Contacts of the helix formed by residues 377 - 392 (chain C) in PDB entry 5U03
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 377 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339C SER* 3.3 17.8 + - - -
340C ALA* 4.4 6.5 - - - +
343C GLU* 3.1 19.3 + - - -
375C VAL 3.3 0.4 + - - -
376C ARG* 1.4 78.2 - - - +
378C THR* 1.3 65.8 + - - +
379C GLU 3.1 3.8 - - - -
380C GLY 3.0 1.7 + - - -
381C LYS* 2.7 29.1 + - - +
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Residues in contact with THR 378 (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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374C GLY 4.2 2.4 + - - -
375C VAL* 2.6 38.3 + - - +
376C ARG 3.2 0.8 - - - -
377C GLY* 1.3 76.1 - - - +
379C GLU* 1.3 58.1 + - - +
381C LYS* 3.1 12.4 + - - +
382C ILE* 2.8 39.2 + - + +
400C LEU* 5.5 1.4 - - - +
404C LEU* 3.7 31.2 - - + +
420C ASN* 5.9 2.5 - - - +
424C PHE* 4.1 13.9 - - + -
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Residues in contact with GLU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C GLU* 3.3 17.7 + - + +
344C PRO* 3.5 33.9 - - - +
345C ILE* 5.0 6.9 - - - +
377C GLY 3.1 0.6 - - - -
378C THR* 1.3 78.7 - - - +
380C GLY* 1.3 58.4 + - - +
382C ILE* 3.0 9.1 + - - +
383C GLN* 2.8 50.5 + - + +
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Residues in contact with GLY 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C SER* 3.4 26.0 - - - -
342C LEU* 3.7 8.2 - - - +
343C GLU* 3.0 21.3 + - - -
377C GLY 3.0 0.8 + - - -
379C GLU* 1.3 75.5 - - - +
381C LYS* 1.3 57.6 + - - +
383C GLN* 3.3 12.2 + - - +
384C ALA* 2.9 29.8 + - - +
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Residues in contact with LYS 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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304C VAL* 4.5 11.0 - - + -
305C GLY* 3.9 14.4 - - - -
306C LYS* 3.7 18.3 - - - +
339C SER* 2.9 34.7 + - - -
369C VAL* 4.5 17.5 - - + +
370C PRO 5.7 2.5 - - - +
371C GLY 6.6 0.2 - - - -
372C GLY* 6.1 3.4 - - - -
374C GLY 5.6 1.6 - - - -
376C ARG 2.9 25.3 + - - -
377C GLY 2.7 14.3 + - - +
378C THR* 3.3 9.4 - - - +
380C GLY* 1.3 78.2 - - - +
382C ILE* 1.3 62.1 + - - +
384C ALA* 3.1 4.9 + - - +
385C ILE* 3.0 27.4 + - - +
400C LEU* 4.5 15.3 - - + -
404C LEU* 4.0 24.9 - - + -
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Residues in contact with ILE 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C THR* 2.8 37.1 + - + +
379C GLU* 3.7 6.3 - - - +
381C LYS* 1.3 71.9 - - - +
383C GLN* 1.3 62.3 + - + +
385C ILE* 3.0 8.9 + - - +
386C ALA* 2.8 28.7 + - + +
404C LEU* 4.1 28.3 - - + +
407C VAL* 4.8 7.0 - - + -
408C GLU* 3.6 27.8 - - + -
411C ARG* 3.5 36.8 - - - +
412C ASN* 5.5 2.5 - - - +
420C ASN* 6.1 0.2 - - - +
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Residues in contact with GLN 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU 2.9 24.4 + - - +
343C GLU* 3.8 3.6 - - - -
344C PRO* 3.9 10.5 - - - +
354C TYR* 5.6 1.8 + - - -
358C TRP* 3.9 18.9 - - + -
379C GLU* 2.8 41.6 + - + +
380C GLY* 3.5 14.7 + - - +
382C ILE* 1.3 79.2 - - + +
384C ALA* 1.3 57.3 + - - +
386C ALA* 3.3 5.8 + - - +
387C TRP* 2.8 29.6 + - - +
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C VAL* 4.2 17.9 - - + -
342C LEU* 3.9 17.7 - - + -
358C TRP* 4.3 2.0 - - - -
361C LEU* 4.2 14.6 - - + -
367C VAL* 5.5 4.1 - - + +
369C VAL* 4.9 5.2 - - + -
380C GLY 2.9 14.2 + - - +
381C LYS 3.1 8.5 + - - +
383C GLN* 1.3 76.5 - - - +
385C ILE* 1.3 57.3 - - - +
387C TRP* 3.2 10.1 + - - +
388C ALA* 2.8 30.2 + - - +
