Contacts of the helix formed by residues 337 - 353 (chain C) in PDB entry 4HH3
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 THR 337 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ALA* 3.6 22.2 - - - +
65A GLU* 6.0 0.8 - - - +
336C GLY* 1.3 67.9 - - - -
338C GLU* 1.3 67.7 + - - +
339C GLN* 3.0 3.1 - - - -
340C GLU* 3.2 45.7 + - - +
341C ALA* 4.2 1.9 + - - +
366C ARG* 4.8 16.4 - - - +
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Residues in contact with GLU 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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63A THR* 3.6 14.6 - - - +
64A ALA* 2.7 40.9 + - + +
65A GLU* 5.1 1.9 + - - +
284C HIS* 5.4 3.1 - - + -
336C GLY* 3.2 7.9 - - - +
337C THR* 1.3 80.8 + - - +
339C GLN* 1.3 61.3 + - - +
340C GLU 3.2 0.3 + - - -
341C ALA* 3.5 8.7 + - - +
342C ASP* 3.1 31.8 + - - +
345C ARG* 4.7 0.3 + - - -
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Residues in contact with GLN 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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281C VAL* 6.4 0.2 - - + -
284C HIS* 3.5 36.1 + - + +
331C PRO* 4.0 7.9 - - - +
332C SER* 2.7 51.7 + - - -
335C GLU* 2.9 24.5 + - - +
336C GLY 3.1 11.4 + - - +
337C THR* 3.0 1.2 - - - -
338C GLU* 1.3 76.1 - - - +
340C GLU* 1.3 62.5 + - + +
342C ASP* 3.5 1.5 - - - +
343C THR* 2.6 45.7 + - - +
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Residues in contact with GLU 340 (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 THR* 3.5 37.7 - - - +
338C GLU 3.2 0.6 - - - -
339C GLN* 1.3 80.7 - - + +
341C ALA* 1.3 61.3 + - - +
343C THR* 3.0 6.9 + - - -
344C LEU* 2.9 34.0 + - + +
366C ARG* 3.3 42.6 + - + +
367C LEU* 3.9 20.6 - - + +
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Residues in contact with ALA 341 (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 THR 4.2 1.3 + - - +
338C GLU* 3.5 8.3 + - - +
340C GLU* 1.3 77.9 - - - +
342C ASP* 1.3 62.1 + - - +
344C LEU* 3.4 13.6 + - + +
345C ARG* 3.0 52.6 + - - +
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Residues in contact with ASP 342 (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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281C VAL* 4.1 12.2 - - + +
282C PRO 5.2 2.3 - - - +
284C HIS* 2.7 32.3 + - - +
338C GLU* 3.1 23.3 + - - +
339C GLN 3.5 5.8 - - - +
340C GLU 3.1 0.2 - - - -
341C ALA* 1.3 76.1 - - - +
343C THR* 1.3 56.8 + - - +
345C ARG* 2.5 39.2 + - - +
346C PHE* 3.0 27.9 + - - +
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Residues in contact with THR 343 (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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281C VAL* 3.6 16.3 - - + +
329C VAL* 4.2 23.3 - - + +
339C GLN* 2.6 31.2 + - - +
340C GLU* 3.6 4.6 - - - -
342C ASP* 1.3 70.2 - - - +
344C LEU* 1.3 60.3 + - - +
346C PHE* 3.1 6.8 + - + +
347C VAL* 2.8 40.5 + - + +
363C VAL* 4.4 8.1 - - + -
364C GLY 6.1 0.2 - - - +
367C LEU* 3.6 21.1 - - + -
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Residues in contact with LEU 344 (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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340C GLU* 2.9 17.6 + - + +
341C ALA* 3.7 14.4 - - + +
343C THR* 1.3 76.9 - - - +
345C ARG* 1.3 57.3 + - + +
347C VAL* 3.4 4.8 + - + +
348C SER* 2.9 34.6 + - - +
367C LEU* 3.8 29.6 - - + -
378C SER* 3.7 33.9 - - - +
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Residues in contact with ARG 345 (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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338C GLU 4.7 0.4 + - - -
341C ALA* 3.0 35.9 + - - +
342C ASP* 2.5 39.4 + - - +
344C LEU* 1.3 76.8 - - + +
346C PHE* 1.3 57.8 + - - +
348C SER* 3.8 6.1 - - - -
349C ALA* 2.9 31.0 + - - +
