Contacts of the strand formed by residues 556 - 564 (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 ILE 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A LEU* 5.4 10.3 - - + -
474A PHE* 6.2 2.9 - - + -
500A LEU* 5.5 0.4 - - + -
501A ASP* 3.8 30.3 - - + +
511A ARG* 3.5 36.6 - - + +
512A ALA* 4.6 11.4 - - + -
543A LEU* 3.8 28.7 - - + -
554A THR 3.9 1.3 - - - +
555A PRO* 1.3 69.8 - - - +
557A THR* 1.3 62.5 + - - +
558A ILE* 3.6 12.4 - - + +
590A GLN* 3.5 2.4 - - - -
591A ALA* 3.3 36.0 + - + +
593A ILE* 4.3 19.0 - - + +
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Residues in contact with THR 557 (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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501A ASP* 3.0 26.4 + - - +
502A LYS* 3.6 7.2 + - + +
503A LEU* 3.4 40.0 - - + +
555A PRO 3.4 3.8 + - - -
556A ILE* 1.3 70.9 - - - +
558A ILE* 1.3 67.3 + - - +
559A PHE* 3.6 6.3 + - + +
588A SER* 4.1 16.4 - - - +
589A ARG 3.4 16.2 - - - +
590A GLN* 3.7 17.6 + - + +
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Residues in contact with ILE 558 (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* 4.0 17.4 - - + +
450A VAL* 4.3 26.5 - - + -
455A LEU* 6.4 0.2 - - + -
474A PHE* 4.9 13.2 - - + -
476A VAL* 4.7 17.3 - - + -
498A LEU* 5.6 6.5 - - + -
499A LEU 4.1 2.9 - - - -
500A LEU* 3.8 29.6 - - + -
556A ILE* 3.6 22.4 - - + +
557A THR* 1.3 71.7 - - - +
559A PHE* 1.3 66.4 + - - +
588A SER* 3.5 3.5 - - - -
589A ARG 2.8 32.7 + - - +
590A GLN* 4.2 3.6 - - - -
591A ALA* 4.1 17.9 - - + +
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Residues in contact with PHE 559 (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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497A GLU 5.3 0.2 - - - -
498A LEU* 3.5 5.2 - - - +
499A LEU* 2.9 64.6 + - + +
502A LYS* 4.4 31.4 - - + -
557A THR* 3.6 4.8 + - + +
558A ILE* 1.3 76.3 - - - +
560A MET* 1.3 60.9 + - - +
561A GLU* 3.5 30.7 - - + -
586A ASN* 3.3 44.9 - - + -
587A ILE 4.3 6.5 - - - -
588A SER* 4.4 13.0 - - - -
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Residues in contact with MET 560 (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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446A ALA* 4.5 4.0 - - + -
447A GLY 3.8 21.8 - - - +
448A LEU* 4.1 17.7 - - + -
478A PHE* 3.8 33.4 - - + -
479A CYS 4.4 9.0 - - - +
480A LEU* 4.4 11.9 - - + -
496A VAL* 4.5 8.7 - - + -
497A GLU 3.9 2.7 - - - -
498A LEU* 3.8 19.7 - - + -
558A ILE* 4.0 1.0 + - + -
559A PHE* 1.3 76.1 - - - +
561A GLU* 1.3 64.1 + - - +
562A TYR* 4.2 20.0 - - + -
586A ASN* 3.1 16.9 - - - +
587A ILE* 3.1 34.6 + - + +
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Residues in contact with GLU 561 (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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496A VAL* 3.3 7.7 - - - +
497A GLU* 2.8 56.7 + - + +
499A LEU* 5.0 6.6 - - - +
559A PHE* 3.5 27.3 - - + -
560A MET* 1.3 73.2 - - - +
562A TYR* 1.3 70.8 + - - +
563A ARG* 3.3 35.2 + - + -
586A ASN* 3.8 15.7 + - + +
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Residues in contact with TYR 562 (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* 3.7 33.4 + - + +
446A ALA* 3.5 32.8 + - + +
480A LEU* 4.7 9.2 - - + -
494A PHE* 5.1 8.5 - + + -
495A GLN 3.7 4.9 - - - -
496A VAL* 4.2 18.8 - - + +
560A MET* 4.2 13.7 - - + -
561A GLU* 1.3 81.6 - - - +
563A ARG* 1.3 74.2 + - - +
579A LEU* 5.3 6.5 - - + +
583A THR 4.3 2.1 + - - -
584A PRO 3.1 20.5 + - - -
585A ALA 2.3 32.3 + - - -
586A ASN* 3.7 16.2 + - - +
587A ILE* 4.6 2.1 - - + +
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Residues in contact with ARG 563 (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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494A PHE* 3.2 17.7 - - - -
495A GLN* 2.9 41.5 + - + +
497A GLU* 6.2 3.4 - - + -
561A GLU* 3.3 29.8 + - + +
562A TYR* 1.3 82.1 - - - +
564A LEU* 1.3 66.0 + - - +
579A LEU* 6.2 4.3 - - - -
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Residues in contact with LEU 564 (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* 4.7 21.8 - - + -
492A LEU* 4.3 9.4 - - + -
493A ASN 3.1 32.5 - - - +
494A PHE* 4.3 24.2 - - + -
495A GLN* 5.0 7.3 - - - +
563A ARG* 1.3 80.1 - - - +
565A ASP* 1.3 63.7 + - + +
566A TYR* 3.4 49.7 - - + +
569A ALA* 4.5 15.5 - - + -
577A PRO* 4.9 4.7 - - + -
578A ILE* 6.3 0.2 - - - -
579A LEU* 5.5 10.9 - - + +
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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