAL* 1.3 68.6 + - - +
399C PHE 2.8 1.8 - - - -
400C PHE* 2.6 15.5 + - + -
401C ALA* 2.7 17.3 + - + +
431C SER 5.5 1.1 - - - +
435C GLY* 2.9 42.4 - - - +
438C ILE* 3.1 39.7 - - + -
439C TYR 4.3 2.5 - - - +
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C THR* 4.7 4.5 - - + -
327C GLY* 4.8 5.4 - - - -
330C THR* 3.4 24.3 - - + +
363C GLY 4.4 1.1 - - - +
366C LEU* 4.1 8.5 - - + -
367C GLY* 3.9 22.7 - - - +
370C LEU* 3.3 29.2 - - + -
394C LEU* 2.7 55.2 + - + +
395C VAL 4.1 0.2 - - - +
397C ILE* 1.3 73.3 - - - +
399C PHE* 1.3 62.5 + - - +
401C ALA* 3.4 4.4 + - - +
402C ASN* 3.0 24.9 + - - +
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Residues in contact with PHE 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C MET* 2.8 59.7 - - + -
363C GLY* 3.5 14.7 + - - -
364C LEU* 2.9 46.9 - - + -
395C VAL 3.3 15.2 + - - +
396C LEU* 4.3 4.7 - - - +
397C ILE 2.6 3.6 + - - -
398C VAL* 1.3 74.6 - - - +
400C PHE* 1.3 78.5 + + - +
401C ALA 2.8 10.3 + - - -
402C ASN* 3.8 0.2 - - - -
403C LEU* 3.1 37.7 + - + +
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Residues in contact with PHE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 3.1 43.7 + - + +
397C ILE* 2.6 8.6 + - + +
399C PHE* 1.3 90.5 - + - +
401C ALA* 1.3 48.7 + - - +
403C LEU* 4.0 7.5 + - + +
404C VAL* 2.7 33.3 + - - +
438C ILE* 4.0 19.3 - - + -
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Residues in contact with ALA 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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327C GLY* 3.0 33.2 - - - +
330C THR* 4.6 0.2 - - + -
331C GLY* 3.9 8.8 - - - +
397C ILE* 2.7 22.5 + - + +
398C VAL* 3.6 5.4 - - - +
399C PHE 2.8 1.0 + - - -
400C PHE* 1.3 70.1 - - - +
402C ASN* 1.3 56.2 + - - +
403C LEU 2.9 1.3 - - - -
404C VAL* 2.6 36.1 + - - +
405C GLY 3.3 5.7 + - - -
431C SER* 3.7 11.2 - - - +
434C THR* 6.2 0.2 - - - -
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Residues in contact with ASN 402 (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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330C THR* 3.2 23.1 - - + +
331C GLY* 4.3 0.9 - - - -
334C SER* 3.0 16.9 + - - -
359C GLU* 2.8 36.9 + - - +
362C VAL* 5.3 0.4 - - - +
363C GLY* 4.6 9.6 - - - -
366C LEU* 3.8 7.4 - - - +
398C VAL 3.0 11.5 + - - +
399C PHE 3.8 3.1 - - - +
401C ALA* 1.3 77.2 - - - +
403C LEU* 1.3 61.1 + - + +
404C VAL 3.1 0.2 - - - -
406C ALA* 2.9 19.4 + - - +
285D ARG* 2.8 33.1 + - - -
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Residues in contact with LEU 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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356C PHE* 3.4 54.5 - - + +
359C GLU* 4.0 33.2 - - + +
360C MET* 4.0 7.2 - - + +
363C GLY* 4.8 1.3 - - - -
399C PHE* 3.1 36.0 + - + +
400C PHE* 4.2 9.6 - - + +
401C ALA 2.9 0.8 - - - -
402C ASN* 1.3 85.1 - - + +
404C VAL* 1.3 60.8 + - - +
406C ALA* 4.1 5.4 - - + -
407C MET* 3.6 21.7 + - + +
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Residues in contact with VAL 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C PHE 2.7 30.3 - - - +
401C ALA* 2.6 19.1 + - - +
403C LEU* 1.3 70.6 - - - +
405C GLY* 1.3 59.6 + - - +
406C ALA 2.9 3.4 - - - -
407C MET* 3.0 3.6 + - - +
408C LEU* 2.9 45.5 + - + +
430C LEU* 5.8 9.9 - - + +
434C THR* 5.3 10.8 - - + +
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Residues in contact with GLY 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C GLY* 3.6 22.3 - - - -
334C SER* 3.0 6.7 - - - -
335C ALA* 2.9 20.7 - - - +
401C ALA 3.3 6.7 + - - -
404C VAL* 1.3 80.6 - - - +
406C ALA* 1.3 56.7 + - - +
408C LEU* 4.5 5.8 - - - -
409C PRO* 2.9 22.7 - - - +
427C VAL* 4.8 8.5 - - - +
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C SER* 2.5 19.2 + - - +
338C ILE* 3.9 15.5 - - + +
355C VAL* 4.8 5.6 - - + +
356C PHE* 6.5 0.4 - - - -
359C GLU* 4.1 20.6 - - + -
402C ASN 2.9 15.2 + - - +
403C LEU* 4.2 6.1 - - + -
404C VAL 2.9 0.6 - - - -
405C GLY* 1.3 80.9 - - - +
407C MET* 1.3 62.9 + - + +
408C LEU 3.4 0.2 - - - -
410C PHE* 3.3 28.2 - - - -
273D TYR* 5.7 0.4 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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