Contacts of the helix formed by residues 328 - 339 (chain C) in PDB entry 3P9K
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 TYR 328 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297C LEU* 3.2 34.0 - - + +
298C PRO 3.5 22.2 + - - -
299C VAL* 4.1 19.5 - - + -
311C PHE* 5.3 1.3 - + - -
327C ARG* 1.3 75.4 - - - +
329C GLU* 1.3 68.9 + - - +
330C ARG* 3.5 41.1 - - + +
331C GLU* 2.8 38.3 + - - +
332C PHE* 3.4 5.4 + - - -
79D ARG* 2.9 39.6 + - - -
101D ARG* 3.1 32.8 + - - -
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Residues in contact with GLU 329 (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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296C ILE* 3.5 28.1 - - + +
297C LEU 4.6 0.4 + - - -
328C TYR* 1.3 73.2 - - - +
330C ARG* 1.3 63.7 + - - +
332C PHE* 2.9 22.4 + - + +
333C GLN* 3.1 37.5 + - + +
344C VAL* 5.8 1.3 - - + +
346C SER* 4.0 27.8 + - - +
354C TRP* 5.6 3.6 - - - -
356C ILE* 6.2 0.9 - - + -
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Residues in contact with ARG 330 (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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299C VAL* 4.2 10.5 - - - +
328C TYR* 3.5 48.6 - - + +
329C GLU* 1.3 78.5 - - - +
331C GLU* 1.3 69.0 + - + +
333C GLN* 3.5 17.8 + - - +
334C ALA* 3.1 26.5 + - - +
337C ARG* 5.3 0.9 + - - -
99D LEU* 3.5 44.5 + - - +
101D ARG* 4.6 6.7 - - - +
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Residues in contact with GLU 331 (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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270C ASP* 5.7 1.3 - - - +
297C LEU* 4.6 0.3 - - - +
325C ARG* 4.9 11.7 + - - -
326C GLU 4.2 2.1 - - - +
327C ARG* 3.1 27.9 - - + +
328C TYR* 2.8 53.1 + - + +
330C ARG* 1.3 87.1 + - + +
332C PHE* 1.3 62.8 + - - +
334C ALA* 3.6 7.5 + - - +
335C LEU* 3.2 28.0 + - - +
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Residues in contact with PHE 332 (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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265C LEU* 4.4 16.2 - - + -
266C HIS* 6.0 2.2 - - + -
292C LEU* 3.7 31.0 - - + -
294C GLN* 3.9 28.5 - - + -
295C CYS 3.8 11.9 - - - -
296C ILE* 4.1 2.9 - - + -
326C GLU* 5.8 0.7 - - - -
327C ARG* 3.6 45.5 - - + -
328C TYR 3.4 14.8 + - - -
329C GLU* 2.9 15.7 + - + +
331C GLU* 1.3 75.9 - - - +
333C GLN* 1.3 62.5 + - + +
335C LEU* 3.2 5.6 + - + +
336C ALA 2.9 23.6 + - - -
344C VAL* 5.7 0.2 - - + -
356C ILE* 3.9 22.0 - - + -
358C PHE* 3.3 21.8 - + + -
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Residues in contact with GLN 333 (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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329C GLU* 3.1 35.6 + - + +
330C ARG* 3.7 18.2 - - - +
332C PHE* 1.3 74.7 - - + +
334C ALA* 1.3 65.6 + - - +
336C ALA* 3.2 2.4 + - - +
337C ARG* 2.9 37.9 + - - +
344C VAL* 4.0 42.5 + - + +
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Residues in contact with ALA 334 (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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330C ARG 3.1 18.3 + - - +
331C GLU* 3.7 8.7 - - - +
332C PHE 3.3 0.2 - - - -
333C GLN* 1.3 76.6 - - - +
335C LEU* 1.3 59.0 + - + +
337C ARG* 3.4 27.6 + - - +
338C GLY* 2.9 25.5 + - - -
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Residues in contact with LEU 335 (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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265C LEU* 4.5 13.7 - - + -
270C ASP* 4.2 31.2 - - + +
273C CYS* 4.1 21.1 - - + -
274C ALA* 4.8 9.5 - - + +
277C LEU* 3.8 15.1 - - + +
327C ARG* 3.9 30.1 - - - +
331C GLU 3.2 15.2 + - - +
332C PHE* 3.2 12.4 + - + +
333C GLN 3.2 0.4 - - - -
334C ALA* 1.3 78.6 - - + +
336C ALA* 1.3 64.8 + - - +
338C GLY* 3.3 2.2 + - - -
339C ALA* 3.2 22.2 + - - +
358C PHE* 5.0 0.9 - - + -
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Residues in contact with ALA 336 (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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277C LEU* 4.7 0.2 - - - -
332C PHE 2.9 6.6 + - - +
333C GLN 3.2 6.9 + - - +
335C LEU* 1.3 75.2 - - - +
337C ARG* 1.3 62.8 + - - +
339C ALA* 3.1 7.0 + - - -
340C GLY 3.3 0.2 + - - -
341C PHE* 3.0 38.1 + - + +
344C VAL* 3.8 14.1 - - + -
358C PHE* 3.5 48.6 - - + -
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Residues in contact with ARG 337 (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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330C ARG 5.3 0.6 + - - -
333C GLN* 2.9 31.7 + - - +
334C ALA* 3.4 29.2 + - - +
336C ALA* 1.3 77.5 - - - +
338C GLY* 1.3 62.6 + - - +
340C GLY* 3.1 14.2 + - - -
341C PHE 3.6 13.1 - - - +
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Residues in contact with GLY 338 (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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278C LYS* 4.8 8.0 + - - +
334C ALA 2.9 15.7 + - - -
335C LEU* 3.8 2.9 - - - -
336C ALA 3.3 0.4 - - - -
337C ARG* 1.3 77.1 - - - +
339C ALA* 1.3 58.7 + - - +
340C GLY 3.5 0.5 + - - -
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Residues in contact with ALA 339 (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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274C ALA* 5.1 3.6 - - - +
277C LEU* 3.6 38.1 - - + -
278C LYS* 4.2 21.3 + - - +
281C TYR* 3.4 23.6 - - - +
335C LEU 3.2 7.7 + - - +
336C ALA 3.1 8.4 + - - +
337C ARG 3.1 1.2 - - - -
338C GLY* 1.3 75.8 - - - +
340C GLY* 1.3 58.7 + - - +
341C PHE* 3.5 12.8 - - + -
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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
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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