Contacts of the helix formed by residues 420 - 433 (chain C) in PDB entry 4PS1
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 TRP 420 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C TYR* 3.2 36.8 + + + +
414C ASN* 5.1 5.5 - - + +
417C GLU* 5.9 2.2 - - - -
418C GLY 5.0 4.3 - - - -
419C THR* 1.3 73.5 - - - +
421C TYR* 1.3 63.4 + - - +
423C GLN* 4.3 2.2 - - - +
424C SER* 3.1 26.9 + - - -
450C VAL* 3.8 12.9 - - + +
453C LYS* 3.3 58.7 - - + +
454C ASP 3.5 34.3 - - - -
455C ASP 3.6 4.0 - - - -
461C LYS 4.7 0.7 - - - -
462C GLN* 3.5 39.7 - - + +
402G LEU* 3.4 38.0 - - + +
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Residues in contact with TYR 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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356C PHE* 3.6 17.9 - + - -
357C ILE 4.4 5.6 - - - -
358C GLN* 3.4 15.0 - - - +
402C GLY* 3.2 38.2 - - - -
403C MET 3.8 13.4 + - - -
404C ALA* 3.6 28.7 - - + -
419C THR* 3.2 1.2 + - - -
420C TRP* 1.3 78.5 - - - +
422C ILE* 1.3 81.6 + - + +
424C SER* 3.2 2.3 + - - -
425C LEU* 2.9 38.0 + - + +
443C LEU* 4.1 10.9 - - + +
446C VAL* 3.8 24.2 - - + -
450C VAL* 4.1 6.5 - - - -
462C GLN* 3.9 7.9 - - - +
464C PRO* 3.9 15.3 - - + -
466C PRO* 5.8 1.4 - - + +
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Residues in contact with ILE 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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266C ASP* 3.4 33.9 - - + +
270C LEU* 3.7 29.2 - - + -
313C CYS* 5.7 0.4 - - + -
315C LEU* 3.9 12.6 - - + -
356C PHE* 4.7 10.3 - - + -
358C GLN* 3.7 22.2 - - + +
419C THR* 3.2 19.5 + - - +
421C TYR* 1.3 98.0 - - + +
423C GLN* 1.3 64.8 + - - +
425C LEU* 3.3 14.2 + - + +
426C CYS* 2.9 26.3 + - - -
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Residues in contact with GLN 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B HIS* 3.2 46.5 + - + +
265C LEU* 3.2 27.1 + - - +
266C ASP* 2.9 24.6 + - - +
269C ALA* 3.8 13.4 - - - +
417C GLU* 3.3 24.4 + - + +
418C GLY 4.1 0.9 - - - -
419C THR 3.0 22.1 + - - +
420C TRP* 4.3 1.8 - - - +
422C ILE* 1.3 77.3 - - - +
424C SER* 1.3 57.3 + - - +
426C CYS* 3.6 2.9 + - - +
427C GLN* 3.0 29.3 + - - +
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Residues in contact with SER 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C TRP 3.1 20.8 + - - -
421C TYR 3.8 2.7 - - - -
423C GLN* 1.3 73.9 - - - +
425C LEU* 1.3 60.2 + - - +
427C GLN* 3.8 7.2 - - - +
428C SER* 3.0 31.4 + - - -
446C VAL* 3.6 15.2 - - - +
449C GLU* 3.5 27.7 - - - +
450C VAL* 3.8 13.7 - - - -
453C LYS* 6.1 1.8 - - - -
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Residues in contact with LEU 425 (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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270C LEU* 4.6 10.1 - - + -
356C PHE* 3.6 43.3 - - + -
421C TYR* 2.9 23.8 + - + +
422C ILE* 3.3 20.6 + - + +
424C SER* 1.3 77.6 - - - +
426C CYS* 1.3 57.9 + - - +
428C SER* 3.8 1.4 - - - -
429C LEU* 2.9 55.7 + - + +
439C ILE* 5.1 0.7 - - + -
442C ILE* 5.0 2.5 - - + -
443C LEU* 3.8 28.5 - - + -
446C VAL* 3.7 14.0 - - + +
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Residues in contact with CYS 426 (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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269C ALA* 3.6 35.0 - - + -
270C LEU* 3.6 26.7 - - - -
273C THR* 3.3 24.7 - - - +
422C ILE* 2.9 20.4 + - - +
423C GLN* 4.1 3.1 - - - +
425C LEU* 1.3 73.2 - - - +
427C GLN* 1.3 67.2 + - - +
429C LEU* 3.8 6.0 - - - +
