Contacts of the helix formed by residues 413 - 421 (chain C) in PDB entry 2IHU
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 PHE 413 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL* 4.0 14.9 - - + +
388C ILE* 5.1 1.2 - - - +
408C SER* 3.4 20.9 - - - -
409C ASP* 3.5 21.8 - - + -
410C ILE 3.3 22.4 - - - -
411C GLY* 3.7 1.6 - - - -
412C PHE* 1.3 75.7 - - - +
414C ARG* 1.3 58.6 + - - +
415C HIS 3.2 0.2 - - - -
416C TYR* 3.0 37.0 + - - +
417C GLY 3.4 4.0 + - - -
460C ILE* 3.4 34.3 - - + -
461C ALA* 3.5 8.1 - - - -
462C GLY* 3.2 29.2 - - - -
488C VAL* 3.9 11.9 - - + -
561C TYR* 3.8 10.1 + - - +
600C TP8 3.1 31.6 + - - +
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Residues in contact with ARG 414 (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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251C TYR* 3.9 20.1 + - - -
408C SER* 3.4 16.8 - - - +
409C ASP 3.2 26.0 - - - +
410C ILE* 3.5 16.7 - - - +
411C GLY 3.1 21.2 + - - +
413C PHE* 1.3 77.5 - - + +
415C HIS* 1.3 66.7 + - - +
417C GLY* 3.2 3.8 + - - +
418C VAL* 2.9 44.2 + - + +
431C THR* 3.0 29.2 + - - +
432C SER 2.9 22.0 + - - -
436C SER* 3.2 25.1 + - - -
495C LEU* 6.3 0.2 - - - +
600C TP8 3.9 17.2 + - - -
120D HIS* 4.7 2.2 - - - -
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Residues in contact with HIS 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C TYR* 4.5 9.2 - - - -
269C THR* 2.8 38.7 + - - +
270C GLY 4.9 1.6 - - - -
271C TYR* 3.2 44.3 - + - +
275C ILE* 3.6 18.6 - - + -
411C GLY 4.0 10.1 - - - -
412C PHE* 3.2 21.5 + + - +
413C PHE 3.2 0.2 - - - -
414C ARG* 1.3 85.9 + - - +
416C TYR* 1.3 55.3 + - - +
418C VAL* 3.4 2.7 + - - +
419C LEU* 3.0 37.7 + - - +
495C LEU* 4.6 5.5 - - + +
600C TP8 4.7 12.5 + - - -
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Residues in contact with TYR 416 (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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275C ILE* 3.7 32.6 + - + +
371C PHE* 4.1 4.5 - + - -
384C VAL* 3.6 26.9 - - + -
385C HIS* 3.5 43.1 + - + -
388C ILE* 3.9 9.9 - - + +
412C PHE* 3.7 46.5 - + - -
413C PHE* 3.0 15.5 + - - +
415C HIS* 1.3 76.2 - - - +
417C GLY* 1.3 58.8 + - - +
419C LEU* 5.2 0.2 - - - -
420C PHE* 2.9 55.3 + + + +
421C ALA 3.7 0.5 + - - -
561C TYR* 5.6 0.9 - - - -
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Residues in contact with GLY 417 (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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254C LYS* 3.8 2.4 - - - -
388C ILE* 3.9 13.0 - - - +
408C SER* 5.1 3.8 - - - -
413C PHE 3.4 5.2 + - - -
414C ARG* 3.2 7.9 + - - -
416C TYR* 1.3 78.7 - - - +
418C VAL* 1.3 61.4 + - - +
421C ALA* 2.9 37.9 + - - +
429C PHE* 3.6 18.3 - - - -
460C ILE* 5.6 0.9 - - - -
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Residues in contact with VAL 418 (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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251C TYR* 3.5 42.4 - - + -
254C LYS* 3.1 26.6 + - - +
267C ALA* 3.6 22.5 + - + +
268C VAL 4.3 1.3 - - - +
269C THR* 3.5 19.1 - - + -
414C ARG* 2.9 41.0 + - - +
415C HIS 3.7 3.8 - - - +
416C TYR 3.4 0.2 - - - -
417C GLY* 1.3 72.3 - - - +
419C LEU* 1.3 59.2 + - - +
429C PHE* 3.7 20.2 - - + -
431C THR* 4.4 0.2 - - + -
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Residues in contact with LEU 419 (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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254C LYS* 4.7 3.4 + - - -
266C GLY* 5.9 1.7 - - - -
267C ALA 3.5 26.9 + - - +
268C VAL* 3.9 0.4 - - - -
269C THR* 3.7 27.1 - - + +
272C MET* 3.7 50.9 - - + +
275C ILE* 4.1 18.8 - - + -
368C ILE* 5.6 3.1 - - - +
415C HIS 3.0 20.0 + - - +
418C VAL* 1.3 77.0 - - - +
420C PHE* 1.3 92.9 + - + +
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Residues in contact with PHE 420 (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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254C LYS* 4.8 0.2 - - - -
272C MET* 5.6 0.4 - - + -
275C ILE* 4.0 6.3 - - + -
276C LEU* 3.6 29.8 - - + -
368C ILE* 3.9 36.3 - - + -
371C PHE* 3.8 22.4 - + - -
372C LEU* 3.6 31.6 - - + +
385C HIS* 4.9 1.1 - - + -
388C ILE* 3.9 5.8 - - + -
392C ASN* 2.8 21.2 + - - -
416C TYR* 2.9 43.3 + + + +
419C LEU* 1.3 105.5 - - + +
421C ALA* 1.3 65.8 + - - +
422C ARG 3.6 0.2 + - - -
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Residues in contact with ALA 421 (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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254C LYS* 2.9 24.0 + - - -
388C ILE* 3.8 9.6 - - + +
392C ASN* 3.5 7.2 - - - +
406C ILE* 4.3 13.2 - - + -
416C TYR 3.7 1.6 + - - -
417C GLY* 2.9 28.9 + - - +
420C PHE* 1.3 79.0 - - - +
422C ARG* 1.3 61.9 + - - +
423C ALA 3.6 0.7 + - - -
429C PHE* 3.7 22.9 - - + -
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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
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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