Contacts of the helix formed by residues 377 - 392 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D SER* 3.3 17.4 + - - -
340D ALA* 4.4 5.8 - - - -
343D GLU* 3.1 21.1 + - - -
375D VAL 3.3 0.4 + - - -
376D ARG* 1.4 78.8 - - - +
378D THR* 1.3 66.3 + - - +
379D GLU 3.1 2.9 - - - -
380D GLY 3.0 2.4 + - - -
381D LYS* 2.7 28.7 + - - +
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Residues in contact with THR 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D GLU* 3.9 0.4 + - - -
374D GLY 4.2 2.4 + - - -
375D VAL* 2.6 39.3 + - + +
376D ARG 3.2 1.5 + - - -
377D GLY* 1.3 75.7 - - - +
379D GLU* 1.3 58.5 + - - +
381D LYS* 3.1 11.7 + - - +
382D ILE* 2.8 40.8 + - + +
400D LEU* 5.6 1.2 - - - +
404D LEU* 3.7 31.0 - - + +
420D ASN* 5.9 2.9 - - - +
424D PHE* 4.1 13.2 - - + -
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Residues in contact with GLU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D GLU* 3.3 17.4 + - + +
344D PRO* 3.5 32.7 - - - +
345D ILE* 5.0 7.1 - - - +
377D GLY 3.1 0.4 - - - -
378D THR* 1.3 78.9 - - - +
380D GLY* 1.3 57.4 + - - +
382D ILE* 3.0 9.5 + - - +
383D GLN* 2.8 51.5 + - + +
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Residues in contact with GLY 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D SER* 3.4 26.7 - - - -
342D LEU* 3.7 8.8 - - - +
343D GLU* 3.0 21.0 + - - -
377D GLY 3.0 0.8 + - - -
379D GLU* 1.3 76.2 - - - +
381D LYS* 1.3 56.4 + - - +
383D GLN* 3.5 10.8 - - - +
384D ALA* 2.9 29.1 + - - +
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Residues in contact with LYS 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D VAL* 4.5 11.9 - - + -
305D GLY* 3.9 14.6 - - - -
306D LYS* 3.7 17.7 - - - +
339D SER* 2.9 34.7 + - - -
369D VAL* 4.5 16.4 - - + +
370D PRO 5.7 2.7 - - - -
371D GLY 6.6 0.2 - - - -
372D GLY* 6.1 3.4 - - - -
374D GLY 5.6 1.6 - - - -
376D ARG 2.9 25.1 + - - +
377D GLY 2.7 13.6 + - - +
378D THR* 3.3 9.2 - - - +
380D GLY* 1.3 75.9 - - - +
382D ILE* 1.3 61.6 + - - +
384D ALA* 3.1 5.5 + - - +
385D ILE* 3.0 26.7 + - - +
400D LEU* 4.5 15.7 - - + -
404D LEU* 4.0 25.1 - - + -
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Residues in contact with ILE 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D THR* 2.8 37.8 + - + +
379D GLU* 3.7 6.5 - - - +
381D LYS* 1.3 72.0 - - - +
383D GLN* 1.3 63.5 + - + +
385D ILE* 3.0 8.9 + - - +
386D ALA* 2.8 27.4 + - + +
404D LEU* 4.1 28.5 - - + +
407D VAL* 4.8 6.7 - - + -
408D GLU* 3.6 28.0 - - + -
411D ARG* 3.5 35.7 - - - +
412D ASN* 5.5 2.2 - - - +
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Residues in contact with GLN 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D LEU 2.9 25.3 + - - +
343D GLU* 3.8 3.6 - - - -
344D PRO* 3.9 10.5 - - - +
354D TYR* 5.6 2.4 + - - -
358D TRP* 3.9 18.4 - - + -
379D GLU* 2.8 41.4 + - + +
380D GLY* 3.5 14.1 + - - +
382D ILE* 1.3 79.7 - - + +
384D ALA* 1.3 57.7 + - - +
386D ALA* 3.3 6.2 + - - +
387D TRP* 2.8 29.3 + - - +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D VAL* 4.2 18.8 - - + -
342D LEU* 3.9 17.3 - - + -
358D TRP* 4.3 2.2 - - - -
361D LEU* 4.2 14.6 - - + -
367D VAL* 5.5 4.1 - - + +
369D VAL* 4.9 5.4 - - + -
380D GLY 2.9 13.5 + - - +
381D LYS 3.1 8.5 + - - +
383D GLN* 1.3 75.7 - - - +