430C ARG* 2.9 34.5 + - - +
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Residues in contact with GLN 427 (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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252B PRO* 3.8 21.5 - - - +
253B LYS* 3.6 27.7 - - - +
255B HIS* 3.4 23.8 + - + -
423C GLN 3.0 18.4 + - - +
424C SER* 3.8 7.1 - - - +
426C CYS* 1.3 75.7 - - - +
428C SER* 1.3 59.0 + - - +
430C ARG* 3.8 2.4 - - - +
431C GLU* 2.9 54.8 + - - +
449C GLU* 5.7 6.7 + - - +
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Residues in contact with SER 428 (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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424C SER* 3.0 18.0 + - - -
425C LEU 3.9 1.3 - - - -
427C GLN* 1.3 77.4 - - - +
429C LEU* 1.3 57.7 + - - +
431C GLU* 4.4 4.3 - - - -
432C ARG* 2.9 37.9 + - - +
442C ILE* 3.1 28.3 + - - +
445C GLU* 3.0 28.2 + - - -
446C VAL* 4.0 10.5 - - - -
449C GLU* 6.4 0.4 - - - -
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Residues in contact with LEU 429 (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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273C THR* 3.7 22.9 - - + -
274C PHE* 3.7 28.9 - - + -
277C LEU* 4.9 1.5 - - + +
356C PHE* 5.3 0.2 - - + -
425C LEU* 2.9 43.5 + - + +
426C CYS* 3.8 1.8 - - - +
428C SER* 1.3 75.7 - - - +
430C ARG* 1.3 59.3 + - - +
433C CYS* 2.8 59.1 + - - +
439C ILE* 3.7 29.2 - - + -
442C ILE* 3.9 9.6 - - + +
476C PHE* 4.3 9.2 - - + -
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Residues in contact with ARG 430 (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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248B ARG 4.9 4.8 + - - -
249B GLU 3.1 27.5 + - - -
250B LYS* 3.7 18.0 + - - +
251B VAL 4.7 1.6 + - - -
252B PRO* 3.6 43.9 + - + +
255B HIS* 5.0 7.1 - - - +
269C ALA* 5.3 3.3 - - - +
272C THR* 4.3 16.5 - - - +
273C THR* 3.4 31.2 - - + +
276C GLU* 4.1 23.5 + - - +
277C LEU* 6.6 0.2 - - - -
426C CYS* 2.9 23.7 + - - +
427C GLN* 3.8 1.9 - - - +
429C LEU* 1.3 76.3 - - - +
431C GLU* 1.3 61.3 + - - +
434C PRO* 3.3 20.0 - - - +
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Residues in contact with GLU 431 (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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252B PRO* 3.8 16.1 - - + +
253B LYS* 3.6 30.5 + - - +
427C GLN* 2.9 40.1 + - - +
428C SER* 4.0 2.8 - - - +
430C ARG* 1.3 79.8 - - - +
432C ARG* 1.3 63.5 + - + +
434C PRO* 3.9 6.7 - - - +
435C ARG* 3.8 22.9 + - - +
445C GLU* 4.3 11.3 - - - +
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Residues in contact with ARG 432 (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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428C SER* 2.9 23.9 + - - +
431C GLU* 1.3 81.9 - - + +
433C CYS* 1.3 65.3 + - - +
434C PRO 3.2 2.2 - - - -
435C ARG* 3.0 46.0 + - - +
437C ASP* 2.8 54.0 + - - +
441C THR* 3.8 17.1 - - - +
442C ILE* 3.8 22.2 - - + +
445C GLU* 2.8 46.2 + - - +
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Residues in contact with CYS 433 (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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277C LEU* 3.9 25.8 - - + -
429C LEU* 2.8 56.6 + - - +
432C ARG* 1.3 71.8 - - - +
434C PRO* 1.4 61.1 - - + +
436C GLY* 2.9 21.4 + - - +
437C ASP 4.7 7.2 - - - -
442C ILE* 3.9 8.3 - - - -
476C PHE* 3.7 36.0 - - - +
477C PRO* 5.2 1.7 - - - +
478C SER* 4.6 3.7 + - - -
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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