Contacts of the strand formed by residues 484 - 490 (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 GLN 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A LYS 4.5 3.8 + - - +
426A ARG* 3.5 36.4 + - + +
427A ILE 3.2 21.8 + - - -
482A GLY 3.2 6.4 + - - +
483A LEU* 1.3 78.7 - - - +
485A PHE* 1.3 60.1 + - - +
553A ASN* 3.8 12.1 - - - +
556A ASN* 3.8 6.5 + - - -
559A ASP* 2.9 37.5 + - + +
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Residues in contact with PHE 485 (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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426A ARG* 4.9 3.6 - - - -
427A ILE* 3.2 27.1 - - + +
474A ILE* 3.6 31.4 - - + -
475A TRP* 3.8 34.8 - + - -
478A GLY* 3.9 19.5 - - - -
483A LEU* 3.6 15.0 - - + -
484A GLN* 1.3 77.2 - - - +
486A THR* 1.3 70.9 + - - +
487A LEU* 4.0 17.7 - - + -
558A CYS 3.5 0.3 - - - +
559A ASP* 3.8 1.4 - - - -
560A GLY* 2.8 59.8 + - - +
561A GLU 4.1 6.5 - - - -
562A ILE* 5.1 0.4 - - + -
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Residues in contact with THR 486 (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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426A ARG* 3.2 22.2 + - - -
427A ILE 3.1 4.1 + - - +
428A ILE* 3.3 7.3 - - - +
429A PHE 2.9 24.6 + - - -
485A PHE* 1.3 74.6 + - - +
487A LEU* 1.3 73.3 + - - +
550A ILE* 3.8 28.7 - - + -
558A CYS* 2.9 30.7 + - + +
561A GLU 3.5 11.0 - - - +
563A ILE* 4.1 14.1 - - + -
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Residues in contact with LEU 487 (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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429A PHE* 3.3 29.6 - - + +
431A SER* 4.5 7.0 - - - -
471A ASP* 3.5 46.9 - - + +
474A ILE* 3.8 25.8 - - + -
475A TRP* 6.2 0.7 - - + -
485A PHE* 4.0 15.3 - - + -
486A THR* 1.3 80.8 - - - +
488A PHE* 1.3 60.8 + - - +
561A GLU 2.9 10.3 + - - +
562A ILE* 3.4 30.3 - - + -
563A ILE* 2.8 25.1 + - - +
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Residues in contact with PHE 488 (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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327A ILE* 4.7 4.7 - - + -
387A LEU* 3.6 27.1 - - + -
389A LEU* 4.6 6.1 - - + -
428A ILE* 3.8 17.5 - - + -
429A PHE 3.0 13.2 + - - -
430A PRO* 3.4 36.6 - - + +
431A SER 2.7 27.7 + - - +
487A LEU* 1.3 74.7 - - - +
489A ARG* 1.3 61.8 + - - +
490A PRO* 3.7 15.7 - - + +
493A TRP* 4.0 22.4 - + - -
547A LEU* 4.4 14.4 - - + -
550A ILE* 3.9 20.0 - - + -
563A ILE 3.2 10.5 - - - +
565A ILE* 3.9 17.7 - - + -
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Residues in contact with ARG 489 (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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431A SER* 3.0 28.6 + - - +
432A THR 3.7 21.1 - - - +
435A VAL* 3.6 14.8 - - - +
436A TYR* 3.0 42.9 + - - -
446A GLU* 3.9 9.7 + - - +
451A LEU* 5.4 6.5 - - - +
468A GLN* 6.2 0.8 - - - +
471A ASP* 3.2 25.7 + - - +
488A PHE* 1.3 73.2 - - - +
490A PRO* 1.3 64.7 - - - +
491A PHE* 3.3 12.3 - - + -
562A ILE* 3.5 38.8 - - + +
563A ILE 3.0 7.7 + - - +
564A ASN* 3.5 13.2 - - - +
565A ILE 2.8 25.6 + - - -
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Residues in contact with PRO 490 (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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327A ILE* 5.7 1.6 - - + -
430A PRO* 5.3 0.7 - - + -
431A SER 3.7 16.4 - - - +
432A THR* 4.9 2.5 - - - -
433A SER* 3.8 15.6 + - - -
488A PHE* 3.7 18.2 - - + +
489A ARG* 1.3 86.7 - - - +
491A PHE* 1.3 62.4 + - - +
492A ASN 3.9 2.6 + - - +
493A TRP* 3.3 40.8 - - + +
506A ILE* 4.8 15.7 - - + -
507A GLY 5.1 6.7 - - - +
565A ILE 3.6 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