Contacts of the strand formed by residues 473 - 484 (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 CYS 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A PRO* 5.3 2.8 - - - +
455A LEU* 5.3 2.1 - - - +
459A ASN* 3.6 16.3 + - - +
461A THR* 4.4 7.4 - - - -
462A CYS* 2.0 62.1 - - - -
471A VAL 2.9 8.4 + - - +
472A SER* 1.3 73.9 + - - +
474A PHE* 1.3 66.4 + - - +
540A ILE* 3.9 7.4 - - + -
541A ALA 3.5 7.0 - - - +
542A TYR* 3.6 16.6 - - + +
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Residues in contact with PHE 474 (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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450A VAL* 4.8 11.0 - - + -
451A TYR 4.3 0.9 - - - +
452A PRO* 3.9 15.5 - - + -
455A LEU* 3.6 48.2 - - + -
472A SER 5.0 0.7 - - - -
473A CYS* 1.3 78.2 - - - +
475A ASN* 1.3 71.0 + - - +
476A VAL* 3.6 27.1 - - + -
500A LEU* 4.8 9.0 - - + -
512A ALA* 5.1 7.6 - - + -
540A ILE* 3.5 6.3 - - - +
541A ALA* 2.7 56.8 + - + +
542A TYR* 4.0 15.5 - - - -
543A LEU* 4.2 2.7 - - - -
556A ILE* 6.2 2.7 - - + -
558A ILE* 4.9 16.8 - - + -
591A ALA* 6.1 0.2 - - + -
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Residues in contact with ASN 475 (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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450A VAL* 4.5 2.6 - - - -
451A TYR* 3.4 49.4 + - + +
452A PRO* 5.7 0.9 - - - +
474A PHE* 1.3 80.6 - - - +
476A VAL* 1.3 63.4 + - - +
477A ARG 4.0 2.1 + - - -
538A GLU* 2.7 33.1 + - + +
539A LEU 3.7 2.5 - - - -
540A ILE* 3.5 27.2 - - - +
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A LEU* 4.7 17.3 - - + -
449A GLU 4.4 4.5 - - - +
450A VAL* 5.6 4.5 - - + +
474A PHE* 3.6 30.7 - - + +
475A ASN* 1.3 71.0 - - - +
477A ARG* 1.3 60.8 + - - +
478A PHE* 4.1 6.8 + - + -
498A LEU* 4.3 23.8 - - + -
500A LEU* 5.0 8.1 - - + -
514A PHE* 5.4 6.7 - - + -
537A GLU 4.0 1.9 - - - +
538A GLU* 3.6 3.1 - - - -
539A LEU* 2.8 37.1 + - + +
541A ALA* 4.2 15.3 - - + -
558A ILE* 4.7 12.3 - - + -
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Residues in contact with ARG 477 (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 5.2 0.2 - - - -
448A LEU* 4.1 3.0 - - - +
449A GLU* 3.1 60.9 + - + +
451A TYR* 3.2 37.9 - - + +
475A ASN 4.0 1.6 + - - -
476A VAL* 1.3 72.3 - - - +
478A PHE* 1.3 60.9 + - - +
479A CYS* 3.6 14.2 - - - -
536A CYS* 3.6 30.7 - - - +
537A GLU 3.9 7.8 - - - +
538A GLU* 4.3 14.1 - - + +
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Residues in contact with PHE 478 (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 3.8 5.4 - - - +
448A LEU* 4.0 7.2 - - + -
476A VAL* 4.3 9.9 - - + -
477A ARG* 1.3 74.8 - - - +
479A CYS* 1.3 60.5 + - - +
480A LEU* 5.6 2.7 - - + -
496A VAL* 4.7 15.5 - - + -
498A LEU* 4.1 26.2 - - + -
514A PHE* 6.4 0.2 - + - -
522A HIS* 5.9 4.3 - - - -
524A LYS* 5.7 7.9 - - + -
526A MET* 4.9 17.5 - - + -
536A CYS* 3.1 14.0 - - - -
537A GLU* 3.2 57.1 + - + -
539A LEU* 5.2 9.4 - - + -
560A MET* 3.8 36.1 - - + -
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Residues in contact with CYS 479 (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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445A ASN 5.0 0.4 - - - -
446A ALA* 3.9 2.3 - - - -
447A GLY* 3.1 38.3 + - - +
449A GLU* 5.3 3.1 - - - -
477A ARG* 3.6 22.7 - - - -
478A PHE* 1.3 74.6 - - - +
480A LEU* 1.3 64.7 + - - +
534A MET* 3.4 27.1 - - - -
536A CYS* 2.0 47.3 - - + +
560A MET* 4.4 2.8 - - - +
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Residues in contact with LEU 480 (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* 4.3 14.8 - - + -
445A ASN 4.2 1.3 - - - -
446A ALA* 4.1 20.6 - - + -
478A PHE* 5.6 2.9 - - + -
479A CYS* 1.3 80.3 - - - +
481A LYS* 1.3 63.9 + - - +
494A PHE* 4.2 24.2 - - + -
496A VAL* 4.0 20.2 - - + -
526A MET* 3.9 28.7 - - + -
528A ILE* 4.4 15.4 - - + +
534A MET* 3.4 2.1 - - - +
535A GLN* 3.1 36.3 + - - +
560A MET* 4.4 11.4 - - + -
562A TYR* 4.7 9.0 - - + -
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Residues in contact with LYS 481 (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* 3.6 5.0 - - - +
445A ASN* 3.0 61.1 + - - +
480A LEU* 1.3 77.4 - - - +
482A ALA* 1.3 71.6 + - - +
483A ASP* 5.7 4.8 - - + +
528A ILE* 4.4 4.3 - - - -
531A GLY 6.1 0.9 - - - +
533A LEU* 4.7 6.3 - - - +
534A MET* 3.7 50.5 - - + +
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Residues in contact with ALA 482 (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* 4.2 10.5 - - + -
443A THR 3.5 9.6 - - - +
444A VAL* 4.7 3.8 - - + -
481A LYS* 1.3 83.9 - - - +
483A ASP* 1.3 65.7 + - - +
492A LEU* 4.4 6.3 - - + -
494A PHE* 3.7 30.5 - - + -
528A ILE* 3.9 12.9 - - + +
529A SER 4.5 1.3 + - - +
530A ARG* 3.3 21.6 - - + -
531A GLY 3.7 3.3 + - - -
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Residues in contact with ASP 483 (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* 3.4 9.3 - - - -
443A THR* 2.9 37.4 + - - +
481A LYS* 5.7 5.2 - - - +
482A ALA* 1.3 78.8 - - - +
484A GLY* 1.3 77.8 + - - +
490A ARG* 4.6 1.4 + - - -
492A LEU* 5.6 0.2 - - - -
530A ARG* 3.3 26.4 + - - +
531A GLY* 3.4 17.8 + - - +
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Residues in contact with GLY 484 (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 3.6 13.7 - - - -
442A ILE* 4.6 0.4 - - - -
483A ASP* 1.3 93.7 + - - +
485A LYS* 1.3 61.7 + - - +
486A GLY 4.3 0.2 + - - -
488A LEU* 4.0 22.6 - - - +
530A ARG* 3.8 11.1 + - - +
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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