Contacts of the helix formed by residues 356 - 373 (chain C) in PDB entry 3RIK
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 SER 356 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C TYR* 4.4 1.5 - - - +
353C ARG* 3.3 27.3 + - - -
354C LEU 3.5 0.4 - - - -
355C GLY* 1.3 73.2 - - - +
357C TRP* 1.3 63.5 + - - +
359C ARG* 3.1 32.4 + - - +
360C GLY 3.5 10.6 + - - -
414C GLN* 4.2 0.4 + - - -
415C PRO* 3.5 13.1 - - - +
416C MET* 5.0 2.6 + - - +
501C SO4 2.7 33.8 + - - -
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Residues in contact with TRP 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C SER* 3.1 19.7 + - - +
13C SER* 4.0 10.1 - - - -
42C SER* 3.5 16.2 - - - -
43C THR 3.3 32.3 - - - -
44C ARG* 3.5 44.2 - - + +
48C ARG* 3.6 14.8 - - - -
355C GLY 3.2 3.6 + - - -
356C SER* 1.3 72.8 - - - +
358C ASP* 1.3 62.6 + - - +
360C GLY* 3.0 12.8 + - - -
361C MET* 3.0 42.6 + - + +
415C PRO* 3.8 12.8 - - + -
418C TYR* 6.1 0.7 - - + -
419C HIS* 3.2 36.8 - + - -
487C TYR* 3.6 25.6 - + + +
488C SER* 4.0 3.6 - - - +
489C ILE* 4.4 0.2 - - + -
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Residues in contact with ASP 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C LYS* 4.4 8.0 + - - -
349C GLU* 5.5 3.1 - - - +
356C SER* 4.0 0.4 + - - +
357C TRP* 1.3 77.3 - - - +
359C ARG* 1.3 65.3 + - - +
361C MET* 3.1 23.9 + - + +
362C GLN* 3.0 48.9 + - - +
501C SO4 3.1 28.6 + - - +
242D SER* 5.8 3.1 - - - -
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Residues in contact with ARG 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C VAL 5.9 2.7 - - - -
344C GLY* 5.6 2.0 - - - -
345C SER* 3.5 17.8 - - - +
349C GLU* 3.2 20.4 + - - +
350C GLN 3.2 15.0 + - - -
351C SER 2.7 26.6 + - - -
353C ARG* 3.2 37.3 - - - +
356C SER* 3.1 20.7 + - - +
358C ASP* 1.3 74.7 - - - +
360C GLY* 1.3 65.1 + - - +
362C GLN* 3.0 31.3 + - - +
363C TYR* 3.1 18.8 + - + -
399C ASP* 2.8 40.9 + - - +
416C MET* 4.0 17.5 - - + -
501C SO4 5.1 0.4 - - - +
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Residues in contact with GLY 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C SER 3.5 6.0 + - - -
357C TRP 3.0 9.1 + - - -
359C ARG* 1.3 77.8 - - - +
361C MET* 1.3 62.3 + - - +
363C TYR* 3.0 12.3 + - - +
364C SER 3.2 9.9 + - - -
415C PRO 4.2 0.7 - - - -
416C MET* 3.9 21.5 - - - +
419C HIS* 3.2 32.3 + - - +
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Residues in contact with MET 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C TRP* 3.0 46.3 + - + +
358C ASP* 3.1 28.5 + - + +
360C GLY* 1.3 75.8 - - - +
362C GLN* 1.3 57.5 + - + +
364C SER* 3.5 7.8 + - - -
365C HIS* 3.0 33.3 + - - +
419C HIS* 3.9 7.6 - - + -
461C LEU* 4.0 5.6 - - + +
462C ASN 4.5 3.1 - - - +
463C ARG* 3.7 36.8 - - + +
487C TYR* 4.0 26.7 - - + -
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Residues in contact with GLN 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C VAL* 4.2 30.9 - - + +
344C GLY 5.1 5.8 + - - +
346C LYS* 4.1 18.0 + - - +
349C GLU* 5.9 0.4 + - - -
358C ASP* 3.0 38.0 + - - +
359C ARG* 3.0 29.0 + - + +
361C MET* 1.3 78.1 - - - +
363C TYR* 1.3 58.1 + - + +
365C HIS* 3.8 4.6 + - - +
366C SER* 2.9 33.0 + - - -
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Residues in contact with TYR 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C TRP* 3.7 16.2 - + - -
341C ALA* 3.3 19.4 + - + -
342C CYS* 3.2 28.5 + - - +
343C VAL* 4.6 7.4 - - + -
359C ARG* 3.1 18.1 + - + -
360C GLY* 3.0 10.5 + - - +
362C GLN* 1.3 77.1 - - + +
364C SER* 1.3 58.0 + - - +
366C SER* 3.2 3.5 + - - -
367C ILE* 2.9 37.1 + - + +
380C ASP* 2.4 35.2 + - + -
399C ASP 5.2 4.2 + - - -
401C PRO* 4.9 2.2 - - + +
416C MET* 3.5 32.8 - - + +
419C HIS* 4.5 8.1 - - + -
420C LEU* 3.6 33.4 - - + -
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Residues in contact with SER 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C GLY 3.2 3.1 + - - -
361C MET 3.5 4.5 + - - -
363C TYR* 1.3 78.2 - - - +
365C HIS* 1.3 54.9 + - - +
367C ILE* 3.2 2.5 + - - +
368C ILE* 2.8 39.9 + - - +
