Contacts of the helix formed by residues 335 - 356 (chain C) in PDB entry 4RQE
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 ASN 335 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C HIS* 5.5 4.6 + - - -
334C ASP* 1.3 81.8 - - - +
336C LYS* 1.3 54.7 + - - +
337C SER 3.0 6.3 - - - +
338C TRP* 2.9 47.8 + - + +
339C GLU* 2.9 25.6 + - + +
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Residues in contact with LYS 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C SER* 5.3 2.0 - - - -
331C SER* 4.6 14.8 - - - +
333C HIS* 3.8 11.3 + - + +
334C ASP* 3.2 37.5 + - + +
335C ASN* 1.3 76.8 - - - +
337C SER* 1.3 57.1 + - - +
339C GLU* 3.7 24.3 - - - +
340C MET* 2.9 30.5 + - - +
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C SER* 3.9 22.2 - - - -
331C SER 3.9 13.2 + - - -
332C PRO 4.7 1.4 + - - -
333C HIS 4.8 0.4 + - - -
334C ASP 4.5 4.0 + - - -
335C ASN* 4.2 3.6 - - - -
336C LYS* 1.3 78.8 - - - +
338C TRP* 1.3 72.8 + - - +
340C MET* 3.4 4.0 + - - +
341C PHE* 2.9 26.3 + - - +
397C ASN* 4.5 7.7 + - - -
424C HIS* 3.9 28.4 - - - -
426C LEU* 3.9 8.4 - - - +
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Residues in contact with TRP 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C HIS* 3.6 38.8 - + + -
334C ASP 5.3 0.4 - - - -
335C ASN* 2.9 39.0 + - + +
337C SER* 1.3 83.8 + - - +
339C GLU* 1.3 60.7 - - + +
341C PHE* 3.2 17.3 - + - +
342C GLU* 2.9 35.2 + - + +
374C SER* 3.5 29.8 - - - -
375C LYS* 3.8 29.4 - - + -
397C ASN* 3.3 30.7 - - + -
399C THR* 4.7 6.3 - - + -
424C HIS* 5.8 2.5 - + - -
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Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ASP* 5.8 0.9 - - - +
335C ASN* 2.9 26.7 + - + +
336C LYS* 3.8 25.1 - - - +
338C TRP* 1.3 74.9 - - + +
340C MET* 1.3 61.1 + - - +
342C GLU* 3.4 8.9 + - - +
343C GLU* 2.9 28.1 + - - +
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Residues in contact with MET 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C TYR* 6.1 0.4 - - - -
291C PRO* 4.1 31.2 - - + -
293C LYS* 5.3 12.8 - - + -
328C VAL* 3.9 32.5 - - + -
330C SER* 4.8 11.4 - - - +
336C LYS 2.9 21.2 + - - +
337C SER* 3.6 7.0 - - - +
339C GLU* 1.3 73.6 - - - +
341C PHE* 1.3 60.0 + - - +
343C GLU* 3.2 28.7 + - - +
344C MET* 2.9 31.3 + - + +
426C LEU* 5.1 4.3 - - + -
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C SER 2.9 15.0 + - - +
338C TRP* 3.2 26.5 - + + +
340C MET* 1.3 76.1 - - - +
342C GLU* 1.3 80.0 + - - +
344C MET* 3.2 6.6 + - - +
345C ILE* 3.1 24.6 + - + +
375C LYS* 4.2 33.9 - - + -
377C LEU* 3.6 41.7 - - + -
395C CYS* 3.3 33.1 - - + -
396C SER 4.5 0.2 - - - -
397C ASN* 4.2 11.9 - - + +
426C LEU* 3.6 24.2 - - + +
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Residues in contact with GLU 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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338C TRP* 2.9 21.9 + - + +
339C GLU* 3.7 8.1 - - - +
341C PHE* 1.3 91.5 - - + +
343C GLU* 1.3 56.3 + - - +
345C ILE* 3.2 14.7 - - - +
346C THR* 2.3 41.7 + - - +
375C LYS* 4.2 11.8 + - - -
377C LEU* 4.9 4.6 - - - +
