Contacts of the strand formed by residues 441 - 451 (chain A) in PDB entry 5FFO
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 VAL 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.7 32.3 - - + -
2A ASN* 3.7 39.0 - - + +
351A ASP* 4.3 15.7 - - + +
420A TYR* 3.3 13.4 + - + +
440A PRO* 1.3 72.2 - - - +
442A ILE* 1.3 65.7 + - - +
443A THR* 3.9 5.0 + - - +
484A GLY* 3.6 19.6 - - - -
485A LYS 4.2 0.9 + - - -
488A LEU* 6.0 0.2 - - - +
578A ILE* 3.1 3.4 - - + +
580A ASN* 3.9 25.1 - - + +
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Residues in contact with ILE 442 (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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440A PRO 4.8 2.0 - - - +
441A VAL* 1.3 76.6 - - - +
443A THR* 1.3 63.4 + - - +
444A VAL* 3.9 1.7 + - + +
482A ALA* 4.2 21.5 - - + -
483A ASP 3.4 11.0 - - - +
488A LEU* 3.5 32.3 - - + -
492A LEU* 4.3 15.7 - - + -
494A PHE* 5.0 4.9 - - + -
564A LEU* 4.7 13.2 - - + -
577A PRO* 3.9 27.8 - - + -
578A ILE 2.8 13.3 + - - +
579A LEU* 3.5 24.9 - - + +
580A ASN 3.0 22.8 + - - -
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Residues in contact with THR 443 (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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441A VAL* 3.9 7.0 + - - +
442A ILE* 1.3 73.5 - - - +
444A VAL* 1.3 63.5 + - - +
445A ASN* 4.3 17.2 + - - +
482A ALA* 3.5 2.3 - - - -
483A ASP* 2.9 37.0 + - - +
580A ASN* 4.2 17.3 + - + +
583A THR* 5.0 7.4 - - - +
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Residues in contact with VAL 444 (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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442A ILE* 4.8 1.8 - - + +
443A THR* 1.3 76.3 - - - +
445A ASN* 1.3 75.2 + - - +
446A ALA 4.1 1.7 + - - +
480A LEU* 4.3 10.8 - - + -
481A LYS 3.6 10.3 - - - +
482A ALA* 4.5 6.3 - - + +
494A PHE* 5.0 9.2 - - + -
562A TYR* 3.7 38.7 + - + +
579A LEU* 4.0 25.8 - - + -
583A THR* 3.7 32.7 + - - +
584A PRO* 4.6 2.9 - - + -
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Residues in contact with ASN 445 (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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443A THR* 4.3 14.8 + - - +
444A VAL* 1.3 79.5 + - - +
446A ALA* 1.3 61.2 + - - +
447A GLY 4.2 0.5 + - - -
479A CYS 4.4 0.3 - - - +
480A LEU* 4.2 1.6 + - - -
481A LYS* 3.0 60.7 + - - +
534A MET* 5.2 5.5 - - + +
583A THR* 6.2 1.0 - - - -
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Residues in contact with ALA 446 (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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444A VAL* 4.0 2.8 + - - +
445A ASN* 1.3 73.4 - - - +
447A GLY* 1.3 59.6 - - - +
479A CYS 3.9 4.0 - - - -
480A LEU* 4.1 10.5 - - + -
560A MET* 4.5 4.0 - - + -
562A TYR* 3.5 42.5 + - + +
587A ILE* 3.5 22.8 - - + +
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Residues in contact with GLY 447 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A ASN 4.2 0.6 + - - -
446A ALA* 1.3 76.0 - - - +
448A LEU* 1.3 63.4 + - - +
449A GLU* 5.8 0.2 - - - -
478A PHE* 3.8 0.5 - - - -
479A CYS* 3.1 37.5 + - - +
534A MET* 6.3 0.2 - - - -
560A MET* 3.8 12.8 - - - +
587A ILE* 3.8 3.4 - - - -
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Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447A GLY* 1.3 74.1 - - - +
449A GLU* 1.3 71.4 + - - +
450A VAL* 4.6 5.2 - - + -
476A VAL* 4.7 13.0 - - + -
477A ARG 4.1 4.9 - - - +
478A PHE* 4.0 22.9 - - + -
498A LEU* 5.8 1.8 - - + -
558A ILE* 4.0 20.4 - - + +
560A MET* 4.1 24.9 - - + -
587A ILE* 4.0 19.4 - - + +
588A SER 4.2 1.8 - - - -
589A ARG* 3.9 47.4 + - + +
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Residues in contact with GLU 449 (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 GLY 5.8 0.2 - - - -
448A LEU* 1.3 80.8 - - - +
450A VAL* 1.3 65.1 + - - +
451A TYR* 3.7 29.7 + - + -
476A VAL* 4.4 2.1 - - - -
477A ARG* 3.1 60.0 + - + +
479A CYS* 5.3 2.8 - - - -
589A ARG* 3.5 8.1 - - - +
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Residues in contact with VAL 450 (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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448A LEU* 4.6 7.6 - - + -
449A GLU* 1.3 77.8 - - - +
451A TYR* 1.3 61.6 + - - +
452A PRO 3.7 20.3 - - - +
453A SER* 3.8 6.6 + - - -
474A PHE* 4.8 15.3 - - + -
475A ASN 4.5 3.4 - - - +
476A VAL* 5.6 4.7 - - + -
558A ILE* 4.3 28.5 - - + -
589A ARG* 2.9 51.3 + - + +
590A GLN 5.0 4.3 - - - +
591A ALA* 4.1 19.1 - - + -
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Residues in contact with TYR 451 (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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449A GLU* 3.7 33.2 - - + -
450A VAL* 1.3 78.0 - - - +
452A PRO* 1.3 66.0 - - + +
474A PHE* 4.8 1.1 - - - -
475A ASN* 3.4 45.7 + - + +
477A ARG* 3.2 42.7 - - + +
538A GLU* 3.9 13.6 + - - -
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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