Contacts of the strand formed by residues 383 - 397 (chain C) in PDB entry 2Y1X
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 GLY 383 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C THR* 5.2 3.4 - - - -
350C MET* 3.7 11.9 - - - +
382C SER* 1.3 76.0 - - - +
384C LEU* 1.3 71.0 + - - -
385C VAL 3.5 1.7 + - - -
427C LEU 3.6 0.2 - - - +
428C PHE* 4.9 3.9 - - - -
429C ALA* 2.8 30.9 + - - +
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C THR* 2.9 31.0 + - - +
301C GLU* 4.7 9.4 - - - +
350C MET* 4.0 0.4 - - - +
383C GLY* 1.3 74.4 - - - -
385C VAL* 1.3 61.5 + - - +
386C HIS* 3.4 25.1 + - + +
426C PRO* 3.8 26.2 - - + -
427C LEU 3.5 6.1 - - - -
428C PHE* 4.3 23.8 - - + -
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Residues in contact with VAL 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C PRO* 3.8 20.9 - - + -
298C PHE 3.7 5.2 - - - +
350C MET* 3.5 25.6 - - + -
379C MET* 4.5 7.4 - - - -
384C LEU* 1.3 71.0 - - - +
386C HIS* 1.3 59.8 + - - +
387C GLY 3.7 22.2 + - - +
423C PHE* 3.8 16.1 - - + -
426C PRO* 3.0 7.0 - - - +
427C LEU* 2.7 48.2 + - + +
429C ALA* 4.3 13.5 - - + -
435C LEU* 4.3 11.9 - - + -
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Residues in contact with HIS 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C PHE* 2.9 26.7 + - + -
299C THR* 3.5 15.2 + - - -
300C ASP 2.8 28.8 + - - +
301C GLU* 3.4 36.7 + - + -
304C TYR* 3.6 23.4 - + + +
384C LEU* 3.4 20.9 + - + +
385C VAL* 1.3 72.7 - - - +
387C GLY* 1.3 57.1 + - - +
422C LEU* 3.3 17.1 - - + +
423C PHE* 2.8 27.8 + - - +
426C PRO* 3.6 25.2 - - + +
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Residues in contact with GLY 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C PRO* 3.4 5.4 - - - +
298C PHE* 3.0 34.3 + - - -
385C VAL* 3.4 6.0 - - - +
386C HIS* 1.3 79.6 - - - +
388C LEU* 1.3 63.6 + - - +
421C CYS 3.0 13.9 - - - -
423C PHE* 3.8 16.3 - - - -
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 4.4 16.4 - - + -
296C ALA 3.3 6.7 - - - +
297C PRO* 3.6 25.4 - - + -
298C PHE* 3.7 2.9 - - - -
375C PHE* 4.0 23.3 - - + -
377C PHE* 4.3 11.0 - - + -
387C GLY* 1.3 81.0 - - - +
389C ALA* 1.3 61.5 + - - +
390C PHE* 3.5 18.9 - - + -
420C ARG* 3.4 1.2 - - - -
421C CYS 2.8 32.3 + - - -
423C PHE* 4.1 16.1 - - + -
435C LEU* 4.8 6.5 - - + -
439C CYS* 5.0 0.9 - - + -
453C ILE* 3.9 30.3 - - + -
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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
----------------------------------------------------------
294C HIS 3.6 0.2 - - - +
295C LEU* 3.0 8.1 - - - +
296C ALA 2.8 36.3 + - - +
298C PHE* 3.7 7.0 - - + -
344C PHE* 3.7 25.1 - - + -
349C LEU* 4.2 10.3 - - + -
388C LEU* 1.3 74.4 - - - +
390C PHE* 1.3 60.8 + - - +
391C TRP* 4.2 6.1 - - + -
419C VAL 3.3 4.7 - - - -
420C ARG* 3.6 19.5 - - + -
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Residues in contact with PHE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C MET* 3.8 45.3 - - + -
293C VAL* 4.4 8.5 - - + -
294C HIS 3.1 5.8 - - - +
295C LEU* 4.0 28.7 - - + -
373C ILE* 5.7 1.3 - - + -
388C LEU* 3.5 31.9 - - + -
389C ALA* 1.3 77.8 - - - +
391C TRP* 1.3 68.4 + - - +
418C GLN* 3.6 5.5 - - - +
419C VAL* 2.7 41.2 + - - +
421C CYS* 3.6 23.1 - - + -
439C CYS* 3.8 28.5 - - - -
441C LEU* 5.9 0.4 - - + -
451C ILE* 5.3 0.2 - - + -
453C ILE* 4.1 11.0 - - + -
