Contacts of the helix formed by residues 401 - 410 (chain A) in PDB entry 1Z7B
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 ASN 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A GLU* 2.8 32.0 + - - +
400A ARG* 1.3 77.1 - - + +
402A PRO* 1.3 62.6 - - - +
403A LEU* 4.0 6.5 - - - +
404A ARG* 3.4 30.8 - - + +
405A VAL* 3.2 19.4 + - - +
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Residues in contact with PRO 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLU 3.5 1.5 - - - +
398A TYR 3.3 20.0 - - - +
399A THR* 3.5 13.2 - - - +
400A ARG 3.4 8.7 - - - +
401A ASN* 1.3 89.4 - - - +
403A LEU* 1.3 74.6 + - + +
405A VAL* 3.2 6.1 + - + +
406A PHE* 2.9 24.0 + - - +
459A PRO* 5.7 5.2 - - + +
462A ILE* 4.5 20.5 - - + +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ASN* 3.3 6.8 + - - +
402A PRO* 1.3 85.2 - - + +
404A ARG* 1.3 57.3 + - - +
406A PHE* 3.2 14.0 + - + +
407A GLU* 2.8 44.2 + - - +
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ILE* 4.5 11.9 - - + -
401A ASN* 3.3 33.7 + - + +
403A LEU* 1.3 75.2 - - - +
405A VAL* 1.3 66.7 + - + +
407A GLU* 3.8 10.4 + - - +
408A LEU* 3.0 29.2 + - + +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A ILE* 3.8 34.1 - - + +
397A GLU* 3.7 27.6 - - + +
398A TYR* 4.2 15.9 - - + +
401A ASN 3.2 14.6 + - - +
402A PRO* 3.2 8.4 + - + +
404A ARG* 1.3 75.7 - - + +
406A PHE* 1.3 58.1 + - - +
409A ASP* 2.9 56.6 + - + +
462A ILE* 5.3 4.3 - - + -
463A TYR* 4.5 12.1 - - + -
466A SER* 6.4 0.9 - - - -
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Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A PRO 2.9 13.2 + - - +
403A LEU* 3.4 19.7 - - + +
405A VAL* 1.3 78.0 - - - +
407A GLU* 1.3 65.5 + - + +
409A ASP* 5.0 0.2 - - - -
410A PHE* 2.9 76.5 + + + +
411A GLU* 3.3 26.6 + - + -
462A ILE* 4.7 15.7 - - + +
466A SER* 3.8 17.0 - - - +
469A LEU* 6.4 0.4 - - + -
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LEU* 2.8 38.2 + - - +
404A ARG* 3.8 8.3 + - - +
406A PHE* 1.3 77.6 - - + +
408A LEU* 1.3 58.6 + - - +
411A GLU* 3.2 29.4 + - - +
412A GLU* 3.0 34.3 + - - +
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ILE* 4.1 10.1 - - + -
370A SER* 3.3 25.1 - - - +
390A VAL* 3.8 22.2 - - + +
391A ALA* 3.4 25.4 - - - +
392A ILE* 3.9 17.9 - - + +
404A ARG* 3.0 16.7 + - + +
407A GLU* 1.3 76.7 - - - +
409A ASP* 1.3 80.3 + - - +
410A PHE 3.5 0.2 + - - -
412A GLU* 3.4 21.9 + - + +
413A ASN* 3.3 12.1 - - - +
504A ALA* 5.0 2.7 - - + -
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Residues in contact with ASP 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ALA* 3.2 12.8 - - + -
392A ILE* 2.6 49.6 + - - +
405A VAL* 2.9 32.3 + - + +
406A PHE* 5.0 0.7 - - - -
408A LEU* 1.3 75.3 - - - +
410A PHE* 1.3 59.5 + - + +
413A ASN* 3.4 18.1 - - - +
429A PHE* 5.4 0.2 - - - -
463A TYR* 3.4 16.0 - - + -
466A SER* 5.3 6.5 - - - -
467A LYS* 4.8 14.1 + - + +
470A LEU* 3.4 18.0 - - - +
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Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A PHE* 2.9 50.6 + + + +
409A ASP* 1.3 81.7 - - - +
411A GLU* 1.3 73.6 + - + +
413A ASN 3.5 1.0 + - - -
414A LEU* 3.0 50.5 + - + +
466A SER* 3.5 31.0 - - - -
469A LEU* 3.6 41.1 - - + -
470A LEU* 3.9 22.0 - - + +
473A VAL* 5.0 7.4 - - + -
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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