Contacts of the helix formed by residues 348 - 367 (chain C) in PDB entry 6S6A
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 ARG 348 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS* 6.1 4.4 - - - +
178B TYR* 3.4 24.9 - - + +
179B GLN* 3.7 45.7 + - - +
184B VAL* 4.0 12.0 - - + +
254C SER 5.9 1.6 - - - +
255C GLY* 5.9 2.2 - - - -
344C GLU* 3.1 49.8 + - - -
345C SER* 3.1 34.2 + - - +
347C GLU* 1.3 80.9 + - - +
349C LYS* 1.3 62.2 + - - +
350C GLY 3.3 2.9 - - - -
351C LEU* 3.2 18.0 + - + +
352C ILE* 3.3 13.3 + - + +
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Residues in contact with LYS 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLN* 5.9 1.3 - - - +
188B GLU* 4.3 1.1 + - - +
189B MET* 6.1 5.8 - - + -
192B ARG* 5.8 3.6 - - - +
315C MET* 4.4 8.2 - - - +
317C ILE* 4.0 14.4 - - - -
327C TYR* 3.2 14.5 + - + +
346C PHE* 3.3 51.3 + - + +
347C GLU 3.2 6.1 + - - +
348C ARG* 1.3 73.4 - - - +
350C GLY* 1.3 60.5 + - - +
352C ILE* 3.2 10.4 + - + +
353C ASP* 2.6 58.7 + - - +
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Residues in contact with GLY 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU* 3.2 24.3 + - - -
216B HIS* 3.4 17.1 + - - -
403B 9JE 3.5 15.5 - - - -
349C LYS* 1.3 73.9 - - - +
351C LEU* 1.3 59.7 + - - +
353C ASP* 3.2 4.4 + - - -
354C TYR* 3.0 26.9 + - - +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER* 3.7 26.5 - - - +
178B TYR* 3.4 26.7 + - + -
179B GLN* 3.7 33.4 - - + +
403B 9JE 3.9 23.1 - - + -
253C ASN 3.6 19.5 - - - +
254C SER* 4.7 6.7 - - - -
348C ARG* 3.2 10.1 + - + +
350C GLY* 1.3 74.0 - - - +
352C ILE* 1.4 63.1 + - + +
354C TYR* 3.5 1.6 + - + +
355C ASN* 3.0 44.9 + - - +
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Residues in contact with ILE 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C PHE* 3.7 11.0 - - + -
254C SER* 3.6 30.1 - - - +
256C ILE* 4.0 20.6 - - + -
327C TYR* 4.1 22.9 - - + -
341C LEU* 3.9 22.4 - - + -
345C SER 3.8 15.7 - - - +
346C PHE* 4.1 11.0 - - + -
348C ARG 3.3 15.4 + - - +
349C LYS* 3.2 16.5 + - + +
350C GLY 3.2 0.8 - - - -
351C LEU* 1.4 77.8 - - + +
353C ASP* 1.3 58.3 + - - +
356C PHE* 2.9 28.0 + - + +
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Residues in contact with ASP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B HIS* 5.1 7.9 - - + +
327C TYR* 2.5 31.5 + - - -
329C LYS* 4.0 12.6 + - - +
349C LYS* 2.6 46.7 + - - +
350C GLY* 3.2 5.3 + - - +
352C ILE* 1.3 75.3 - - - +
354C TYR* 1.3 62.8 + - - +
356C PHE* 3.2 18.3 + - - +
357C HIS* 3.4 20.4 + - + +
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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
----------------------------------------------------------
171B LYS* 3.6 28.3 - - - -
216B HIS* 4.4 6.1 + + - +
218B GLN* 5.5 2.5 - - - -
225B VAL* 3.5 18.1 - - - +
226B HIS* 3.2 13.5 - - - -
227B ARG* 4.3 13.9 - - - -
228B PHE* 3.1 57.3 + + + -
229B GLU* 2.5 30.5 + - - -
403B 9JE 3.8 20.4 - - + -
350C GLY 3.0 16.9 + - - +
351C LEU* 4.0 5.6 - - - +
353C ASP* 1.3 75.2 - - - +
355C ASN* 1.3 62.4 + - - +
357C HIS* 3.4 18.6 + + + +
358C CYS* 3.7 11.1 + - - -
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Residues in contact with ASN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 6.1 1.6 - - - -
171B LYS* 2.8 31.9 + - - +
175B SER* 5.6 0.4 + - - -
250C PHE* 4.0 9.3 + - + -
253C ASN* 3.4 27.0 + - - +
254C SER* 3.2 26.9 + - - +
351C LEU* 3.0 31.5 + - - +
352C ILE 3.9 1.1 - - - +
354C TYR* 1.3 75.7 - - - +
356C PHE* 1.3 63.5 + - - +
357C HIS 3.2 0.2 - - - -
358C CYS* 3.1 12.1 + - + +
359C PHE* 3.0 20.6 + - - +
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Residues in contact with PHE 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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250C PHE* 3.6 14.5 - + + -
329C LYS* 3.4 45.1 - - + -
330C GLU 3.3 26.5 - - - -
331C VAL* 4.1 5.6 - - + -
337C LEU* 3.6 36.6 - - + -
352C ILE* 2.9 15.6 + - + +
353C ASP* 3.3 13.7 - - - +
355C ASN* 1.3 75.5 - - - +
357C HIS* 1.3 66.6 + + - +
359C PHE* 3.1 13.6 + + - +
360C ARG* 2.7 55.0 + - + +
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Residues in contact with HIS 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLN* 3.7 34.0 + - - -
225B VAL* 3.8 19.4 - - + +
227B ARG* 6.4 0.2 - - - +
329C LYS* 5.5 5.9 + - - -
353C ASP* 3.4 24.3 + - + +
354C TYR* 3.7 11.0 - + + +
355C ASN 3.2 0.6 - - - -
356C PHE* 1.3 95.9 - + - +
358C CYS* 1.3 63.4 + - - +
360C ARG* 3.9 17.4 + - - +
361C LYS* 3.1 25.1 + - - +
