Contacts of the helix formed by residues 349 - 362 (chain C) in PDB entry 4YCG
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 349 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LEU* 4.4 3.6 - - - -
347C THR 4.7 0.2 - - - +
348C PRO* 1.3 76.1 - - - +
350C LYS* 1.3 63.8 + - - +
351C HIS* 3.6 2.8 + - - +
352C ALA* 3.1 24.9 + - - +
353C ILE* 3.1 27.3 + - - +
406C CYS 4.1 0.8 + - - -
407C ARG* 3.6 36.1 + - - +
373D PRO* 5.7 0.9 - - - +
376D LEU* 3.9 26.9 - - + +
398D GLY* 5.7 0.2 - - - -
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Residues in contact with LYS 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B THR* 4.8 6.7 - - - +
248B GLU* 2.4 52.6 + - - -
249B LEU* 4.6 10.9 - - + +
252B MET* 3.6 24.5 - - + +
349C THR* 1.3 74.3 - - - +
351C HIS* 1.3 58.7 + - - +
353C ILE* 3.2 4.4 + - - +
354C VAL* 2.9 33.9 + - - +
396D TYR* 3.5 38.8 - - + -
397D GLU* 3.1 27.1 + - - +
398D GLY* 3.3 12.1 + - - +
399D MET* 3.7 8.7 - - - -
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Residues in contact with HIS 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C THR* 3.3 6.2 + - - +
350C LYS* 1.3 77.0 - - - +
352C ALA* 1.3 53.7 + - - +
354C VAL* 3.3 6.6 + - + +
355C GLN* 2.8 62.4 + - + +
407C ARG 4.4 8.5 + - - -
310D LEU* 4.8 1.0 - - + +
329D TYR* 5.1 0.2 - - - -
331D ALA* 3.1 23.4 + - + +
332D TYR 2.8 28.3 + - - -
333D GLU* 4.7 2.2 - - - -
334D CYS 5.5 0.9 - - - -
373D PRO* 4.4 6.0 - - + +
376D LEU* 4.1 11.9 - - + -
398D GLY 3.0 16.9 + - - +
399D MET 3.5 17.5 - - - +
400D SER* 4.1 2.2 - - - -
401D VAL* 3.3 21.8 - - + +
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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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342C LEU* 3.9 13.5 - - + -
348C PRO* 4.5 0.2 - - + -
349C THR* 3.1 25.4 + - - +
351C HIS* 1.3 77.0 + - - +
353C ILE* 1.3 54.1 + - - +
355C GLN* 4.0 3.3 - - - +
356C THR* 2.7 38.0 + - - -
369C ALA* 4.2 7.6 - - + +
406C CYS 3.7 21.3 - - - +
407C ARG* 3.9 16.8 + - - +
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Residues in contact with ILE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 3.7 24.9 - - + -
252B MET* 3.9 18.8 - - + -
253B ILE* 3.9 18.6 - - + +
256B GLU* 3.8 35.1 - - + +
342C LEU* 4.2 7.9 - - + -
348C PRO* 4.2 12.6 - - + -
349C THR 3.1 16.2 + - - +
350C LYS 3.6 5.8 - - - +
352C ALA* 1.3 74.5 - - - +
354C VAL* 1.3 65.3 + - - +
356C THR* 3.4 4.2 + - - -
357C LEU* 3.1 22.7 + - + +
319D TRP* 3.8 22.4 - - + -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C LYS 2.9 21.0 + - - +
351C HIS* 3.6 6.5 - - + +
353C ILE* 1.3 76.1 - - - +
355C GLN* 1.3 59.7 + - - +
357C LEU* 3.1 7.9 + - - +
358C VAL* 2.8 31.4 + - + +
310D LEU* 6.2 0.4 - - + -
312D VAL* 3.8 38.4 - - + -
314D PHE* 5.3 0.4 - - + -
317D ILE* 4.8 3.5 - - + +
319D TRP* 3.6 31.0 - - + -
329D TYR* 3.8 22.9 - - + +
331D ALA* 4.9 2.7 - - + -
399D MET* 4.1 9.9 - - + -
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Residues in contact with GLN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C HIS* 2.8 49.0 + - + +
352C ALA* 4.0 4.3 - - - +
354C VAL* 1.3 73.5 - - - +
356C THR* 1.3 53.4 + - - +
358C VAL* 3.2 9.4 + - - +
359C HIS* 2.7 34.1 + - - +
366C VAL* 4.0 10.5 - - + +
367C GLY 2.8 30.6 + - - +
