Contacts of the helix formed by residues 418 - 429 (chain C) in PDB entry 4ZZ7
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 ASP 418 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A SER 4.4 0.2 - - - +
486A VAL* 3.8 17.7 + - + +
487A ARG 4.7 0.2 + - - -
417B ARG* 3.0 52.0 + - - +
418B ASP* 4.9 0.2 - - - +
258C ASP* 3.3 14.5 + - - +
416C THR* 3.2 8.5 + - - +
417C ARG* 1.3 76.7 - - - +
419C GLY* 1.3 62.7 + - - +
420C GLU* 3.3 12.0 + - - +
421C ALA* 2.9 30.9 + - + +
422C ALA* 3.3 21.3 + - - +
481D TRP* 4.0 2.5 - - - -
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Residues in contact with GLY 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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481A TRP* 3.4 41.6 + - - -
417B ARG 2.7 19.8 + - - -
419B GLY 4.0 1.5 - - - +
417C ARG 3.8 2.2 + - - -
418C ASP* 1.3 70.6 - - - +
420C GLU* 1.3 59.9 + - - +
422C ALA* 3.5 2.9 + - - +
423C ARG 3.2 17.0 + - - -
481D TRP* 4.2 12.1 - - - -
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Residues in contact with GLU 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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481A TRP* 3.4 42.9 - - + +
483A SER 3.3 23.3 - - - +
484A ALA* 3.6 16.9 - - - +
487A ARG* 2.5 49.3 + - - +
418C ASP* 3.3 8.5 + - - +
419C GLY* 1.3 74.0 - - - +
421C ALA* 1.3 62.3 + - - +
423C ARG* 3.4 1.7 + - - +
424C TYR* 3.0 30.3 + - - +
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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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486A VAL* 4.7 4.0 - - + -
487A ARG* 4.5 11.9 - - + +
256C MET* 4.7 1.1 - - + -
396C MET* 3.4 27.0 - - - +
414C ILE* 4.5 3.4 - - + -
416C THR* 4.4 11.2 - - + +
418C ASP* 2.9 26.9 + - + +
419C GLY 3.4 0.2 - - - -
420C GLU* 1.3 80.4 + - - +
422C ALA* 1.3 58.3 + - - +
424C TYR* 4.6 1.6 - - - -
425C PHE* 3.1 30.5 + - - +
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Residues in contact with ALA 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ILE* 4.6 3.6 - - - -
416C THR* 4.4 4.6 - - + +
418C ASP 3.3 4.6 + - - +
419C GLY 3.7 6.7 - - - +
420C GLU 3.3 0.2 - - - -
421C ALA* 1.3 79.1 - - - +
423C ARG* 1.3 57.4 + - - +
425C PHE* 3.6 4.1 - - - +
426C SER* 3.0 29.7 + - - -
436C ILE* 3.6 27.9 - - + +
479D GLN* 5.1 4.0 - - - +
481D TRP* 3.6 33.2 - - + -
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Residues in contact with ARG 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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124A ARG* 4.8 1.2 - - - +
125A ASN* 3.7 19.4 + - - +
129A GLY* 4.0 23.3 + - - -
131A ASP* 2.9 52.5 + - - +
479A GLN* 5.0 7.6 - - - +
480A ARG* 6.3 0.7 - - - +
481A TRP* 3.9 24.0 - - + +
419C GLY 3.2 15.5 + - - +
420C GLU* 3.4 2.9 + - - +
422C ALA* 1.3 73.0 - - - +
424C TYR* 1.3 61.1 + - - +
426C SER* 3.2 8.6 + - - +
427C ASP* 2.7 76.4 + - + +
428C ASN* 5.9 0.2 + - - -
135D GLU* 5.7 0.2 + - - -
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Residues in contact with TYR 424 (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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487A ARG* 3.5 50.9 + - + +
396C MET* 4.5 0.7 - - + -
397C GLN* 2.9 21.7 + - - -
400C MET* 3.4 34.9 - - + +
420C GLU* 3.0 22.0 + - - +
421C ALA 4.1 2.7 - - - +
423C ARG* 1.3 79.8 - - - +
425C PHE* 1.3 61.7 + - - +
427C ASP* 4.7 1.8 - - - -
428C ASN* 3.0 53.4 + - + +
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Residues in contact with PHE 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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254C ILE* 3.5 30.5 - - + -
396C MET* 3.8 4.7 - - + -
400C MET* 4.0 18.6 - - - -
403C ILE* 4.4 0.2 - - + -
412C THR* 3.5 29.6 - - + -
413C CYS 3.7 12.6 - - - -
414C ILE* 3.2 38.8 - - + -
421C ALA 3.1 20.9 + - - +
422C ALA 3.6 3.1 - - - +
424C TYR* 1.3 75.0 - - - +
426C SER* 1.3 65.0 + - - +
429C ILE* 3.0 48.6 + - + +
434C VAL* 3.5 27.8 - - + -
435C GLY 4.0 0.9 - - - -
436C ILE* 4.4 1.8 - - + -
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Residues in contact with SER 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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422C ALA 3.0 20.4 + - - -
423C ARG* 3.4 12.8 + - - +
425C PHE* 1.3 77.8 - - - +
427C ASP* 1.3 56.6 + - - +
429C ILE* 4.5 0.2 - - - -
434C VAL* 3.9 20.2 - - - -
436C ILE* 4.4 3.7 - - - +
133D TRP* 4.7 6.9 - - - -
135D GLU* 5.0 3.0 + - - +
137D GLN* 4.2 0.5 + - - -
475D LYS* 2.8 32.2 + - - +
477D VAL* 3.8 33.2 - - - +
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Residues in contact with ASP 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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124A ARG* 2.7 46.2 + - - +
423C ARG* 2.7 57.4 + - + +
424C TYR* 4.2 2.9 - - - +
426C SER* 1.3 75.3 + - - +
428C ASN* 1.3 67.5 + - - +
57D ARG* 2.9 22.5 + - - -
58D ASN* 4.2 3.3 - - - +
135D GLU* 4.0 5.5 - - - +
137D GLN* 3.1 20.0 + - - +
475D LYS* 3.2 5.7 + - - -
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Residues in contact with ASN 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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400C MET* 5.2 4.0 - - - -
404C ASP* 4.4 4.2 - - - +
423C ARG* 5.9 0.2 + - - -
424C TYR* 3.0 57.9 + - + +
427C ASP* 1.3 85.1 + - - +
429C ILE* 1.3 66.6 + - - +
430C GLN* 3.0 20.1 + - - +
57D ARG* 3.4 22.1 - - - +
58D ASN* 4.7 10.9 - - - +
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Residues in contact with ILE 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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400C MET* 3.8 33.3 - - + +
403C ILE* 3.8 21.3 - - + -
404C ASP* 3.5 16.4 - - - +
412C THR* 4.1 10.3 - - + -
425C PHE* 3.0 40.6 + - + +
428C ASN* 1.3 77.2 - - - +
430C GLN* 1.3 62.9 + - - +
431C VAL* 3.3 19.7 + - + +
434C VAL* 3.8 30.3 - - + -
452C TRP* 4.1 0.3 - - - -
475D LYS* 2.6 31.4 + - - +
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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