Contacts of the helix formed by residues 350 - 364 (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 GLU 350 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C THR* 2.6 17.2 + - - +
349C GLU* 1.3 76.8 - - - +
351C PRO* 1.3 69.2 - - + +
352C VAL* 3.0 26.0 - - + +
353C ARG* 2.8 56.3 + - - +
354C TYR 3.1 8.0 + - - -
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Residues in contact with PRO 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C SER* 3.3 28.3 - - - +
348C GLN 4.5 1.8 - - - +
349C GLU 3.6 5.8 - - - +
350C GLU* 1.3 85.2 - - + +
352C VAL* 1.3 69.9 + - + +
353C ARG 3.3 0.2 - - - -
354C TYR* 3.6 9.4 - - + -
355C HIS* 2.9 45.1 + - + +
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Residues in contact with VAL 352 (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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350C GLU* 3.0 22.3 - - + +
351C PRO* 1.3 82.5 - - + +
353C ARG* 1.3 59.2 + - + +
355C HIS* 4.0 1.8 - - - +
356C GLU* 2.8 43.1 + - + +
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Residues in contact with ARG 353 (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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341C ASP* 2.7 42.4 + - - +
346C THR* 3.5 12.6 + - + +
349C GLU* 3.9 20.8 + - - +
350C GLU* 2.8 53.3 + - - +
352C VAL* 1.3 77.7 - - + +
354C TYR* 1.3 61.0 + - - +
356C GLU* 3.6 12.7 - - - +
357C ALA* 2.8 33.1 + - - +
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Residues in contact with TYR 354 (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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341C ASP 3.2 18.8 - - - -
342C LEU 3.2 21.9 + - - -
343C GLU 3.0 27.8 - - - -
344C PRO* 3.8 7.1 - - + +
346C THR* 3.6 2.8 - - + +
347C SER* 3.6 39.0 - - - +
350C GLU 3.1 4.8 + - - -
351C PRO* 3.5 8.1 - - + +
352C VAL 3.2 0.2 - - - -
353C ARG* 1.3 78.9 - - - +
355C HIS* 1.3 92.3 + + - +
357C ALA* 3.2 8.8 + - - +
358C TRP* 3.2 41.8 + + - -
383C GLN* 5.6 1.9 + - - -
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Residues in contact with HIS 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C SER* 5.0 2.6 + - - -
351C PRO* 2.9 38.2 + - + +
352C VAL* 4.2 1.8 - - - +
354C TYR* 1.3 99.8 - + - +
356C GLU* 1.3 56.4 + - - +
358C TRP* 3.3 6.2 + - - +
359C GLN* 2.7 36.0 + - - +
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Residues in contact with GLU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C VAL* 2.8 32.5 + - + +
353C ARG* 3.6 12.5 - - - +
355C HIS* 1.3 77.0 - - - +
357C ALA* 1.3 56.7 + - - +
359C GLN* 3.2 9.1 + - - +
360C LYS* 2.9 64.0 + - + +
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Residues in contact with ALA 357 (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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337C ILE* 3.6 15.8 - - + +
341C ASP* 3.7 22.4 - - + +
342C LEU* 3.6 18.8 - - + -
353C ARG 2.8 17.3 + - - +
354C TYR 3.2 5.3 + - - +
356C GLU* 1.3 76.8 - - - +
358C TRP* 1.3 57.4 + - - +
360C LYS* 3.1 11.2 + - - +
361C LEU* 2.8 27.5 + - - +
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Residues in contact with TRP 358 (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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342C LEU* 2.9 48.0 + - + +
354C TYR* 3.2 48.6 + + - -
355C HIS* 3.9 8.7 - - - +
357C ALA* 1.3 76.3 - - - +
359C GLN* 1.3 67.2 + - - +
361C LEU* 3.5 32.6 - - + +
362C CYS* 3.0 23.2 + - - +
383C GLN* 3.9 37.5 - - + -
384C ALA* 4.3 1.8 - - - -
387C TRP* 3.8 28.9 - + + -
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Residues in contact with GLN 359 (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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355C HIS 2.7 23.2 + - - +
356C GLU* 3.2 10.2 + - - +
358C TRP* 1.3 72.2 - - - +
360C LYS* 1.3 81.4 + - - +
362C CYS* 3.2 7.0 + - - +
363C SER* 3.0 33.3 + - - -
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Residues in contact with LYS 360 (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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335C LYS* 3.7 24.8 - - + +
336C TYR 5.4 6.3 + - - +
337C ILE* 3.9 20.6 - - + -
356C GLU* 2.9 49.7 + - + +
357C ALA* 3.4 9.0 - - - +
359C GLN* 1.3 84.9 - - - +
361C LEU* 1.3 63.5 + - - +
363C SER* 2.5 24.0 + - - +
364C ALA 2.9 7.6 + - - -
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Residues in contact with LEU 361 (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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302C ALA* 3.6 25.8 - - + -
304C VAL* 4.2 13.5 - - + -
337C ILE* 3.7 8.7 - - + +
342C LEU* 4.4 8.3 - - + -
357C ALA 2.8 14.4 + - - +
358C TRP* 3.5 44.6 - - + +
359C GLN 3.2 0.4 - - - -
360C LYS* 1.3 74.6 - - - +
362C CYS* 1.3 61.9 + - - +
364C ALA* 3.1 17.8 + - - +
367C VAL* 3.6 20.4 - - + +
384C ALA* 4.2 15.9 - - + -
387C TRP* 3.5 27.5 - - + -
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Residues in contact with CYS 362 (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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358C TRP 3.0 13.6 + - - +
359C GLN* 3.7 8.7 - - - +
361C LEU* 1.3 76.3 - - - +
363C SER* 1.3 61.8 + - - +
364C ALA 3.1 10.7 - - - +
387C TRP* 3.6 29.1 - - + +
393C LYS* 5.0 11.4 + - - -
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Residues in contact with SER 363 (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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300C SER* 3.6 7.9 + - - -
335C LYS* 3.4 15.2 + - - -
359C GLN* 3.0 25.9 + - - -
360C LYS* 2.5 29.3 + - - -
362C CYS* 1.3 75.8 - - - +
364C ALA* 1.3 60.9 + - - +
365C HIS* 3.6 9.4 + - - -
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Residues in contact with ALA 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C SER* 3.3 12.6 - - - +
301C ILE 4.1 1.8 - - - -
302C ALA* 3.7 23.6 - - + +
335C LYS* 4.2 4.5 - - + +
360C LYS 2.9 10.3 + - - +
361C LEU 3.4 13.5 - - - +
362C CYS 3.1 13.4 - - - +
363C SER* 1.3 76.3 + - - +
365C HIS* 1.3 62.7 + - - +
366C GLY* 3.4 18.6 - - - +
367C VAL* 4.9 1.0 - - + +
387C TRP* 5.1 1.4 - - - -
393C LYS* 5.1 9.2 + - - +
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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