Contacts of the strand formed by residues 289 - 297 (chain C) in PDB entry 5DX1
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 ILE 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287C PRO* 4.3 0.2 - - - +
288C THR* 1.3 86.9 - - + +
290C GLY* 1.3 61.8 + - - +
291C ASP* 3.9 19.5 - - - +
356C THR* 4.5 10.3 - - + -
357C VAL 3.4 9.0 - - - +
358C ASN* 3.8 25.8 - - + +
359C PHE* 3.4 7.9 - - - -
393C VAL* 3.2 8.8 - - - +
394C ALA* 3.0 38.1 + - + +
396C ILE* 4.3 19.1 - - + -
403C TRP* 3.8 30.5 - - + -
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Residues in contact with GLY 290 (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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263C LEU* 4.7 9.9 - - - -
289C ILE* 1.3 74.7 - - - +
291C ASP* 1.3 63.6 + - - +
292C VAL 4.2 0.6 + - - -
355C TYR 3.8 1.2 - - - +
356C THR* 3.3 2.6 - - - +
357C VAL* 2.7 44.5 + - - +
359C PHE* 3.5 15.9 - - - -
392C ASP 3.5 7.9 - - - -
393C VAL* 4.2 4.3 - - - -
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Residues in contact with ASP 291 (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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263C LEU* 4.9 0.6 - - - +
289C ILE* 3.9 7.0 - - - +
290C GLY* 1.3 70.8 - - - -
292C VAL* 1.3 62.5 + - - +
293C HIS* 3.8 12.0 + - + +
354C LYS* 3.5 30.8 + - + +
355C TYR 3.4 2.5 - - - -
356C THR* 2.3 37.6 + - - +
391C PHE* 3.1 8.3 - - - +
392C ASP* 2.9 37.7 + - + +
403C TRP* 3.6 26.4 - - - -
502C GOL 5.2 1.9 - - - -
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C MET* 5.1 6.5 - - + +
263C LEU* 3.5 27.6 - - + -
264C PHE* 3.5 33.9 - - + -
290C GLY 4.2 0.6 - - - +
291C ASP* 1.3 72.1 - - - +
293C HIS* 1.3 70.4 + - - +
294C LEU* 5.5 2.1 - - + +
353C VAL 3.7 0.9 - - - +
354C LYS* 3.5 3.3 - - - -
355C TYR* 2.8 52.7 + - + +
357C VAL* 5.9 0.7 - - + -
372C ILE* 5.0 8.1 - - + -
389C PHE* 4.1 21.1 - - + -
390C TRP 3.5 10.3 - - - +
391C PHE* 4.7 0.7 - - + -
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Residues in contact with HIS 293 (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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291C ASP* 4.1 13.3 + - + +
292C VAL* 1.3 81.9 - - - +
294C LEU* 1.3 62.7 + - - +
352C SER* 3.0 22.6 + - - +
353C VAL 3.4 6.9 + - - -
354C LYS* 3.9 30.9 - - + +
388C ALA 3.7 0.4 - - - +
389C PHE* 3.2 5.5 - - - -
390C TRP* 2.7 75.8 + + + +
392C ASP* 3.6 21.2 + - - -
502C GOL 5.7 2.9 - - - -
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Residues in contact with LEU 294 (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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292C VAL* 5.5 2.9 - - + +
293C HIS* 1.3 76.2 - - - +
295C ALA* 1.3 61.3 + - - +
352C SER* 3.1 4.9 - - - -
353C VAL* 2.8 43.8 + - + +
372C ILE* 3.9 26.7 - - + -
374C PHE* 4.0 17.0 - - + -
376C PHE* 3.0 42.5 - - + -
387C LEU* 4.7 7.9 - - + -
388C ALA 3.1 10.1 - - - +
389C PHE* 3.4 34.8 - - + -
390C TRP* 5.1 0.9 - - - -
438C CYS* 4.2 12.6 - - + -
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Residues in contact with ALA 295 (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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294C LEU* 1.3 77.6 - - - +
296C PRO* 1.4 75.3 - - + +
348C LEU* 4.1 18.6 - - + +
350C ALA 3.8 15.7 - - - +
352C SER* 3.9 14.4 - - - +
376C PHE* 3.7 2.4 - - - -
387C LEU* 3.4 5.1 - - - +
388C ALA* 2.8 32.2 + - - +
390C TRP* 4.2 8.7 - - + -
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Residues in contact with PRO 296 (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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295C ALA* 1.4 89.3 - - + +
297C PHE* 1.3 59.3 + - - +
348C LEU* 3.5 6.1 - - - +
349C MET* 3.0 25.0 + - + -
350C ALA* 3.8 25.4 - - + +
376C PHE* 3.6 28.7 - - + -
378C MET* 4.1 18.2 - - + -
384C VAL* 3.7 20.9 - - + -
386C GLY 3.3 8.7 - - - +
387C LEU* 3.8 5.5 - - + -
434C LEU* 4.1 10.3 - - + -
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Residues in contact with PHE 297 (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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296C PRO* 1.3 75.0 - - - +
298C THR* 1.3 71.1 + - - +
299C ASP* 3.9 17.0 - - + -
302C LEU* 4.5 2.0 - - + -
347C ILE* 3.2 24.5 - - + +
348C LEU* 4.1 8.1 - - + -
349C MET* 3.8 6.1 - - - -
384C VAL* 3.6 2.3 - - - -
385C HIS* 2.8 41.2 + - + -
386C GLY* 3.0 44.2 + - - -
387C LEU 3.5 22.4 - - - -
388C ALA* 3.7 2.5 - - + -
419C ARG* 3.7 36.3 - - + -
420C CYS 4.0 2.7 - - - -
421C LEU* 4.0 21.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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