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Residues in contact with CYS 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LYS* 4.7 16.8 - - - -
225B VAL* 3.4 41.1 - - + -
226B HIS* 4.5 12.3 - - + -
354C TYR* 3.7 11.1 + - - -
355C ASN* 3.1 13.2 + - - +
357C HIS* 1.3 75.4 - - - +
359C PHE* 1.3 65.0 + - - +
361C LYS* 3.3 2.6 + - - +
362C ALA* 3.0 24.1 + - - +
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Residues in contact with PHE 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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243C LEU 5.0 0.2 - - - -
246C LEU* 4.0 25.1 - - + +
247C LEU* 3.6 38.8 - - + -
250C PHE* 4.1 22.7 - + + -
261C LEU* 4.1 11.0 - - + -
331C VAL* 4.2 16.2 - - + -
337C LEU* 4.1 16.6 - - + -
355C ASN 3.0 11.8 + - - +
356C PHE* 3.1 20.6 + + - +
358C CYS* 1.3 75.0 - - - +
360C ARG* 1.3 62.4 + - - +
362C ALA* 3.2 8.9 + - - +
363C ILE* 2.9 61.7 + - + +
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Residues in contact with ARG 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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221B GLU* 4.2 19.1 + - - -
312C LYS* 5.0 13.9 + - - +
330C GLU* 3.1 41.8 + - - -
331C VAL* 2.8 33.0 + - - +
332C THR* 5.3 0.2 - - - +
356C PHE* 2.7 38.5 + - + +
357C HIS* 3.9 20.3 + - - +
358C CYS 3.2 0.2 - - - -
359C PHE* 1.3 79.4 - - - +
361C LYS* 1.3 64.2 + - - +
363C ILE* 3.1 2.8 + - - +
364C HIS* 3.0 46.1 + - - +
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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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223B ARG 4.4 15.0 + - - -
224B ASP* 5.6 1.8 + - - +
225B VAL* 3.9 32.5 - - + +
226B HIS* 5.2 7.0 + - - +
357C HIS 3.1 17.6 + - - +
358C CYS 3.9 2.7 - - - +
360C ARG* 1.3 75.6 - - - +
362C ALA* 1.3 58.8 + - - +
364C HIS* 3.2 13.7 + - + +
365C GLU* 3.0 49.8 + - + +
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Residues in contact with ALA 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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142B LYS* 6.2 0.2 - - - +
246C LEU* 3.9 28.3 - - + -
358C CYS 3.0 13.5 + - - +
359C PHE* 3.3 12.8 - - - +
361C LYS* 1.3 74.9 - - - +
363C ILE* 1.3 63.6 + - - +
365C GLU* 3.4 14.7 + - - +
366C VAL* 3.1 25.3 + - - +
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Residues in contact with ILE 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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243C LEU* 3.5 26.9 - - + -
246C LEU* 4.1 14.1 - - + -
261C LEU* 4.5 7.0 - - + -
331C VAL* 3.6 19.7 - - + -
332C THR* 4.7 8.3 - - + -
335C LEU* 4.8 4.9 - - + -
359C PHE* 2.9 57.7 + - + +
360C ARG 3.1 7.2 + - - +
362C ALA* 1.3 72.4 - - - +
364C HIS* 1.3 66.8 + - - +
366C VAL* 3.3 4.3 + - - +
367C PHE* 3.2 43.3 + - + -
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Residues in contact with HIS 364 (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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331C VAL 2.7 22.5 + - - -
332C THR* 3.4 26.1 - - + +
360C ARG* 3.0 51.4 + - + -
361C LYS* 3.2 14.5 + - - +
363C ILE* 1.3 78.2 - - + +
365C GLU* 1.3 55.1 + - + +
367C PHE* 3.1 3.1 + - - -
368C GLU 3.1 7.6 + - - -
369C VAL* 2.8 55.0 + - + +
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Residues in contact with GLU 365 (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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361C LYS* 3.0 47.3 + - + +
362C ALA* 3.7 15.2 - - - +
363C ILE 3.3 0.2 - - - -
364C HIS* 1.3 74.0 - - + +
366C VAL* 1.3 65.8 + - - +
368C GLU* 3.2 18.2 + - - +
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Residues in contact with VAL 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLN* 3.7 41.0 + - + +
242C THR* 3.4 28.3 - - + -
243C LEU* 4.2 16.8 - - + -
246C LEU* 4.0 11.2 - - + -
362C ALA 3.1 19.9 + - - +
363C ILE* 3.6 9.4 - - - +
364C HIS 3.3 0.4 - - - -
365C GLU* 1.3 76.4 - - - +
367C PHE* 1.3 66.2 + - + +
368C GLU* 3.2 10.6 + - - +
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Residues in contact with PHE 367 (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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60C SER* 6.2 3.8 - - - -
109C PHE* 3.6 34.8 - + - -
237C ILE* 5.2 1.6 - - + -
239C GLN* 4.3 22.9 - - + -
243C LEU* 4.0 38.1 - - + -
261C LEU* 5.1 0.2 - - + -
270C ILE* 4.1 2.9 - - + -
332C THR* 5.7 2.9 - - + -
335C LEU* 3.8 22.2 - - + -
363C ILE* 3.2 28.1 + - + +
364C HIS 3.1 3.2 + - - -
366C VAL* 1.3 81.7 - - + +
368C GLU* 1.3 71.7 + - - +
369C VAL* 3.0 23.9 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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