Contacts of the helix formed by residues 350 - 364 (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 GLU 350 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346D THR* 2.6 16.8 + - - +
349D GLU* 1.3 75.4 - - - +
351D PRO* 1.3 67.2 - - + +
352D VAL* 3.0 26.1 - - + +
353D ARG* 2.8 57.2 + - - +
354D TYR 3.1 8.0 + - - -
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Residues in contact with PRO 351 (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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347D SER* 3.3 29.2 - - - +
348D GLN 4.5 1.6 - - - +
349D GLU 3.6 6.1 - - - +
350D GLU* 1.3 84.8 - - + +
352D VAL* 1.3 69.3 + - + +
353D ARG 3.3 0.2 - - - -
354D TYR* 3.6 9.2 - - + -
355D HIS* 2.9 44.4 + - + +
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Residues in contact with VAL 352 (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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350D GLU* 3.0 21.7 - - + +
351D PRO* 1.3 82.3 - - + +
353D ARG* 1.3 59.8 + - + +
355D HIS* 4.0 1.5 - - - +
356D GLU* 2.8 42.8 + - + +
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Residues in contact with ARG 353 (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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341D ASP* 2.7 41.7 + - - +
346D THR* 3.5 16.4 + - + +
349D GLU* 3.9 20.8 + - - +
350D GLU* 2.8 53.3 + - - +
352D VAL* 1.3 77.9 - - + +
354D TYR* 1.3 61.6 + - - +
356D GLU* 3.6 12.1 - - - +
357D ALA* 2.8 32.7 + - - +
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Residues in contact with TYR 354 (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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341D ASP 3.2 18.4 - - - -
342D LEU 3.2 21.7 + - - -
343D GLU 3.0 27.6 - - - -
344D PRO* 3.8 7.3 - - + +
346D THR* 3.7 3.0 - - + +
347D SER* 3.6 37.5 - - - +
350D GLU 3.1 5.1 + - - -
351D PRO* 3.5 7.9 - - + +
353D ARG* 1.3 79.5 - - - +
355D HIS* 1.3 93.3 + + - +
357D ALA* 3.2 8.3 + - - +
358D TRP* 3.2 40.5 + + - -
383D GLN* 5.6 2.1 + - - -
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Residues in contact with HIS 355 (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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347D SER* 5.0 2.8 + - - -
351D PRO* 2.9 38.2 + - + +
352D VAL* 4.2 1.6 - - - +
354D TYR* 1.3 99.9 - + - +
356D GLU* 1.3 55.3 + - - +
358D TRP* 3.3 6.8 + - - +
359D GLN* 2.7 36.7 + - - +
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Residues in contact with GLU 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D VAL* 2.8 31.8 + - + +
353D ARG* 3.6 12.6 - - - +
355D HIS* 1.3 77.4 - - - +
357D ALA* 1.3 57.4 + - - +
359D GLN* 3.2 9.4 + - - +
360D LYS* 2.9 63.7 + - + +
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Residues in contact with ALA 357 (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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337D ILE* 3.6 15.7 - - + +
341D ASP* 3.7 22.2 - - + +
342D LEU* 3.6 20.2 - - + -
353D ARG 2.8 17.8 + - - +
354D TYR 3.2 5.1 + - - +
356D GLU* 1.3 76.3 - - - +
358D TRP* 1.3 57.4 + - - +
360D LYS* 3.1 11.7 + - - +
361D LEU* 2.8 27.5 + - - +
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Residues in contact with TRP 358 (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 48.5 + - + +
354D TYR* 3.2 49.5 + + - -
355D HIS* 3.9 8.5 - - - +
357D ALA* 1.3 75.9 - - - +
359D GLN* 1.3 66.7 + - - +
361D LEU* 3.2 34.9 + - + +
362D CYS* 3.0 23.4 + - - +
383D GLN* 3.9 36.8 - - + -
384D ALA* 4.3 2.0 - - - -
387D TRP* 3.8 27.8 - + + -
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Residues in contact with GLN 359 (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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355D HIS 2.7 22.8 + - - +
356D GLU* 3.5 9.2 - - - +
358D TRP* 1.3 71.6 - - - +
360D LYS* 1.3 78.8 + - - +
362D CYS* 3.2 7.5 + - - +
363D SER* 3.0 32.7 + - - -
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Residues in contact with LYS 360 (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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335D LYS* 3.7 24.8 - - + +
336D TYR 5.4 6.6 + - - +
337D ILE* 3.9 20.2 - - + -
356D GLU* 2.9 49.8 + - + +
357D ALA* 3.4 8.7 - - - +
359D GLN* 1.3 84.8 - - - +
361D LEU* 1.3 63.9 + - - +
363D SER* 2.5 23.7 + - - +
364D ALA 2.9 7.8 + - - -
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Residues in contact with LEU 361 (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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302D ALA* 3.6 26.0 - - + -
304D VAL* 4.2 12.8 - - + -
337D ILE* 3.7 9.1 - - + +
342D LEU* 4.4 7.9 - - + -
357D ALA 2.8 14.4 + - - +
358D TRP* 3.5 43.7 - - + +
359D GLN 3.2 0.2 - - - -
360D LYS* 1.3 76.3 - - - +
362D CYS* 1.3 63.2 + - - +
364D ALA* 3.1 17.8 + - - +
367D VAL* 3.6 20.5 - - + +
384D ALA* 4.2 16.6 - - + -
387D TRP* 3.5 28.8 - - + -
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Residues in contact with CYS 362 (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 3.0 12.6 + - - +
359D GLN* 3.7 8.7 - - - +
361D LEU* 1.3 76.2 - - - +
363D SER* 1.3 62.7 + - - +
364D ALA 3.1 10.7 - - - +
387D TRP* 3.6 27.6 - - + +
393D LYS* 5.0 11.4 + - - -
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Residues in contact with SER 363 (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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300D SER* 3.6 7.7 + - - -
335D LYS* 3.4 14.5 + - - -
359D GLN* 3.0 24.9 + - - -
360D LYS* 2.5 29.1 + - - -
362D CYS* 1.3 74.5 - - - +
364D ALA* 1.3 60.5 + - - +
365D HIS* 3.6 9.5 + - - -
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Residues in contact with ALA 364 (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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300D SER* 3.3 12.1 - - - +
301D ILE 4.1 1.3 - - - -
302D ALA* 3.7 22.7 - - + +
335D LYS* 4.2 4.5 - - + +
360D LYS 2.9 10.4 + - - +
361D LEU 3.4 14.6 - - - +
362D CYS 3.1 14.5 - - - +
363D SER* 1.3 77.8 + - - +
365D HIS* 1.3 62.5 + - - +
366D GLY* 3.4 20.2 - - - +
367D VAL* 4.9 1.0 - - + +
387D TRP* 5.1 1.2 - - - -
393D LYS* 5.1 9.0 + - - +
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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