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Residues in contact with GLU 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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293C LYS* 4.6 14.4 + - - -
339C GLU 2.9 18.6 + - - +
340C MET* 3.2 32.5 + - - +
342C GLU* 1.3 75.7 - - - +
344C MET* 1.3 51.8 + - - +
346C THR* 3.5 7.2 + - - -
347C THR* 2.5 40.2 + - - +
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Residues in contact with MET 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C TYR* 4.0 8.3 - - - +
326C GLN* 3.6 41.3 + - - +
328C VAL* 3.7 31.0 - - + -
340C MET* 2.9 17.3 + - + +
341C PHE* 3.5 4.5 - - - +
342C GLU 3.2 0.2 - - - -
343C GLU* 1.3 76.2 - - - +
345C ILE* 1.3 60.3 + - - +
346C THR 3.2 0.2 - - - -
347C THR* 3.1 8.9 + - - -
348C ALA* 3.0 23.7 + - - +
395C CYS* 3.9 12.6 - - - -
426C LEU* 3.9 32.3 - - + -
427C ASN 4.2 5.6 - - - +
428C ALA* 3.8 20.0 - - + -
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Residues in contact with ILE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C PHE* 3.1 21.2 + - + +
342C GLU* 3.2 33.0 - - - +
344C MET* 1.3 76.5 - - - +
346C THR* 1.3 58.2 - - - +
348C ALA* 3.4 13.3 + - + +
349C GLU* 2.9 39.7 + - + +
361C ILE* 4.6 19.5 - - + -
377C LEU* 4.3 22.9 - - + +
379C LEU* 5.4 5.8 - - + +
393C VAL* 5.1 8.3 - - + -
395C CYS* 4.2 27.7 - - + -
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Residues in contact with THR 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C GLU* 2.3 29.4 + - - +
343C GLU* 3.6 8.6 - - - -
345C ILE* 1.3 78.9 - - - +
347C THR* 1.3 59.9 + - - +
349C GLU* 3.3 17.4 + - + +
350C GLU* 2.8 44.5 + - + +
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Residues in contact with THR 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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214C THR* 6.1 0.7 - - + -
215C LEU* 5.0 0.2 - - + -
218C ARG* 4.0 38.0 + - + +
220C TYR* 4.5 11.1 + - + +
326C GLN* 4.0 14.6 - - - +
343C GLU* 2.5 27.6 + - - +
344C MET* 3.1 10.9 + - - -
346C THR* 1.3 78.5 - - - +
348C ALA* 1.3 56.0 + - - +
350C GLU* 3.4 12.9 + - - +
351C PHE* 2.9 27.3 + - - +
430C MET* 4.6 7.6 - - + -
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Residues in contact with ALA 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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326C GLN* 4.3 13.9 - - - +
344C MET 3.0 12.3 + - - +
345C ILE* 3.7 20.0 - - + +
346C THR 3.3 0.2 - - - -
347C THR* 1.3 73.1 - - - +
349C GLU* 1.3 61.0 + - - +
351C PHE* 3.2 8.5 + - - +
352C TYR* 3.0 39.6 + - + +
379C LEU* 5.1 4.0 - - + +
393C VAL* 4.7 15.0 - - + -
429C THR 5.2 1.3 - - - +
430C MET* 4.7 8.7 - - - -
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Residues in contact with GLU 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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157C SER* 4.5 8.5 - - - -
345C ILE* 2.9 22.2 + - + +
346C THR* 3.5 26.2 + - + +
348C ALA* 1.3 75.3 - - - +
350C GLU* 1.3 64.4 - - + +
352C TYR 4.0 0.2 - - - -
353C GLN* 3.1 34.9 + - - +
359C TYR* 3.4 26.2 + - + +
361C ILE* 3.4 38.1 - - + +
379C LEU* 5.0 3.4 - - + -