419C HIS* 2.7 27.5 + - - -
423C PHE* 3.5 18.1 - - - -
461C LEU* 3.6 15.2 - - - +
489C ILE* 3.5 27.4 - - - -
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Residues in contact with HIS 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C MET 3.0 19.8 + - - +
362C GLN* 3.8 5.5 + - - +
364C SER* 1.3 77.8 - - - +
366C SER* 1.3 57.7 + - - +
368C ILE* 3.8 3.7 - - + +
369C THR* 2.9 49.9 + - - -
445C ASP* 3.5 18.8 + - + -
461C LEU* 3.7 11.3 - - + +
463C ARG* 3.3 47.7 + - - -
506C SO4 5.0 8.5 - - - -
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Residues in contact with SER 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C TRP* 3.0 43.5 + - - +
315C ASP* 4.3 5.9 + - - -
343C VAL* 5.2 3.6 - - - +
362C GLN 2.9 19.0 + - - -
363C TYR 3.4 4.5 - - - -
365C HIS* 1.3 82.3 + - - +
367C ILE* 1.3 55.9 + - - +
369C THR* 3.9 4.5 - - - -
370C ASN* 3.0 36.6 + - - -
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Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PHE* 4.3 15.5 - - + -
312C TRP* 3.5 21.1 - - + -
363C TYR* 2.9 30.3 + - + +
364C SER* 3.6 4.5 - - - +
366C SER* 1.3 70.4 - - - +
368C ILE* 1.3 62.2 + - - +
370C ASN* 3.2 2.9 + - - +
371C LEU* 2.8 38.7 + - + +
378C TRP* 4.2 16.6 - - + +
419C HIS 4.5 3.4 - - - +
420C LEU* 4.3 24.0 - - + -
423C PHE* 3.5 46.9 - - + -
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Residues in contact with ILE 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C SER 2.8 25.1 + - - +
365C HIS* 3.8 4.3 - - + +
367C ILE* 1.3 72.9 - - - +
369C THR* 1.3 64.5 + - - +
371C LEU* 3.0 9.6 + - - +
372C LEU* 2.9 34.1 + - + +
423C PHE* 3.6 22.7 - - + -
445C ASP* 3.7 37.7 - - + +
446C ALA* 3.8 29.4 - - - +
447C VAL* 4.2 8.7 - - + -
459C VAL* 4.7 5.6 - - + +
461C LEU* 3.8 19.1 - - + +
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Residues in contact with THR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 4.9 3.1 - - - +
320C ALA* 3.9 19.7 - - + -
365C HIS* 2.9 38.9 + - - -
366C SER* 3.9 5.6 - - - -
368C ILE* 1.3 75.7 - - - +
370C ASN* 1.3 65.8 + - - +
372C LEU* 3.4 8.7 + - - +
373C TYR* 3.1 37.1 + - + +
506C SO4 3.6 21.9 + - - +
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Residues in contact with ASN 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 4.3 10.5 - - - +
310C VAL* 5.3 2.7 - - - +
312C TRP* 2.8 29.1 + - - +
315C ASP* 5.1 0.2 + - - -
324C LEU* 3.6 21.6 - - - +
338C ALA* 3.7 7.1 - - - +
366C SER* 3.0 23.2 + - - +
367C ILE 3.5 0.2 - - - +
369C THR* 1.3 75.1 - - - +
371C LEU* 1.3 65.8 + - - +
373C TYR 2.8 12.3 + - - -
375C VAL* 3.2 31.9 + - + +
378C TRP* 2.9 29.3 + - + +
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Residues in contact with LEU 371 (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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76C GLN* 2.9 36.0 + - - +
78C VAL* 4.5 7.4 - - + -
81C PHE* 5.3 1.3 - - + -
367C ILE* 2.8 34.8 + - + +
368C ILE 3.0 7.2 + - - +
370C ASN* 1.3 74.9 - - - +
372C LEU* 1.3 61.4 + - - +
373C TYR 3.0 0.5 + - - -
374C HIS 3.1 2.8 + - - -
375C VAL 4.1 0.7 - - - +
378C TRP* 3.5 29.4 - - + -
423C PHE* 4.3 7.6 - - + -
427C ILE* 4.9 3.4 - - + -
433C ARG* 3.4 14.0 + - + -
447C VAL* 3.9 35.0 - - + -
449C LEU* 4.5 24.5 - - + -
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C ILE* 2.9 37.3 + - + +
369C THR* 3.9 7.6 - - - +
371C LEU* 1.3 70.8 - - - +
373C TYR* 1.3 76.7 + - + +
374C HIS* 3.5 7.3 + - - -
433C ARG* 3.6 39.6 + - - +
446C ALA 4.1 12.1 - - - +
447C VAL* 4.1 15.7 - - + -
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Residues in contact with TYR 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ALA* 3.8 22.2 - - + -
321C LYS* 3.8 38.1 - - + +
324C LEU* 3.7 20.1 - - + +
325C GLY* 3.8 22.9 - - - +
336C LEU* 3.7 13.3 - - - +
369C THR* 3.1 29.3 + - + +
370C ASN 2.8 10.2 + - - +
372C LEU* 1.3 92.6 - - + +
374C HIS* 1.3 73.4 + + - +
375C VAL* 3.1 8.1 + - - +
506C SO4 4.8 5.0 + - - -
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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