Contacts of the helix formed by residues 424 - 434 (chain C) in PDB entry 5ZR1
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 LEU 424 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C ASN* 2.5 36.7 + - + +
281C PHE* 3.6 24.2 - - + -
282C GLN* 3.6 29.8 - - + +
285C LEU* 4.4 7.2 - - + -
406C ALA* 4.0 15.3 - - + +
410C ALA* 3.7 29.4 - - + -
422C PHE* 4.1 4.7 - - + -
423C ASN* 1.3 72.9 - - - +
425C ILE* 1.3 56.8 + - - +
427C LEU* 3.7 17.7 - - + -
428C TYR* 2.9 25.4 + - + +
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Residues in contact with ILE 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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277C GLY 4.3 12.3 - - - +
278C ASN* 4.9 2.2 - - - +
281C PHE* 3.6 35.0 - - + -
299C VAL* 3.7 19.2 - - + +
302C ILE* 4.5 10.5 - - + -
303C LEU* 3.8 26.0 - - + -
306C MET* 3.7 35.0 - - + -
317C LEU* 4.2 14.1 - - + -
423C ASN* 3.2 8.6 - - + +
424C LEU* 1.3 79.0 - - - +
426C GLU* 1.3 57.8 + - - +
428C TYR* 3.3 4.2 + - - +
429C HIS* 2.9 24.8 + - - +
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Residues in contact with GLU 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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274C PHE* 6.0 0.7 - - - -
303C LEU* 3.7 27.0 - - + +
422C PHE* 5.7 0.2 - - - -
423C ASN* 3.6 25.1 + - + +
425C ILE* 1.3 76.1 - - - +
427C LEU* 1.3 59.8 + - - +
429C HIS* 3.6 10.1 - - + -
430C ASN* 3.0 40.7 + - - +
439C TYR* 2.9 40.2 + - + +
442C ARG* 4.1 6.8 + - - -
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Residues in contact with LEU 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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406C ALA* 4.6 4.3 - - + +
409C VAL* 3.9 22.9 - - + -
410C ALA* 4.3 13.7 - - + +
413C LEU* 5.3 5.4 - - + -
422C PHE* 4.4 11.9 - - + -
423C ASN 3.3 17.1 + - - +
424C LEU* 3.7 24.9 - - + +
425C ILE 3.3 0.4 - - - -
426C GLU* 1.3 81.5 - - - +
428C TYR* 1.3 58.2 + - - +
430C ASN* 3.7 1.2 + - - +
431C LEU* 3.1 28.9 + - + +
436C LEU* 3.7 25.4 - - + +
439C TYR* 3.6 30.3 - - + -
440C LEU* 4.1 8.1 - - + -
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Residues in contact with TYR 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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281C PHE* 3.9 22.0 - + + -
285C LEU* 3.8 25.9 - - + +
293C ASN* 5.3 1.4 + - - -
294C LEU* 3.8 35.5 + - + +
299C VAL* 4.0 6.3 - - + -
402C ILE* 4.2 30.4 - - + +
403C ASN* 3.5 20.4 + - - -
406C ALA* 4.0 16.4 - - + -
424C LEU* 2.9 21.4 + - + +
425C ILE 3.3 4.0 + - - +
427C LEU* 1.3 74.8 - - - +
429C HIS* 1.3 63.2 + - - +
431C LEU* 3.5 6.3 + - + +
432C LEU* 3.2 52.6 + - + +
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Residues in contact with HIS 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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296C ASP* 3.6 26.5 + - + +
299C VAL* 3.7 13.2 - - + +
300C GLU* 3.3 44.4 + - + +
303C LEU* 4.6 13.2 - - + -
425C ILE 2.9 15.9 + - - +
426C GLU* 3.8 9.6 - - + +
427C LEU 3.3 0.4 - - - -
428C TYR* 1.3 77.4 - - - +
430C ASN* 1.3 76.0 + - - +
432C LEU* 3.4 13.7 + - - +
433C ILE* 3.5 36.1 + - + +
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Residues in contact with ASN 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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426C GLU* 3.0 27.6 + - - +
427C LEU 4.3 2.2 - - - +
429C HIS* 1.3 87.0 - - - +
431C LEU* 1.3 56.4 + - - +
432C LEU 3.4 0.2 - - - -
433C ILE* 3.7 7.2 + - - +
434C GLY 3.1 4.9 + - - -
435C LYS* 2.9 67.7 + - - +
436C LEU* 3.5 3.1 + - + -
439C TYR* 3.3 36.2 - - + +
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Residues in contact with LEU 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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402C ILE* 3.8 29.5 - - + +
405C HIS* 4.1 13.9 - - - +
406C ALA* 3.8 31.4 - - + +
409C VAL* 5.6 2.0 - - + -
427C LEU* 3.1 20.7 + - + +
428C TYR* 3.8 6.7 - - + +
429C HIS 3.2 0.4 - - - -
430C ASN* 1.3 76.5 - - - +
432C LEU* 1.3 64.1 + - - +
433C ILE 3.3 0.6 + - - -
434C GLY* 3.7 6.7 + - - +
436C LEU* 3.8 35.9 - - + +
455C PHE* 4.1 24.4 - - + +
457C PRO* 3.8 14.6 - - - +
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Residues in contact with LEU 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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294C LEU 3.4 27.6 - - - +
296C ASP* 3.8 34.5 - - + +
299C VAL* 3.9 9.2 - - + -
402C ILE* 3.7 24.0 - - + -
428C TYR* 3.2 39.6 + - + +
429C HIS* 3.4 8.0 + - - +
431C LEU* 1.3 77.5 - - - +
433C ILE* 1.3 61.0 + - - +
457C PRO* 3.5 15.2 - - + +
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Residues in contact with ILE 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ASP* 3.8 19.1 - - + +
429C HIS* 3.5 44.0 + - + +
430C ASN* 4.1 10.1 - - - +
431C LEU 3.3 0.4 - - - -
432C LEU* 1.3 80.9 - - - +
434C GLY* 1.3 57.7 + - - +
435C LYS* 3.7 32.1 - - + +
456C GLU* 4.7 4.9 - - - +
457C PRO* 4.5 5.2 - - - +
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Residues in contact with GLY 434 (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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430C ASN 3.1 4.7 + - - -
431C LEU* 3.7 6.7 + - - -
432C LEU 3.6 1.6 - - - -
433C ILE* 1.3 78.5 - - - +
435C LYS* 1.3 60.7 + - - +
436C LEU* 3.3 10.1 + - - +
437C ASP* 4.4 6.8 - - - +
454C HIS* 5.6 5.4 - - - -
455C PHE 4.8 6.4 - - - +
456C GLU* 4.3 15.9 - - - +
457C PRO* 4.4 6.1 - - - -
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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