Contacts of the helix formed by residues 349 - 365 (chain C) in PDB entry 5FI6
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 349 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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348C VAL* 1.3 79.9 - - - +
350C ASN* 1.3 61.7 + - - +
351C ALA* 3.4 11.9 + - - +
352C GLU* 3.1 35.8 + - - +
353C LYS* 2.9 25.5 + - - +
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Residues in contact with ASN 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C VAL 5.0 0.2 - - - +
349C ASN* 1.3 73.1 - - - +
351C ALA* 1.3 64.7 + - - +
352C GLU 3.3 0.2 - - - -
353C LYS* 4.0 20.1 + - - +
354C PHE* 3.0 26.8 + - - +
408C GLY* 3.0 33.2 + - - +
409C ILE* 5.4 0.5 - - - +
411C ASP* 4.1 8.3 + - - +
412C PHE* 3.5 27.3 - - + +
415C GLN* 4.3 17.0 - - - +
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Residues in contact with ALA 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ASN* 3.2 14.8 + - - +
350C ASN* 1.3 78.7 - - - +
352C GLU* 1.3 60.2 + - + +
354C PHE* 3.7 3.4 - - - +
355C ASP* 3.1 35.4 + - - +
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Residues in contact with GLU 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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345C LYS* 5.3 0.9 - - + -
348C VAL* 3.5 32.3 - - + +
349C ASN* 3.1 22.8 + - - +
351C ALA* 1.3 76.7 - - + +
353C LYS* 1.3 55.3 + - - +
354C PHE 3.1 1.6 - - - -
355C ASP* 3.1 7.8 + - - +
356C TYR* 2.7 38.1 + - - +
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Residues in contact with LYS 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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342C SER 5.4 2.8 + - - -
344C ILE* 3.7 12.3 + - - +
345C LYS* 3.1 45.9 - - + +
346C GLN* 4.2 8.9 - - - +
347C GLY 4.3 2.3 - - - +
348C VAL* 3.2 20.2 + - + +
349C ASN 2.9 14.7 + - - +
350C ASN* 4.0 15.8 + - - +
352C GLU* 1.3 74.8 - - - +
354C PHE* 1.3 63.8 + - - +
356C TYR* 3.2 3.7 + - - +
357C VAL* 3.0 20.6 + - - +
409C ILE* 3.8 23.8 - - - +
412C PHE* 3.5 34.2 - - + -
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Residues in contact with PHE 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ASN 3.0 22.3 + - - +
351C ALA* 3.7 4.3 - - - +
353C LYS* 1.3 75.2 - - - +
355C ASP* 1.3 73.9 + - - +
357C VAL* 2.9 6.2 + - - +
358C MET* 2.8 51.5 + - + +
372C PHE* 3.8 30.1 - + + -
412C PHE* 3.7 9.3 - + + -
415C GLN* 3.8 38.4 - - + +
416C LEU* 4.2 11.0 - - + -
419C ILE* 3.8 21.5 - - + -
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Residues in contact with ASP 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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351C ALA* 3.1 23.0 + - - +
352C GLU* 3.7 7.2 - - - +
354C PHE* 1.3 88.3 - - - +
356C TYR* 1.3 63.6 + - - +
358C MET* 3.8 7.6 - - - +
359C GLN* 3.0 26.7 + - - +
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Residues in contact with TYR 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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294C ILE* 4.0 13.5 - - + -
298C ASP* 2.6 41.5 + - - -
344C ILE* 4.0 16.8 - - + -
345C LYS* 3.4 45.1 - - + -
352C GLU 2.7 20.5 + - - +
353C LYS 3.4 5.2 - - - +
355C ASP* 1.3 73.3 - - - +
357C VAL* 1.3 64.9 + - + +
359C GLN* 3.4 24.1 + - - +
360C PHE* 3.3 40.2 + + - +
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Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 5.6 2.5 - - + -
291C LYS* 5.4 4.0 - - + -
294C ILE* 4.0 23.6 - - + -
344C ILE* 3.9 31.4 - - + -
353C LYS 3.0 14.7 + - - +
354C PHE 2.9 7.6 + - - +
356C TYR* 1.3 74.4 - - + +
358C MET* 1.3 60.8 + - - +
360C PHE* 2.9 5.2 + - - +
361C LEU* 2.8 46.6 + - + +
412C PHE* 4.2 10.8 - - + -
416C LEU* 3.8 26.0 - - + -
419C ILE* 4.6 1.3 - - + -
