Contacts of the helix formed by residues 408 - 422 (chain C) in PDB entry 5I4A
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 LYS 408 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403C LYS 4.7 3.2 + - - -
406C ASP* 3.2 20.2 + - + +
407C ILE* 1.3 75.2 - - - +
409C PRO* 1.3 71.4 - - + +
410C PHE* 3.4 21.6 - - + -
411C ILE* 3.1 42.6 + - + +
412C ILE* 3.3 12.9 + - - +
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Residues in contact with PRO 409 (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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322C VAL* 4.1 24.7 - - + -
407C ILE* 3.9 11.2 - - + +
408C LYS* 1.3 82.6 - - + +
410C PHE* 1.3 60.6 + - + +
412C ILE* 3.0 7.5 + - + +
413C LYS* 2.8 36.7 + - + +
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Residues in contact with PHE 410 (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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408C LYS* 4.1 27.6 - - + -
409C PRO* 1.3 80.0 - - + +
411C ILE* 1.3 81.8 + - + +
413C LYS* 4.0 10.8 - - + +
414C SER* 3.0 31.6 + - - -
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Residues in contact with ILE 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C ILE* 5.1 7.9 - - + -
403C LYS* 4.4 47.1 - - + +
408C LYS* 3.1 40.4 + - + +
410C PHE* 1.3 98.5 - - + +
412C ILE* 1.3 68.5 + - + +
414C SER* 3.0 9.3 + - - +
415C TYR* 2.9 28.6 + - + +
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Residues in contact with ILE 412 (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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315C LEU* 4.1 22.9 - - + -
322C VAL* 4.1 13.7 - - + -
323C PHE* 3.9 41.5 - - + +
399C ILE* 5.0 11.9 - - + -
403C LYS 4.5 14.6 - - - +
404C LEU* 5.1 2.9 - - + -
407C ILE* 3.9 19.7 - - + -
408C LYS 3.5 13.5 - - - +
409C PRO 3.0 5.7 + - - +
411C ILE* 1.3 81.9 - - + +
413C LYS* 1.3 62.7 + - - +
415C TYR* 3.2 9.8 + - + +
416C VAL* 2.9 23.1 + - + +
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Residues in contact with LYS 413 (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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282C PHE* 3.4 48.4 - - + -
322C VAL* 4.0 16.7 - - + +
325C ARG* 4.9 3.8 - - - +
326C ALA* 3.9 25.9 - - + +
329C GLU* 2.9 27.3 + - - -
409C PRO* 2.8 26.4 + - + +
410C PHE* 4.0 8.5 - - - +
412C ILE* 1.3 76.2 - - - +
414C SER* 1.3 57.0 + - - +
416C VAL* 3.2 4.0 + - - +
417C TYR* 2.8 26.9 + - - +
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Residues in contact with SER 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 5.0 2.2 - - - -
410C PHE* 3.0 18.9 + - - -
411C ILE* 3.0 14.4 + - - +
413C LYS* 1.3 73.2 - - - +
415C TYR* 1.3 63.0 + - - +
417C TYR* 3.1 11.5 + - - +
418C LYS* 2.8 29.8 + - - +
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Residues in contact with TYR 415 (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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316C PHE* 5.9 2.9 - + - -
323C PHE* 4.6 13.0 - + - -
373C ILE* 3.4 31.0 - - + +
397C GLN* 2.6 45.6 + - + +
398C PRO 4.0 12.3 - - - -
399C ILE* 3.7 33.3 - - + +
411C ILE* 2.9 19.6 + - + +
412C ILE* 3.3 11.9 - - + +
414C SER* 1.3 78.1 + - - +
416C VAL* 1.3 62.2 + - - +
418C LYS* 3.3 13.5 + - + +
419C MET* 3.1 48.9 + - + +
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Residues in contact with VAL 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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293C LEU* 4.3 5.8 - - + -
323C PHE* 3.5 45.5 - - + +
326C ALA* 4.2 8.7 - - + -
327C ALA* 3.9 23.3 - - + +
330C LEU* 3.9 9.1 - - + +
332C PHE* 3.9 22.7 - - + -
412C ILE* 2.9 19.3 + - + +
413C LYS 3.6 6.3 - - - +
415C TYR* 1.3 72.2 - - - +
417C TYR* 1.3 65.3 + - - +
419C MET* 3.3 9.4 + - - +
420C GLY* 3.1 18.4 + - - -
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Residues in contact with TYR 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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278C ALA* 5.6 1.1 - - - +
281C VAL* 3.9 28.3 - - + -
282C PHE* 4.5 6.5 - + + -
286C PHE* 3.9 16.0 - + - -
330C LEU* 3.8 12.3 - - + +
413C LYS 2.8 14.7 + - - +
414C SER* 3.1 14.8 + - - +
416C VAL* 1.3 77.9 - - - +
418C LYS* 1.3 61.7 + - - +
420C GLY* 3.1 3.5 + - - -
421C ASN* 2.8 41.3 + - - -
428C PRO* 3.5 26.2 - - + +
429C PHE* 3.3 28.9 - + - -
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Residues in contact with LYS 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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396C LEU 5.5 1.9 + - - -
397C GLN* 3.3 24.8 + - - +
398C PRO* 5.2 13.7 + - - +
414C SER 2.8 16.3 + - - +
415C TYR* 3.3 17.2 + - + +
417C TYR* 1.3 75.7 - - - +
419C MET* 1.3 63.5 + - - +
421C ASN* 3.1 8.8 + - + +
422C PHE* 3.0 56.7 + - + -
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Residues in contact with MET 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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293C LEU* 3.9 31.9 - - + -
295C ALA* 5.4 0.4 - - + -
323C PHE* 4.4 10.5 - - + -
371C MET* 3.2 49.3 - - + +
373C ILE* 3.8 23.6 - - + -
397C GLN* 4.0 14.4 - - + +
415C TYR* 3.1 52.4 + - + +
416C VAL* 3.5 11.7 - - - +
417C TYR 3.2 0.2 - - - -
418C LYS* 1.3 75.5 - - - +
420C GLY* 1.3 62.9 + - - +
422C PHE 3.1 9.4 + - - -
423C ILE* 3.4 6.2 + - - +
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Residues in contact with GLY 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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286C PHE* 3.7 17.5 - - - -
332C PHE* 3.6 25.7 - - - -
416C VAL 3.1 11.7 + - - -
417C TYR 3.1 3.8 + - - -
419C MET* 1.3 75.6 - - - +
421C ASN* 1.3 61.8 + - - +
423C ILE* 3.0 13.7 + - - +
426C CYS* 3.4 18.4 - - - +
428C PRO* 5.1 0.5 - - - +
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Residues in contact with ASN 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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286C PHE* 4.4 1.6 - - - -
417C TYR* 2.8 29.0 + - + +
418C LYS* 3.1 16.7 + - + +
420C GLY* 1.3 74.8 - - - +
422C PHE* 1.3 68.7 + - + +
423C ILE 3.6 4.0 + - - +
428C PRO* 3.6 23.9 - - - +
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Residues in contact with PHE 422 (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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371C MET* 4.4 1.1 - - + -
395C ILE* 3.7 37.2 - - + +
396C LEU 5.4 4.3 - - - -
397C GLN* 3.7 15.0 - - - +
418C LYS* 3.0 48.0 + - + +
419C MET 3.6 9.6 - - - +
420C GLY 3.1 0.8 - - - -
421C ASN* 1.3 85.9 - - + +
423C ILE* 1.3 59.2 + - - +
424C PRO* 3.4 10.7 - - - +
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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