Contacts of the strand formed by residues 491 - 496 (chain A) in PDB entry 5FS9
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 GLY 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A SER 3.4 7.6 - - - -
485A ASP* 3.7 10.8 - - - -
490A VAL* 1.3 75.9 - - - +
492A TYR* 1.3 65.6 + - - -
517A PRO* 3.5 6.8 - - - +
579A TRP* 3.7 6.9 - - - -
580A ASN* 2.9 36.4 + - - +
582A PHE* 3.9 9.4 - - - -
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Residues in contact with TYR 492 (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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310A PHE* 4.0 23.1 - + + -
340A MET* 4.2 8.3 - - + -
344A LEU* 3.9 26.5 - - + -
348A LEU* 4.3 7.6 - - + -
351A TRP* 3.8 14.2 - - - -
352A THR* 2.7 36.8 + - - +
482A PHE* 5.5 2.0 - - + -
483A TRP* 3.2 7.2 - - - +
484A SER* 2.8 42.9 + - - +
485A ASP* 4.6 0.7 + - - +
486A LEU* 3.9 19.1 - - + +
490A VAL* 3.8 20.2 - - + -
491A GLY* 1.3 75.1 - - - -
493A GLU* 1.3 65.4 + - - +
529A ARG* 5.6 0.2 - - - -
577A VAL* 4.9 4.7 - - + -
578A LEU 3.3 8.1 - - - +
579A TRP* 3.8 22.4 - + + -
582A PHE* 5.7 0.4 - - - -
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Residues in contact with GLU 493 (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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481A MET* 3.9 13.0 - - + -
482A PHE* 3.2 7.2 - - - +
483A TRP* 4.1 4.9 - - + +
492A TYR* 1.3 80.6 - - - +
494A ALA* 1.3 61.4 + - - +
529A ARG* 2.9 35.4 - - + +
577A VAL* 3.3 6.8 - - - +
578A LEU* 2.8 42.3 + - + +
581A ILE 4.2 15.7 - - - +
582A PHE* 3.7 15.7 - - + -
583A ASN 4.7 5.2 + - - -
585A MET* 3.3 37.7 + - + +
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Residues in contact with ALA 494 (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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310A PHE* 6.6 0.2 - - + -
343A ILE* 6.2 0.9 - - + -
454A HIS* 5.8 0.4 - - - -
481A MET* 3.3 6.6 - - - +
482A PHE* 2.7 54.8 + - + +
493A GLU* 1.3 78.5 - - - +
495A ILE* 1.3 62.5 + - - +
498A VAL* 4.2 10.8 - - + -
576A ILE 3.2 11.9 - - - +
577A VAL* 3.8 15.7 - - + -
585A MET* 4.2 2.9 - - - -
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Residues in contact with ILE 495 (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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479A GLN* 3.8 30.7 - - + +
480A SER 3.6 15.0 - - - +
494A ALA* 1.3 76.6 - - - +
496A GLY* 1.3 67.9 + - - +
498A VAL* 3.6 2.9 - - - +
575A GLY* 3.2 1.2 - - - -
576A ILE* 2.9 36.2 + - + +
585A MET* 3.7 27.4 - - + -
588A ALA* 3.9 13.2 - - + -
589A ARG* 3.7 36.3 - - + +
592A ILE* 3.6 20.2 - - + -
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Residues in contact with GLY 496 (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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447A LEU* 4.0 15.0 - - - -
450A ARG* 3.5 23.6 + - - +
454A HIS* 5.9 3.5 - - - -
479A GLN* 4.7 3.2 + - - -
480A SER 4.5 3.2 + - - -
495A ILE* 1.3 84.4 - - - +
497A LEU* 1.3 59.9 + - - +
498A VAL* 3.4 7.6 + - - +
574A VAL 3.4 9.9 - - - -
575A GLY* 4.2 0.2 - - - -
592A ILE* 4.4 4.9 - - - -
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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