385D ILE* 1.3 57.8 + - - +
387D TRP* 3.2 10.3 + - - +
388D ALA* 2.8 30.5 + - - +
395D PHE* 6.0 0.4 - - - -
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Residues in contact with ILE 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D VAL* 4.2 13.5 - - + -
381D LYS 3.0 19.8 + - - +
382D ILE* 3.0 12.7 + - - +
384D ALA* 1.3 75.3 - - - +
386D ALA* 1.3 57.5 + - - +
388D ALA* 3.1 5.4 + - - +
389D ARG* 2.8 26.7 + - - +
395D PHE* 3.8 23.1 - - + -
401D GLY 3.9 8.1 - - - +
404D LEU* 3.8 18.2 - - + +
405D ALA* 3.7 32.1 - - + +
408D GLU* 3.9 15.3 - - + +
520D PHE* 3.8 27.1 - - + -
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Residues in contact with ALA 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D ILE* 2.8 18.4 + - + +
383D GLN* 3.8 6.3 - - - +
385D ILE* 1.3 73.5 - - - +
387D TRP* 1.3 57.1 + - - +
389D ARG* 3.2 3.6 + - - +
390D ASN* 2.8 44.0 + - - +
408D GLU* 3.3 31.6 - - + +
412D ASN* 4.1 9.4 - - - +
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Residues in contact with TRP 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D TRP* 3.8 27.1 - + + -
361D LEU* 3.5 45.8 - - + -
362D CYS* 3.6 34.1 - - + +
364D ALA 5.1 1.6 - - - -
367D VAL* 4.0 13.9 - - + -
383D GLN 2.8 18.1 + - - +
384D ALA 3.3 6.5 - - - +
386D ALA* 1.3 76.7 - - - +
388D ALA* 1.3 71.7 + - + +
390D ASN* 3.1 6.6 + - - +
391D GLN* 2.9 62.0 + - + +
393D LYS* 3.7 31.6 - - + -
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Residues in contact with ALA 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D VAL* 3.9 27.1 - - + -
384D ALA 2.8 16.2 + - - +
385D ILE 3.6 4.0 - - - +
387D TRP* 1.3 89.0 - - + +
389D ARG* 1.3 59.4 + - - +
392D LYS* 2.7 25.3 + - - -
393D LYS* 2.9 26.3 + - + +
395D PHE* 4.2 10.5 - - + -
517D HIS* 3.5 2.4 + - - -
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Residues in contact with ARG 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ILE 2.8 17.1 + - - +
386D ALA* 3.2 3.5 + - - +
388D ALA* 1.3 77.3 - - - +
390D ASN* 1.3 80.8 + - - +
392D LYS* 3.4 25.3 + - - +
408D GLU* 2.8 41.4 + - - -
409D PHE* 4.9 11.6 - - - +
412D ASN* 3.6 19.8 + - - +
413D VAL* 3.9 23.7 - - - +
514D LEU* 3.6 32.3 - - + -
517D HIS* 3.7 8.4 - - + -
520D PHE* 3.7 15.4 - - + -
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Residues in contact with ASN 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D ALA* 2.8 30.1 + - - +
387D TRP* 3.8 5.8 - - - +
389D ARG* 1.3 100.8 + - - +
391D GLN* 1.3 71.4 + - - +
392D LYS* 3.2 10.8 + - - +
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Residues in contact with GLN 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D TRP* 2.9 49.5 + - + +
390D ASN* 1.3 84.1 + - - +
392D LYS* 1.3 72.0 + - - +
393D LYS* 3.3 33.1 + - + +
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Residues in contact with LYS 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D ALA 2.7 10.5 + - - -
389D ARG* 3.4 14.8 + - - +
390D ASN* 3.2 10.0 - - - +
391D GLN* 1.3 82.0 - - - +
393D LYS* 1.3 61.2 + - - +
394D PRO* 4.1 3.1 - - - +
514D LEU* 5.5 3.2 - - - +
516D ASP* 2.9 26.1 + - - +
517D HIS* 3.4 25.6 - - + +
518D PRO* 3.8 31.3 - - + +
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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