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Residues in contact with GLU 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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218C ARG* 3.9 34.5 + - - +
346C THR* 2.8 31.7 + - + +
347C THR* 3.4 14.1 + - - +
349C GLU* 1.3 77.0 - - + +
351C PHE* 1.3 55.9 + - - +
353C GLN* 4.2 9.7 - - - +
354C SER* 3.1 28.2 + - - -
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Residues in contact with PHE 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 5.6 2.0 - - + -
210C TYR* 3.4 28.9 - + - -
211C ALA* 3.9 24.9 - - + -
214C THR* 3.6 25.1 - - + -
218C ARG* 6.1 0.7 - - - +
347C THR 2.9 14.8 + - - +
348C ALA 3.3 9.0 - - - +
349C GLU 3.1 0.2 - - - -
350C GLU* 1.3 76.2 - - - +
352C TYR* 1.3 83.6 + + - +
354C SER* 2.3 26.3 + - - -
355C LEU* 2.9 39.1 + - + +
430C MET* 3.6 40.6 - - + -
431C CYS* 4.5 7.4 - - + -
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Residues in contact with TYR 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 ALA* 3.0 30.6 + - + +
349C GLU 4.6 1.6 - - - +
351C PHE* 1.3 85.3 - + - +
353C GLN* 1.3 60.3 - - - +
355C LEU* 3.5 25.1 - - + +
356C GLY 3.0 17.8 + - - -
357C ILE* 3.1 29.9 + - + +
359C TYR* 4.8 14.8 - - + -
379C LEU* 4.9 12.3 - - + -
392C LEU* 4.6 14.9 + - + +
393C VAL* 3.6 28.2 - - + +
430C MET 3.1 28.5 + - - -
431C CYS* 3.4 8.0 - - - +
432C ALA 4.3 0.5 + - - -
436C THR* 3.2 34.0 - - + +
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Residues in contact with GLN 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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158C ILE 5.1 0.6 + - - -
159C TRP* 3.3 24.2 - - + +
349C GLU* 3.1 23.8 + - - +
350C GLU* 4.2 8.6 - - - +
352C TYR* 1.3 74.9 - - - +
354C SER* 1.3 60.4 + - - +
355C LEU 3.1 0.4 - - - -
356C GLY* 3.0 18.4 + - - +
357C ILE 4.9 1.8 - - - +
359C TYR* 3.0 34.3 + - + -
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Residues in contact with SER 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C TYR* 3.4 23.2 + - - -
214C THR* 5.8 0.3 - - - +
350C GLU 3.1 16.1 + - - -
351C PHE* 2.3 30.7 + - - -
353C GLN* 1.3 76.3 - - - +
355C LEU* 1.3 60.0 + - - +
356C GLY 3.3 0.2 - - - -
455C LYS* 3.6 25.8 - - - +
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Residues in contact with LEU 355 (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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207C LEU* 5.5 11.4 - - + -
210C TYR* 3.8 29.2 - - + -
351C PHE* 2.9 41.3 + - + +
352C TYR* 3.5 32.1 - - + +
353C GLN 3.1 0.4 - - - -
354C SER* 1.3 80.5 + - - +
356C GLY* 1.3 51.1 + - - +
357C ILE* 4.4 10.2 - - + +
436C THR* 5.8 1.1 - - + -
440C ILE* 5.9 7.7 - - + +
444C TYR* 2.5 27.2 + - - -
453C PRO* 4.7 10.4 - - + +
455C LYS* 5.2 8.8 - - + +
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Residues in contact with GLY 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ASP* 5.3 2.2 - - - +
352C TYR 3.0 3.8 + - - -
353C GLN* 3.0 15.2 + - - -
354C SER 4.5 0.2 - - - -
355C LEU* 1.3 79.1 - - - +
357C ILE* 1.3 61.3 + - - +
358C PRO* 4.1 5.8 - - - +
443C ASN* 5.5 1.4 - - - +
444C TYR* 3.1 16.6 + - - -
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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