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Residues in contact with MET 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C PHE* 2.8 50.2 + - + +
355C ASP* 3.8 9.0 - - - +
357C VAL* 1.3 72.0 - - - +
359C GLN* 1.3 52.7 + - - +
361C LEU* 2.9 6.1 + - - +
362C ASN* 2.6 52.1 + - - +
370C VAL* 3.5 44.9 - - + +
371C GLY 4.1 9.0 - - - +
372C PHE* 5.6 0.4 - - - -
419C ILE* 3.8 23.8 - - + -
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Residues in contact with GLN 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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355C ASP 3.0 16.2 + - - +
356C TYR* 3.7 28.3 + - - +
358C MET* 1.3 77.0 - - - +
360C PHE* 1.3 71.9 + - + +
362C ASN* 3.4 10.8 + - - +
363C LYS* 3.2 49.2 + - - +
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Residues in contact with PHE 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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294C ILE* 3.6 41.7 - - + -
297C ASN* 4.1 16.2 - - - -
298C ASP* 4.0 11.4 - - - -
356C TYR* 3.3 41.5 + + - +
357C VAL 2.9 8.8 + - - +
359C GLN* 1.3 88.6 - - + +
361C LEU* 1.3 65.3 + - - +
363C LYS* 3.3 21.7 + - + +
364C MET* 3.0 31.3 + - + +
446C VAL* 4.1 17.7 - - + +
447C LEU* 4.9 5.8 - - + -
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Residues in contact with LEU 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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283C LEU* 4.8 3.4 - - + -
287C VAL* 4.5 9.4 - - + -
290C LEU* 3.9 27.4 - - + -
294C ILE* 4.5 3.6 - - + -
357C VAL* 2.8 35.4 + - + +
358C MET* 3.5 7.6 - - - +
360C PHE* 1.3 73.0 - - - +
362C ASN* 1.3 61.9 + - - +
364C MET* 3.5 26.1 + - + +
365C ALA* 3.2 18.4 + - - +
370C VAL* 3.7 16.3 - - + +
419C ILE* 3.5 43.1 - - + -
429C MET* 3.5 16.4 - - + +
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Residues in contact with ASN 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 MET* 2.6 41.3 + - - +
359C GLN* 3.7 9.3 - - - +
360C PHE 3.2 0.2 - - - -
361C LEU* 1.3 71.6 - - - +
363C LYS* 1.3 65.5 + - + +
365C ALA 3.3 5.2 + - - -
367C ASN* 2.8 45.5 + - - +
368C GLU 4.2 6.1 + - - -
370C VAL* 3.6 28.1 + - - +
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Residues in contact with LYS 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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359C GLN* 3.2 41.9 + - - +
360C PHE* 3.3 21.3 + - + +
362C ASN* 1.3 76.1 - - + +
364C MET* 1.3 62.5 + - - +
366C GLY* 3.3 10.0 + - - -
367C ASN* 4.6 7.4 + - - +
439C CYS* 3.5 17.8 - - - +
442C THR* 4.9 1.6 + - - +
444C GLU* 3.1 35.4 + - - +
445C ARG 5.6 0.7 - - - +
446C VAL* 3.6 22.5 - - + +
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Residues in contact with MET 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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290C LEU* 4.1 35.7 - - + +
294C ILE* 4.7 8.3 - - + -
360C PHE* 3.0 17.9 + - + +
361C LEU* 3.5 34.5 - - + +
363C LYS* 1.3 76.4 - - - +
365C ALA* 1.3 56.9 + - - +
366C GLY 3.4 3.1 + - - -
428C VAL* 3.3 11.8 - - - +
429C MET* 4.1 21.8 - - + +
432C THR* 2.7 30.2 + - + +
433C LEU* 5.2 2.0 - - - -
439C CYS* 3.6 0.7 - - - -
446C VAL* 3.4 25.6 - - + -
447C LEU* 3.8 24.0 - - + -
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Residues in contact with ALA 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 LEU 3.2 15.8 + - - +
362C ASN 3.3 2.2 + - - +
364C MET* 1.3 76.0 - - - +
366C GLY* 1.3 60.7 + - - +
367C ASN 3.0 3.6 - - - -
368C GLU* 2.9 28.5 + - - +
370C VAL* 4.1 9.9 - - + -
425C SER* 3.5 22.0 - - - +
428C VAL* 3.4 16.0 - - - +
429C MET* 3.6 16.8 - - + -
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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