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Residues in contact with ILE 385 (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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369C VAL* 4.2 13.0 - - + -
381C LYS 3.0 20.9 + - - +
382C ILE* 3.0 12.2 + - - +
384C ALA* 1.3 75.5 - - - +
386C ALA* 1.3 57.2 + - - +
388C ALA* 3.1 4.8 + - - +
389C ARG* 2.8 27.0 + - - +
395C PHE* 3.8 22.2 - - + -
401C GLY 3.9 8.5 - - - +
404C LEU* 3.8 18.2 - - + +
405C ALA* 3.7 32.8 - - + +
408C GLU* 3.9 13.9 - - + +
520C PHE* 3.8 26.7 - - + -
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Residues in contact with ALA 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ILE* 2.8 17.8 + - + +
383C GLN* 3.8 6.5 - - - +
385C ILE* 1.3 72.7 - - - +
387C TRP* 1.3 58.9 + - - +
389C ARG* 3.2 2.9 + - - +
390C ASN* 2.8 44.3 + - - +
408C GLU* 3.3 32.8 - - + +
412C ASN* 4.1 9.4 - - - +
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Residues in contact with TRP 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C TRP* 3.8 26.9 - + + -
361C LEU* 3.5 46.7 - - + -
362C CYS* 3.6 33.1 - - + +
364C ALA 5.1 1.3 - - - -
367C VAL* 4.0 14.1 - - + -
383C GLN 2.8 18.3 + - - +
384C ALA 3.3 6.1 - - - +
385C ILE 3.1 0.2 - - - -
386C ALA* 1.3 77.1 - - - +
388C ALA* 1.3 72.4 + - + +
390C ASN* 3.1 6.2 + - - +
391C GLN* 2.9 63.5 + - + +
393C LYS* 3.6 32.5 - - + -
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Residues in contact with ALA 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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367C VAL* 3.9 27.6 - - + -
384C ALA 2.8 15.3 + - - +
385C ILE 3.6 4.5 - - - +
387C TRP* 1.3 87.5 - - + +
389C ARG* 1.3 58.4 + - - +
392C LYS* 2.7 25.6 + - - -
393C LYS* 2.9 26.4 + - + +
395C PHE* 4.2 10.3 - - + -
517C HIS* 3.5 2.4 + - - -
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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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385C ILE 2.8 16.6 + - - +
386C ALA* 3.6 4.2 - - - +
388C ALA* 1.3 77.0 - - - +
390C ASN* 1.3 79.9 + - - +
392C LYS* 3.4 25.8 + - - +
408C GLU* 2.8 40.2 + - - +
409C PHE* 4.9 11.6 - - - +
412C ASN* 3.6 19.6 + - - +
413C VAL* 3.9 23.7 - - - +
514C LEU* 3.6 32.5 - - + -
517C HIS* 3.7 9.2 - - + -
520C PHE* 3.7 16.6 - - + -
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Residues in contact with ASN 390 (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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386C ALA* 2.8 31.1 + - - +
387C TRP* 3.8 5.2 - - - +
389C ARG* 1.3 99.1 + - - +
391C GLN* 1.3 71.8 + - - +
392C LYS* 3.2 11.4 + - - +
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Residues in contact with GLN 391 (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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387C TRP* 2.9 47.7 + - + +
390C ASN* 1.3 84.3 + - + +
392C LYS* 1.3 72.7 + - - +
393C LYS* 3.2 33.4 - - + +
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Residues in contact with LYS 392 (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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388C ALA 2.7 9.2 + - - -
389C ARG* 3.4 15.6 + - - +
390C ASN 3.2 9.0 - - - +
391C GLN* 1.3 82.0 - - - +
393C LYS* 1.3 60.9 + - - +
394C PRO* 4.1 2.9 - - - +
514C LEU* 5.5 2.6 - - - +
515C GLU 5.3 0.6 + - - -
516C ASP* 2.9 25.1 + - - +
517C HIS* 3.4 25.4 - - + +
518C PRO* 3.8 31.8 - - + +
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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
------------------------------------------------------------
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