368C LYS* 3.6 16.4 + - - -
369C ALA* 3.9 6.1 - - - +
407C ARG 4.7 5.0 - - - +
310D LEU* 4.7 7.2 - - + -
333D GLU* 3.9 21.5 + - - +
334D CYS 5.3 2.0 + - - -
373D PRO* 5.7 1.7 - - - +
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Residues in contact with THR 356 (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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256B GLU* 4.8 1.8 - - - +
338C CYS 4.4 8.5 + - - +
340C PHE* 3.9 42.0 - - + +
342C LEU* 3.5 19.9 - - + +
352C ALA 2.7 23.3 + - - -
353C ILE* 3.6 5.8 - - - -
354C VAL 3.2 0.2 - - - -
355C GLN* 1.3 76.2 - - - +
357C LEU* 1.3 62.0 + - - +
359C HIS* 3.3 9.6 + - + +
360C LEU* 3.1 23.8 + - + +
368C LYS* 5.1 6.5 - - + +
369C ALA* 4.2 12.1 + - - +
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Residues in contact with LEU 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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256B GLU* 4.0 13.5 - - + +
340C PHE* 3.5 35.2 - - + -
353C ILE* 3.1 14.1 + - + +
354C VAL 3.1 7.7 + - - +
356C THR* 1.3 74.8 - - - +
358C VAL* 1.3 64.3 + - - +
360C LEU* 3.2 15.4 + - + +
361C LYS* 3.2 19.2 + - - +
317D ILE* 4.0 27.4 - - + +
319D TRP* 3.4 48.2 - - + +
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Residues in contact with VAL 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C VAL* 2.8 20.5 + - + +
355C GLN* 3.4 10.5 - - - +
357C LEU* 1.3 74.3 - - - +
359C HIS* 1.3 54.1 + - - +
361C LYS* 3.0 5.5 + - - +
362C PHE* 2.7 45.7 + - + -
366C VAL* 3.7 31.0 - - + -
310D LEU* 4.3 9.6 - - + -
311D ARG 5.9 0.7 - - - +
312D VAL* 3.8 36.6 - - + -
317D ILE* 4.0 13.7 - - + -
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Residues in contact with HIS 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLN 2.7 20.5 + - - +
356C THR* 3.4 9.2 - - + +
358C VAL* 1.3 74.4 - - - +
360C LEU* 1.3 66.4 + - + +
362C PHE 4.2 0.4 - - - -
363C PRO* 2.9 55.3 - - + +
366C VAL* 2.7 32.6 + - - +
367C GLY* 3.5 13.9 - - - +
368C LYS* 3.9 32.9 - - + +
502C ZN 2.4 36.3 - - - -
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Residues in contact with LEU 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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340C PHE* 3.7 49.4 - - + -
356C THR* 3.1 15.0 + - + +
357C LEU* 3.4 17.7 - - + +
358C VAL 3.2 0.4 - - - -
359C HIS* 1.3 86.9 - - + +
361C LYS* 1.3 61.6 + - - +
363C PRO* 3.9 7.4 - - - +
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Residues in contact with LYS 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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357C LEU 3.2 8.1 + - - +
358C VAL* 3.0 10.4 + - - +
360C LEU* 1.3 82.1 - - - +
362C PHE* 1.3 95.8 + - + +
363C PRO* 3.4 7.5 - - - +
316D ASP* 3.8 36.8 + - + +
317D ILE* 5.1 3.6 - - + -
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Residues in contact with PHE 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 VAL* 2.7 28.2 + - + +
359C HIS 3.3 2.9 - - - -
361C LYS* 1.3 112.2 - - + +
363C PRO* 1.3 60.0 - - - +
364C THR* 3.2 4.5 - - - +
365C LYS* 4.3 25.8 - - + -
366C VAL* 2.9 34.4 + - + +
316D ASP* 4.0 24.5 - - + -
317D ILE* 6.5 0.2 - - + -
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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