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Residues in contact with TRP 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C MET* 5.8 2.7 - - - +
293C VAL* 3.6 5.3 - - - +
294C HIS* 2.8 60.6 + + + +
296C ALA* 4.1 9.6 - - + -
344C PHE* 4.6 2.0 - + - -
349C LEU* 3.8 28.7 - - + -
353C SER* 4.0 21.5 - - - -
389C ALA* 4.2 20.6 - - + -
390C PHE* 1.3 85.9 - - - +
392C PHE* 1.3 72.1 + - - +
393C ASP* 4.4 4.8 + - - -
407C THR* 3.5 20.0 - - - +
408C ALA* 3.5 29.1 - - + +
409C PRO* 3.5 23.1 - - + -
418C GLN* 3.9 8.1 - - + +
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Residues in contact with PHE 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C MET* 3.7 30.3 - - + -
261C GLY 3.4 21.1 - - - -
263C MET* 4.1 6.5 - - - -
264C LEU* 3.3 42.0 - - + -
292C ASP 3.1 17.7 - - - +
293C VAL* 4.3 1.6 - - + -
294C HIS* 4.6 0.4 - - - +
391C TRP* 1.3 84.1 - - - +
393C ASP* 1.3 71.8 + - - +
394C VAL* 4.5 1.3 - - + -
405C LEU* 4.3 2.4 - - + +
407C THR* 2.8 50.4 + - + +
416C TRP* 3.6 41.7 - + + -
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Residues in contact with ASP 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C GLY* 3.4 0.2 - - - -
292C ASP* 2.8 33.6 + - + +
294C HIS* 3.4 25.5 + - - -
391C TRP* 4.4 4.3 + - - -
392C PHE* 1.3 78.8 - - - +
394C VAL* 1.3 67.4 + - - +
404C TRP* 3.8 24.7 - - + -
405C LEU 3.2 10.1 - - - +
406C SER* 2.6 34.5 + - - -
407C THR 3.6 0.5 + - - -
408C ALA* 4.2 3.3 + - - +
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Residues in contact with VAL 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C MET* 4.0 44.0 - - + -
264C LEU* 4.7 3.6 - - + -
288C PRO* 3.8 14.8 - - + -
290C ILE 3.2 13.5 - - - +
291C GLY* 4.1 6.7 - - - -
360C PHE* 4.7 2.9 - - + -
392C PHE* 4.5 7.4 - - + -
393C ASP* 1.3 78.9 - - - +
395C ALA* 1.3 61.4 + - - +
396C PHE* 4.0 14.3 - - + -
404C TRP* 3.3 9.3 - - - -
405C LEU* 2.9 53.3 + - + +
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Residues in contact with ALA 395 (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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288C PRO* 3.6 1.4 - - - -
289C THR* 2.7 33.8 + - - -
290C ILE* 3.0 31.1 + - + -
394C VAL* 1.3 75.0 - - - +
396C PHE* 1.3 56.6 + - - +
397C ILE* 3.8 5.4 - - + -
402C THR* 4.3 9.4 - - + -
403C VAL 3.4 5.6 - - - +
404C TRP* 3.7 29.6 - - + -
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Residues in contact with PHE 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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172C THR* 4.7 5.4 - - + -
173C TYR* 3.5 47.8 - + - -
176C ALA* 3.7 29.2 - - + -
177C ILE* 6.2 0.2 - - + -
180C ASN* 4.6 0.8 + - - +
287C PHE* 3.7 31.6 - + + -
288C PRO* 3.4 35.4 - - + -
289C THR* 3.8 3.4 - - - -
394C VAL* 4.0 17.0 - - + -
395C ALA* 1.3 72.6 - - - +
397C ILE* 1.3 61.4 + - - +
398C GLY 3.3 3.2 + - - -
401C MET 3.7 1.2 - - - +
402C THR* 3.1 4.1 - - - -
403C VAL* 2.7 49.5 + - + +
405C LEU* 4.3 13.9 - - + -
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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
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285C ASN* 3.2 20.8 + - - +
287C PHE* 3.8 2.7 - - - -
289C THR* 2.8 38.7 + - + +
290C ILE* 4.3 22.0 - - + -
395C ALA* 4.5 5.4 - - + -
396C PHE* 1.3 69.7 - - - +
398C GLY* 1.3 63.6 + - - +
402C THR* 3.6 27.1 - - + +
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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