Contacts of the strand formed by residues 484 - 490 (chain A) in PDB entry 1RS0
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 GLU 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ILE 3.9 0.4 - - - +
475A SER* 3.7 4.7 + - - -
476A VAL* 3.0 46.5 + - + -
478A ARG* 3.2 28.6 + - - +
482A GLY 3.6 2.6 + - - +
483A HIS* 1.3 75.4 - - - +
485A SER* 1.3 72.6 + - - +
486A CYS* 4.3 6.1 - - - -
501A HIS* 4.1 7.3 - - - +
502A CYS* 3.4 25.7 - - - +
750A DFP 3.2 33.0 - - + +
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Residues in contact with SER 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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473A LYS* 3.6 24.8 + - - +
474A ILE 3.5 6.8 + - - -
475A SER* 5.5 1.1 + - - -
483A HIS 4.1 1.7 + - - -
484A GLU* 1.3 78.7 - - - +
486A CYS* 1.3 73.6 + - - +
672A GLY* 3.6 25.4 + - - -
750A DFP 4.1 7.1 - - - +
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Residues in contact with CYS 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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473A LYS* 3.7 4.2 - - - +
474A ILE* 2.7 50.2 + - + +
476A VAL* 6.2 1.5 - - + +
484A GLU* 4.3 6.1 - - + -
485A SER* 1.3 84.5 + - - +
487A MET* 1.3 64.0 + - - +
498A THR* 4.5 1.6 - - - +
502A CYS* 2.0 54.3 - - + -
672A GLY 3.8 7.2 - - - -
674A SER* 3.4 16.8 - - - +
750A DFP 4.1 7.6 - - - -
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Residues in contact with MET 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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471A GLN* 3.7 24.7 - - + +
472A ALA 3.5 13.7 - - - +
473A LYS* 4.0 25.8 - - + -
474A ILE* 3.9 3.3 - - - +
486A CYS* 1.3 74.6 - - - +
488A GLY* 1.3 59.3 + - - +
498A THR* 2.8 22.0 + - - -
608A VAL* 4.9 5.2 - - + +
609A SER 4.9 1.3 - - - -
610A GLU* 4.0 23.1 - - + +
615A LEU* 3.8 29.6 - - + -
672A GLY 3.3 18.8 + - - +
673A ASP* 4.0 8.7 - - - +
674A SER 3.1 5.9 + - - -
675A GLY* 3.1 10.3 - - - -
676A GLY* 3.6 19.7 - - - +
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Residues in contact with GLY 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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471A GLN* 3.8 5.4 + - - -
472A ALA* 2.9 32.7 + - - -
474A ILE* 4.5 0.7 - - - -
487A MET* 1.3 77.1 - - - +
489A ALA* 1.3 60.6 + - - +
496A VAL* 4.1 9.6 - - - -
497A LEU 3.2 13.0 - - - -
498A THR* 4.2 2.0 - - - -
675A GLY 3.4 6.3 + - - -
676A GLY* 4.1 0.2 - - - -
677A PRO* 4.0 10.1 - - - +
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Residues in contact with ALA 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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470A TRP* 3.4 10.3 - - + +
472A ALA* 4.9 0.2 - - - -
488A GLY* 1.3 75.1 - - - +
490A VAL* 1.3 62.6 + - - +
491A VAL* 3.4 2.2 + - + +
496A VAL* 3.0 9.0 - - - +
497A LEU* 2.7 38.4 + - + +
570A ILE* 4.3 11.0 - - + -
677A PRO* 4.0 18.6 - - + -
688A GLN* 3.5 25.8 - - - +
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Residues in contact with VAL 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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469A PRO 4.9 0.4 - - - +
470A TRP* 2.9 22.1 + - - +
472A ALA* 4.7 0.7 - - + -
489A ALA* 1.3 71.1 - - - +
491A VAL* 1.3 59.8 + - - +
492A SER 3.3 24.5 - - - +
495A PHE 3.7 4.5 - - - +
496A VAL* 4.4 11.2 - - + +
516A VAL* 4.4 15.0 - - + -
561A LEU* 4.0 24.5 - - + -
563A TYR* 4.5 4.9 - - + -
567A ILE* 4.7 8.5 - - + -
568A ARG 3.7 13.9 - - - +
569A PRO* 3.1 17.2 - - + +
570A ILE* 2.9 27.9 + - - +
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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