Contacts of the strand formed by residues 378 - 389 (chain C) in PDB entry 5IXM
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 378 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358C TYR* 3.5 28.2 - - - -
359C TYR 2.9 30.9 + - - -
377C THR* 1.3 76.5 + - - +
379C SER* 1.3 60.9 + - - -
380C LEU* 3.0 14.5 + - - +
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Residues in contact with SER 379 (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 GLN* 2.8 25.5 + - - +
357C ILE 3.4 7.6 - - - -
358C TYR* 3.3 14.1 - - - -
378C GLY* 1.3 68.0 - - - -
380C LEU* 1.3 63.5 + - - +
382C TRP* 2.9 35.9 + - - -
404C THR* 4.1 6.1 + - - -
607C C8E 5.6 2.9 - - - -
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Residues in contact with LEU 380 (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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357C ILE 3.0 3.4 + - - -
359C TYR* 3.9 24.2 - - + -
376C ALA* 3.7 35.0 - - + +
377C THR* 3.6 20.2 - - - +
378C GLY 3.0 13.6 + - - +
379C SER* 1.3 79.3 - - - +
381C VAL* 1.3 62.5 + - + +
382C TRP* 4.1 3.6 + - - -
402C TYR 3.9 0.5 - - - +
403C ASP* 3.5 5.4 - - - +
404C THR* 3.1 49.0 + - + +
405C ARG* 3.7 35.9 - - + +
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Residues in contact with VAL 381 (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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310C SER* 5.0 10.8 - - - +
315C LEU* 3.8 23.1 - - + -
356C GLN* 3.2 6.6 - - - +
357C ILE* 2.8 44.9 + - + +
359C TYR* 3.8 15.0 - - + +
380C LEU* 1.3 81.8 - - - +
382C TRP* 1.3 68.5 + - - +
383C ALA* 5.4 0.9 - - + -
402C TYR 3.4 7.6 - - - +
403C ASP* 3.8 11.7 - - - +
405C ARG* 3.6 27.1 - - - +
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Residues in contact with TRP 382 (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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601A C8E 3.8 46.1 + - - -
315C LEU* 4.8 0.2 - - - -
354C VAL* 4.3 17.9 - - + -
355C GLY 3.5 17.0 - - - -
356C GLN* 3.7 19.5 - - + +
379C SER* 2.9 37.1 + - - -
380C LEU 4.5 3.6 - - - -
381C VAL* 1.3 86.4 - - - +
383C ALA* 1.3 64.6 + - - +
401C GLN* 3.6 1.6 - - - +
402C TYR* 2.9 40.9 + - + +
404C THR* 5.5 2.5 - - - -
607C C8E 6.1 2.9 - - + -
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Residues in contact with ALA 383 (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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601A C8E 4.4 6.9 - - - -
310C SER 5.1 1.3 - - - +
311C ASP 4.0 17.3 - - - +
312C TYR* 3.9 10.7 - - - +
315C LEU* 4.0 21.8 - - + -
354C VAL* 3.6 2.3 - - - +
355C GLY* 2.9 33.1 + - - +
381C VAL* 5.4 0.7 - - + -
382C TRP* 1.3 78.1 - - - +
384C GLY* 1.3 57.8 + - - +
400C ALA 3.3 11.7 - - - +
401C GLN* 4.4 7.4 - - + +
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Residues in contact with GLY 384 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A C8E 3.4 23.7 - - - -
312C TYR* 4.7 4.9 + - - +
353C SER 3.1 13.0 - - - -
354C VAL* 4.3 0.2 - - - -
383C ALA* 1.3 77.0 - - - +
385C ASP* 1.3 63.0 + - - +
399C GLY* 3.2 2.3 - - - -
400C ALA 2.9 32.6 + - - +
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Residues in contact with ASP 385 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601A C8E 3.7 4.1 + - - +
311C ASP* 6.2 0.2 - - - -
312C TYR* 3.7 18.8 - - + +
351C ASN* 4.4 7.9 - - - +
352C VAL* 3.6 2.1 - - - +
353C SER* 2.8 52.6 + - - +
384C GLY* 1.3 75.2 - - - +
386C THR* 1.3 65.4 + - - +
398C GLY 3.2 13.2 - - - +
399C GLY* 4.0 4.0 - - - -
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Residues in contact with THR 386 (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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181A PHE* 5.2 0.7 - - + -
601A C8E 3.5 52.7 - - + +
350C PHE* 3.9 17.3 - - - -
351C ASN* 2.9 20.4 + - - -
352C VAL* 4.4 7.9 - - - -
385C ASP* 1.3 78.8 - - - +
387C PHE* 1.3 62.5 + - - +
388C TRP* 5.3 0.5 - - - +
396C LEU* 6.4 1.1 - - + -
397C LYS* 3.1 7.9 - - - +
398C GLY 2.9 35.9 + - - +
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Residues in contact with PHE 387 (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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348C GLU* 3.8 28.9 - - + -
349C ARG 4.1 11.2 - - - -
350C PHE* 3.4 5.1 - - - -
351C ASN* 2.7 63.6 + - + +
386C THR* 1.3 76.0 + - - +
388C TRP* 1.3 69.2 + - - +
389C ARG* 4.0 20.9 - - + -
395C GLY* 5.6 1.3 - - - -
396C LEU 3.5 4.0 - - - -
397C LYS* 4.1 5.6 - - + -
556C PHE* 3.8 37.7 - + + -
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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
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226A ALA* 3.6 27.8 - - + -
227A LYS 5.0 0.9 - - - -
259A PRO* 4.2 15.0 - - + +
260A GLN 3.8 14.1 - - - -
261A PHE* 3.7 36.6 - + + -
601A C8E 5.2 2.5 - - + -
349C ARG 3.5 11.2 - - - -
350C PHE* 3.8 21.3 - + + -
386C THR* 5.3 0.9 - - - +
387C PHE* 1.3 80.9 - - - +
389C ARG* 1.3 68.4 + - - +
390C ILE* 3.4 30.2 + - + +
395C GLY* 3.6 1.0 - - - -
396C LEU* 2.8 65.3 + - + +
602C C8E 3.7 38.0 + - - -
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Residues in contact with ARG 389 (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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347C VAL* 3.4 33.6 - - - +
348C GLU 4.6 3.6 - - - -
349C ARG* 2.6 50.0 + - - +
387C PHE* 4.0 16.9 - - + -
388C TRP* 1.3 76.9 + - - +
390C ILE* 1.3 63.0 + - - +
391C ASN 3.4 21.4 + - - +
392C ASP* 3.1 36.9 + - - +
394C LEU 3.9 4.0 - - - +
395C GLY* 4.7 2.5 - - - -
602C C8E 5.5 0.5 - - - +
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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