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Residues in contact with PHE 346 (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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279C ALA* 5.5 0.9 - - + -
280C GLY 4.3 7.0 - - - -
281C VAL* 4.0 21.1 - - + -
282C PRO* 3.5 31.2 - - + -
309C PRO* 5.1 0.7 - - + -
312C VAL* 3.8 27.6 - - + -
315C LEU* 3.3 33.0 - - + -
327C LEU* 4.8 0.2 - - + -
329C VAL* 4.1 28.3 - - + -
342C ASP 3.0 17.8 + - - +
343C THR* 3.1 8.3 + - - +
345C ARG* 1.3 74.8 - - - +
347C VAL* 1.3 67.3 - - + +
349C ALA* 3.3 5.2 + - - +
350C LEU* 3.0 43.5 + - + +
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Residues in contact with VAL 347 (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 VAL* 5.0 1.6 - - + -
343C THR* 2.8 27.8 + - + +
344C LEU* 4.0 4.9 - - + +
346C PHE* 1.3 78.1 - - + +
348C SER* 1.3 62.4 + - - +
350C LEU* 3.3 10.6 + - + +
351C ARG* 3.0 22.4 + - + +
361C ILE* 4.4 16.6 - - + -
363C VAL* 3.9 27.4 - - + -
367C LEU* 6.0 0.9 - - + -
378C SER* 3.3 25.4 - - - +
379C GLY* 3.7 23.8 - - - +
380C ALA* 4.0 2.9 - - + +
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Residues in contact with SER 348 (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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344C LEU* 2.9 19.2 + - - +
345C ARG* 3.8 7.0 - - - -
347C VAL* 1.3 78.2 - - - +
349C ALA* 1.3 51.9 + - - +
351C ARG* 3.1 8.3 + - - +
352C ALA* 2.8 35.7 + - - +
378C SER 4.4 8.3 + - - -
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Residues in contact with ALA 349 (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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312C VAL* 3.9 24.8 - - + +
345C ARG 2.9 19.0 + - - +
346C PHE 3.6 4.7 - - - +
347C VAL 3.3 0.2 - - - -
348C SER* 1.3 75.1 - - - +
350C LEU* 1.3 62.4 + - - +
352C ALA* 3.3 14.3 + - - +
353C ARG* 3.3 20.6 + - - +
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Residues in contact with LEU 350 (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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312C VAL* 4.1 21.8 - - + +
315C LEU* 4.4 16.6 - - + -
316C ALA 5.2 0.2 - - - +
319C LEU* 5.0 1.8 - - + -
327C LEU* 3.6 28.9 - - + -
346C PHE* 3.0 40.3 + - + +
347C VAL* 3.5 11.4 - - + +
349C ALA* 1.3 76.1 - - - +
351C ARG* 1.3 62.3 + - - +
353C ARG* 3.3 23.9 + - - +
356C LEU* 3.8 33.7 - - + +
359C LEU* 5.0 2.2 - - + -
361C ILE* 4.2 17.9 - - + -
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Residues in contact with ARG 351 (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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347C VAL* 3.0 20.7 + - + +
348C SER* 3.7 7.0 - - - +
350C LEU* 1.3 73.7 - - - +
352C ALA* 1.3 64.9 + - - +
353C ARG 3.1 9.2 - - - +
356C LEU 5.2 2.0 + - - -
359C LEU* 2.9 32.1 + - - +
361C ILE* 3.5 22.2 - - + +
379C GLY* 2.8 38.8 + - - +
381C ASP* 2.6 34.4 + - - -
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Residues in contact with ALA 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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348C SER 2.8 16.5 + - - +
349C ALA* 3.6 10.1 - - - +
350C LEU 3.2 0.2 - - - -
351C ARG* 1.3 73.6 - - - +
353C ARG* 1.3 66.7 + - - +
354C THR* 4.5 5.7 - - - +
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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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312C VAL* 3.8 23.8 - - + +
313C ALA* 3.9 26.5 + - - +
316C ALA* 3.7 16.4 - - - +
320C LYS* 4.5 2.4 - - - +
349C ALA 3.3 13.5 - - - +
350C LEU* 3.4 12.6 - - - +
351C ARG 3.1 11.5 - - - +
352C ALA* 1.3 82.3 - - - +
354C THR* 1.3 64.6 + - - +
355C ASP* 2.7 44.1 + - - +
356C LEU* 4.2 13.9 + - + +
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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