Contacts of the helix formed by residues 350 - 364 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B THR* 2.6 16.2 + - - +
349B GLU* 1.3 77.2 - - - +
351B PRO* 1.3 69.5 - - + +
352B VAL* 3.0 27.2 - - + +
353B ARG* 2.8 56.6 + - - +
354B TYR 3.1 8.0 + - - -
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Residues in contact with PRO 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B SER* 3.3 28.3 - - - +
348B GLN 4.5 2.0 - - - +
349B GLU 3.6 6.1 - - - +
350B GLU* 1.3 84.6 - - + +
352B VAL* 1.3 69.5 + - + +
354B TYR* 3.6 9.9 - - + -
355B HIS* 2.9 45.1 + - + +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B GLU* 3.0 20.6 - - + +
351B PRO* 1.3 82.5 - - + +
353B ARG* 1.3 57.8 + - + +
355B HIS* 3.9 1.9 - - - +
356B GLU* 2.8 43.7 + - + +
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Residues in contact with ARG 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASP* 2.7 42.5 + - - +
346B THR* 3.5 12.8 + - + +
349B GLU* 3.9 21.0 + - - +
350B GLU* 2.8 52.8 + - - +
352B VAL* 1.3 78.2 - - + +
354B TYR* 1.3 60.3 + - - +
356B GLU* 3.6 12.7 - - - +
357B ALA* 2.8 32.6 + - - +
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Residues in contact with TYR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASP 3.2 18.6 - - - -
342B LEU 3.2 22.4 + - - -
343B GLU 3.0 28.3 - - - -
344B PRO* 3.8 7.9 - - + +
346B THR* 3.7 2.6 - - + +
347B SER* 3.6 38.1 - - - +
350B GLU 3.1 4.9 + - - -
351B PRO* 3.5 9.0 - - + +
352B VAL 3.2 0.2 - - - -
353B ARG* 1.3 78.3 - - - +
355B HIS* 1.3 92.2 + + - +
357B ALA* 3.2 8.7 + - - +
358B TRP* 3.2 41.1 + + - -
383B GLN* 5.6 1.9 + - - -
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Residues in contact with HIS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B SER* 5.0 3.0 + - - -
351B PRO* 2.9 38.2 + - + +
352B VAL* 4.2 1.3 - - - +
354B TYR* 1.3 99.4 - + - +
356B GLU* 1.3 56.9 + - - +
358B TRP* 3.3 6.0 + - - +
359B GLN* 2.7 36.9 + - - +
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Residues in contact with GLU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B VAL* 2.8 32.1 + - + +
353B ARG* 3.6 12.1 - - - +
355B HIS* 1.3 78.2 - - - +
357B ALA* 1.3 56.8 + - - +
359B GLN* 3.2 9.4 + - - +
360B LYS* 2.9 62.3 + - + +
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Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ILE* 3.6 15.5 - - + +
341B ASP* 3.7 22.4 - - + +
342B LEU* 3.6 19.3 - - + -
353B ARG 2.8 18.0 + - - +
354B TYR 3.2 4.9 + - - +
356B GLU* 1.3 76.4 - - - +
358B TRP* 1.3 56.7 + - - +
360B LYS* 3.1 11.5 + - - +
361B LEU* 2.8 27.2 + - - +
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Residues in contact with TRP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B LEU* 2.9 47.7 + - + +
354B TYR* 3.2 48.6 + + - -
355B HIS* 3.9 7.9 - - - +
357B ALA* 1.3 75.1 - - - +
359B GLN* 1.3 66.7 + - - +
361B LEU* 3.5 32.6 - - + +
362B CYS* 3.0 23.4 + - - +
383B GLN* 3.9 37.2 - - + -
384B ALA* 4.3 1.8 - - - -
387B TRP* 3.8 27.8 - + + -
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B HIS 2.7 23.4 + - - +
356B GLU* 3.2 10.4 + - - +
358B TRP* 1.3 70.6 - - - +
360B LYS* 1.3 78.4 + - - +
362B CYS* 3.2 7.5 + - - +
363B SER* 3.0 32.8 + - - -
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Residues in contact with LYS 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LYS* 3.7 24.6 - - + +
336B TYR 5.4 6.3 + - - +
337B ILE* 3.9 20.4 - - + -
356B GLU* 2.9 48.9 + - + +
357B ALA* 3.4 8.7 - - - +
359B GLN* 1.3 85.9 - - - +
361B LEU* 1.3 64.0 + - - +
363B SER* 2.5 24.3 + - - +
364B ALA 2.9 7.8 + - - -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ALA* 3.6 26.2 - - + -
304B VAL* 4.2 13.0 - - + -
337B ILE* 3.7 8.7 - - + +
342B LEU* 4.4 7.9 - - + -
357B ALA 2.8 14.3 + - - +
358B TRP* 3.5 44.2 - - + +
359B GLN 3.2 0.2 - - - -
360B LYS* 1.3 77.1 - - - +
362B CYS* 1.3 63.0 + - - +
364B ALA* 3.1 17.8 + - - +
367B VAL* 3.6 20.1 - - + +
384B ALA* 4.2 16.2 - - + -
387B TRP* 3.5 28.5 - - + -
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Residues in contact with CYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B TRP 3.0 12.3 + - - +
359B GLN* 3.7 9.0 - - - +
361B LEU* 1.3 76.8 - - - +
363B SER* 1.3 62.5 + - - +
364B ALA 3.1 10.6 - - - +
387B TRP* 3.6 27.5 - - + +
393B LYS* 5.0 11.8 + - - -
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Residues in contact with SER 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B SER* 3.6 8.3 + - - -
335B LYS* 3.4 15.6 + - - -
359B GLN* 3.0 24.9 + - - -
360B LYS* 2.5 28.8 + - - -
362B CYS* 1.3 76.4 - - - +
364B ALA* 1.3 59.8 + - - +
365B HIS* 3.6 9.7 + - - -
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B SER* 3.3 12.6 - - - +
301B ILE 4.1 1.6 - - - -
302B ALA* 3.7 22.4 - - + +
335B LYS* 4.2 4.5 - - + +
360B LYS 2.9 10.0 + - - +
361B LEU 3.4 14.6 - - - +
362B CYS 3.1 14.5 - - - +
363B SER* 1.3 77.8 + - - +
365B HIS* 1.3 62.3 + - - +
366B GLY* 3.4 18.8 - - - +
367B VAL* 4.9 1.2 - - + +
387B TRP* 5.1 1.2 - - - -
393B 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