Contacts of the helix formed by residues 333 - 342 (chain C) in PDB entry 5FI2
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 VAL 333 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C LYS* 3.8 2.7 - - - -
320C LEU 6.0 0.9 - - - +
321C PHE 5.3 1.6 - - - +
329C HIS* 4.6 17.5 - - + +
330C ASN* 3.6 33.7 - - - +
332C MET* 1.3 80.9 - - - +
334C ASN* 1.3 54.5 + - - +
335C ALA* 3.8 9.2 - - + +
336C GLY 3.0 18.2 + - - +
337C ALA* 2.7 34.1 + - - +
462C CYS 5.7 1.8 - - - +
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Residues in contact with ASN 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C SER* 4.3 2.4 + - - -
288C LYS* 3.1 26.9 + - - +
333C VAL* 1.3 74.0 - - - +
335C ALA* 1.3 57.8 + - - +
337C ALA* 3.7 0.3 - - - +
338C ILE* 2.8 37.0 + - + +
386C ARG* 4.4 18.6 - - - +
387C ASN* 4.0 14.4 + - - +
390C ILE* 4.0 14.8 - - + +
413C TYR* 3.2 14.3 + - - +
465C TYR* 6.0 1.6 - - - -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C PHE* 3.6 35.4 - - + +
328C PRO* 3.7 7.0 - - + -
333C VAL* 3.2 6.8 - - + +
334C ASN* 1.3 78.2 - - - +
336C GLY* 1.3 61.4 + - - +
338C ILE* 3.6 2.1 + - - +
339C VAL* 3.2 29.3 + - - +
390C ILE* 3.7 32.3 - - + +
394C LEU* 4.0 3.6 - - + +
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Residues in contact with GLY 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C VAL* 3.7 4.9 - - - +
328C PRO* 3.4 13.7 - - - +
330C ASN 3.2 26.0 - - - -
331C PRO* 4.1 4.5 - - - -
333C VAL* 3.0 8.5 + - - +
335C ALA* 1.3 76.9 - - - +
337C ALA* 1.3 58.6 + - - +
339C VAL* 3.2 4.2 + - - +
340C VAL* 2.9 31.7 + - - +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LYS* 3.3 36.8 - - + -
291C LYS* 3.7 9.0 - - - +
331C PRO 3.6 7.7 + - - +
333C VAL 2.7 19.4 + - - +
334C ASN 3.7 2.7 - - - +
336C GLY* 1.3 70.6 - - - +
338C ILE* 1.3 55.3 + - - +
340C VAL* 3.2 4.4 + - - +
341C THR* 2.6 39.2 + - - -
413C TYR* 3.8 11.4 - - + -
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Residues in contact with ILE 338 (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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334C ASN 2.8 23.0 + - - +
335C ALA 3.8 3.6 - - - +
337C ALA* 1.3 75.1 - - - +
339C VAL* 1.3 62.8 + - - +
341C THR* 3.4 9.3 - - - -
342C SER* 3.3 16.8 + - - -
387C ASN* 4.0 23.3 - - + +
390C ILE* 3.9 20.0 - - + -
391C GLY* 5.0 1.8 - - - +
394C LEU* 3.6 20.2 - - + -
400C PHE* 3.9 13.5 - - + -
409C ILE* 3.7 13.8 - - + +
410C LEU* 3.8 27.1 - - + -
413C TYR* 3.6 24.2 - - + -
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Residues in contact with VAL 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 3.7 39.7 - - + +
308C VAL* 4.7 3.8 - - + -
328C PRO* 3.6 18.8 - - + -
335C ALA 3.2 16.5 + - - +
336C GLY* 3.2 7.4 + - - +
338C ILE* 1.3 75.9 - - - +
340C VAL* 1.3 62.0 + - - +
342C SER* 2.6 28.4 + - - +
343C LEU* 3.3 8.4 - - + +
394C LEU* 3.7 21.3 - - + -
399C CYS* 4.0 14.4 - - + +
400C PHE* 4.1 8.3 - - + -
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Residues in contact with VAL 340 (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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288C LYS 5.3 0.2 - - - +
291C LYS* 3.8 20.9 - - + +
292C TYR* 3.8 48.7 - - + +
295C ALA* 4.3 5.6 - - + -
304C VAL* 4.7 1.8 - - + -
308C VAL* 4.3 18.4 - - + -
331C PRO* 4.3 8.1 - - + +
336C GLY 2.9 18.5 + - - +
337C ALA* 3.2 6.3 + - - +
339C VAL* 1.3 75.0 - - - +
341C THR* 1.3 63.9 + - - +
343C LEU* 3.0 31.0 + - + +
344C ILE* 3.6 9.1 - - + +
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Residues in contact with THR 341 (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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291C LYS* 3.4 20.4 + - - +
337C ALA 2.6 22.6 + - - -
338C ILE* 3.4 10.1 - - - -
340C VAL* 1.3 78.8 - - - +
342C SER* 1.3 58.8 + - - +
343C LEU 3.4 0.7 + - - -
344C ILE* 3.7 15.7 + - - +
353C LYS* 5.4 0.5 + - - -
409C ILE* 4.0 11.5 - - + +
412C PHE* 3.5 37.8 - - + -
413C TYR* 3.6 20.0 - - - +
416C LEU* 3.6 14.4 - - + -
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Residues in contact with SER 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 ILE 3.3 5.2 + - - -
339C VAL* 2.6 20.3 + - - +
341C THR* 1.3 78.0 - - - +
343C LEU* 1.3 60.1 + - - +
344C ILE 3.4 1.3 - - - +
346C GLN* 3.6 18.0 - - - +
353C LYS* 5.2 2.4 + - - -
400C PHE* 3.4 27.3 - - - -
401C PRO* 3.3 25.0 - - - +
404C THR* 4.5 4.8 + - - -
409C ILE* 3.8 26.1 - - - +
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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