Contacts of the helix formed by residues 422 - 433 (chain C) in PDB entry 3ZXR
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 GLN 422 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327C TYR* 3.7 14.3 - - + -
420C PRO* 3.5 1.4 - - - +
421C THR* 1.3 91.5 - - - +
423C LEU* 1.3 65.4 + - - +
424C SER* 2.9 26.3 + - - +
425C ASP* 3.1 37.4 + - - +
426C VAL* 3.6 7.6 + - - +
507C CL 3.9 12.8 - - + +
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Residues in contact with LEU 423 (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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318C ALA* 5.0 0.7 - - - -
321C ASN 3.9 7.6 - - - +
322C PRO* 3.4 36.6 - - + +
323C THR* 3.6 18.6 - - - +
324C VAL* 3.7 10.2 - - + +
327C TYR* 3.5 16.6 - - + -
422C GLN* 1.3 73.0 - - - +
424C SER* 1.3 63.2 + - - +
426C VAL* 3.0 24.1 + - + +
427C ILE* 2.9 36.8 + - + +
455C LYS* 4.3 9.0 - - + -
459C GLU* 3.9 9.6 - - + +
460C ILE* 4.0 16.8 - - + -
507C CL 3.8 9.9 - - + +
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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
----------------------------------------------------------
422C GLN* 2.9 29.5 + - - -
423C LEU* 1.3 79.0 - - - +
425C ASP* 1.3 60.5 + - - +
427C ILE* 4.0 1.2 - - - +
428C ASP* 3.0 41.9 + - - +
460C ILE* 3.8 26.9 - - - -
464C ASN* 5.8 1.1 - - - -
507C CL 3.4 14.2 - - - +
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Residues in contact with ASP 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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314C PRO 5.0 0.2 - - - -
420C PRO* 4.7 10.0 - - + +
421C THR* 4.0 12.8 + - - -
422C GLN* 3.1 38.3 + - - +
424C SER* 1.3 88.8 + - - +
426C VAL* 1.3 57.3 + - - +
428C ASP* 3.4 9.0 + - - +
429C ARG* 3.0 27.5 + - - +
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Residues in contact with VAL 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C PRO 3.5 17.4 - - - +
315C SER* 4.3 0.5 - - - -
317C LEU* 4.1 6.1 - - + -
318C ALA* 3.6 25.1 - - + +
327C TYR* 3.3 29.6 - - + +
420C PRO* 3.5 35.9 - - + -
422C GLN 3.6 1.5 + - - +
423C LEU* 3.0 29.8 + - + +
425C ASP* 1.3 74.3 - - - +
427C ILE* 1.3 60.8 - - - +
429C ARG* 3.7 1.0 - - - +
430C LEU* 2.8 30.0 + - - +
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Residues in contact with ILE 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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318C ALA* 4.0 20.9 - - + -
423C LEU* 2.9 35.9 + - + +
424C SER* 4.0 3.6 - - - +
426C VAL* 1.3 73.8 - - - +
428C ASP* 1.3 64.1 + - - +
430C LEU* 3.3 6.0 + - + +
431C GLU* 3.0 22.9 + - - +
451C TRP* 4.1 13.0 - - + +
452C ILE* 3.7 26.2 - - + +
455C LYS* 3.9 24.0 - - + -
456C ARG* 3.6 30.5 - - + +
460C ILE* 4.0 10.8 - - + -
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Residues in contact with ASP 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 30.5 + - - +
425C ASP* 3.6 9.9 - - - +
427C ILE* 1.3 73.0 - - - +
429C ARG* 1.3 63.4 + - - +
431C GLU* 3.3 6.8 + - - +
432C ALA* 3.0 21.9 + - - +
456C ARG* 2.9 30.1 + - - +
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Residues in contact with ARG 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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311C HIS 5.4 2.4 + - - -
314C PRO* 3.4 59.9 - - + +
315C SER* 3.8 7.0 - - - +
425C ASP 3.0 15.4 + - - +
426C VAL 3.7 0.4 - - - +
427C ILE 3.2 0.2 - - - -
428C ASP* 1.3 74.1 - - - +
430C LEU* 1.3 54.9 + - - +
432C ALA* 3.1 9.3 + - - +
433C ASP* 2.8 55.3 + - - +
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Residues in contact with LEU 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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315C SER* 3.8 21.7 - - - +
318C ALA* 3.8 20.0 - - + -
319C PHE* 3.9 20.2 - - + -
426C VAL 2.8 20.6 + - - +
427C ILE* 3.3 5.1 + - + +
429C ARG* 1.3 73.1 - - - +
431C GLU* 1.3 53.0 + - - +
433C ASP 3.4 2.1 + - - -
434C HIS* 2.8 44.3 + - + +
437C LEU* 3.6 31.0 - - + -
448C ILE* 4.1 13.9 - - + -
451C TRP* 4.0 11.7 - - + -
452C ILE* 3.9 20.6 - - + -
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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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427C ILE 3.0 12.6 + - - +
428C ASP* 3.4 10.3 - - - +
430C LEU* 1.3 78.2 - - - +
432C ALA* 1.3 60.6 + - - +
434C HIS* 3.4 17.9 + - + -
452C ILE* 3.6 25.7 - - + +
456C ARG* 2.9 38.9 + - - +
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Residues in contact with ALA 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 ASP 3.0 13.6 + - - +
429C ARG* 3.1 14.5 + - - +
431C GLU* 1.3 80.1 - - - +
433C ASP* 1.3 62.6 + - + +
434C HIS* 4.3 2.0 + - - -
435C GLU* 5.7 0.9 - - - +
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Residues in contact with ASP 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C HIS* 5.8 1.0 + - - -
312C HIS* 4.6 16.5 + - - -
315C SER* 3.6 19.1 + - - -
429C ARG* 2.8 38.4 + - - +
430C LEU 3.4 4.4 + - - +
432C ALA* 1.3 78.2 - - + +
434C HIS* 1.3 64.3 + - - +
435C GLU* 4.1 13.7 + - - +
436C TYR* 4.1 3.9 - - - -
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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