Contacts of the strand formed by residues 732 - 741 (chain C) in PDB entry 3FBY
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 732 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561C VAL* 3.1 2.9 - - - +
562C GLN* 3.0 31.2 + - - +
586C PHE* 4.1 15.0 - - + -
587C HIS 3.7 6.7 - - - +
588C VAL* 4.4 5.2 - - + +
597C ALA* 3.7 23.3 - - + -
726C CYS* 3.5 27.1 - - + -
729C GLN* 3.4 49.1 - - + +
731C ASN* 1.3 73.6 - - - +
733C ILE* 1.3 61.6 + - - +
734C TRP* 3.3 36.2 - - + -
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Residues in contact with ILE 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C VAL* 3.8 17.9 - - + -
296C PRO* 3.8 41.3 - - + +
311C ALA* 6.1 0.4 - - + -
559C GLU* 4.1 11.4 - - + +
560C ILE 3.7 8.3 - - - +
561C VAL* 4.1 16.2 - - + -
585C THR 3.4 2.8 - - - +
586C PHE* 3.7 0.9 - - - -
587C HIS* 2.8 39.0 + - + +
589C ASN* 3.8 22.4 - - + +
731C ASN 4.2 5.4 - - - +
732C ILE* 1.3 76.0 - - - +
734C TRP* 1.3 62.2 + - - +
735C ALA* 4.0 16.6 - - + -
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Residues in contact with TRP 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C TRP* 3.6 24.5 - + - -
559C GLU* 3.5 2.6 - - - -
560C ILE* 2.8 54.2 + - + +
561C VAL 4.0 1.6 - - - -
562C GLN* 3.7 20.0 - - + -
585C THR 3.1 6.7 - - - +
586C PHE* 4.9 7.2 - + + -
598C GLY 2.9 26.2 + - - +
684C TRP* 3.8 20.9 - + + -
724C VAL* 3.4 28.2 - - + +
725C PHE 3.6 20.2 - - - -
726C CYS* 4.7 0.2 - - + -
732C ILE* 3.3 50.8 - - + +
733C ILE* 1.3 71.8 - - - +
735C ALA* 1.3 60.8 + - - +
737C LEU* 3.6 19.8 - - + +
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Residues in contact with ALA 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C ASP* 4.8 1.3 - - + -
296C PRO* 3.8 27.4 - - + -
298C SER* 4.1 3.8 - - - +
559C GLU* 2.9 26.2 - - - +
585C THR* 2.7 39.9 + - - +
683C ARG* 3.4 0.2 + - - -
733C ILE* 3.8 5.4 - - + -
734C TRP* 1.3 73.1 - - - +
736C ASN* 1.3 73.2 + - + +
737C LEU* 3.3 4.1 + - - +
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Residues in contact with ASN 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU 3.9 4.4 + - - -
273C ASP* 3.7 27.1 - - - +
274C GLY* 4.0 7.3 - - - +
298C SER* 3.1 31.1 + - - -
558C ARG* 2.5 39.6 + - - +
683C ARG* 2.8 49.1 + - - +
735C ALA* 1.3 70.4 - - - +
737C LEU* 1.3 60.2 + - - +
738C ARG* 3.9 7.3 + - - +
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Residues in contact with LEU 737 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C THR* 3.3 12.8 - - + +
531C PHE* 4.1 20.6 - - + -
557C GLY 4.9 0.2 - - - +
558C ARG* 2.7 56.1 + - - +
559C GLU* 3.6 4.7 - - - +
560C ILE* 3.9 22.0 - - + +
582C PHE* 4.7 6.3 - - + -
583C GLU 3.4 2.9 - - - +
584C GLY* 3.7 15.3 - - - -
684C TRP* 3.7 17.0 - - + -
724C VAL* 5.7 1.6 - - + -
734C TRP* 3.6 28.7 - - + +
735C ALA 3.3 9.6 + - - +
736C ASN* 1.3 73.4 - - - +
738C ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 738 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C THR* 3.5 12.8 + - - +
558C ARG* 3.0 40.0 - - - +
581C ASP 4.5 0.3 - - - -
582C PHE* 3.4 6.6 - - - -
583C GLU* 2.7 61.7 + - + +
683C ARG* 4.1 5.4 - - - +
736C ASN* 3.9 13.7 + - - +
737C LEU* 1.3 81.2 + - - +
739C TYR* 1.3 61.9 + - - +
740C ARG* 4.7 8.0 + - - +
1001C SO4 2.6 43.4 + - - -
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Residues in contact with TYR 739 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C VAL* 3.2 34.4 - - + +
526C VAL* 4.3 8.3 - - + +
528C LEU 3.5 8.7 + - - -
529C THR* 2.8 29.2 + - + -
530C ASP* 3.0 37.6 + - - +
531C PHE* 3.6 37.7 - + - -
575C THR* 3.1 23.6 - - + +
577C PHE* 3.4 26.7 - + + -
581C ASP 3.2 11.0 - - - +
582C PHE* 4.2 2.0 - + + -
722C LEU* 3.5 24.7 - - + -
738C ARG* 1.3 75.5 - - - +
740C ARG* 1.3 66.4 + - - +
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Residues in contact with ARG 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518C ASP 5.6 0.7 - - - +
519C VAL* 3.6 20.0 - - + +
521C PRO* 6.3 0.7 - - + -
577C PHE* 4.5 4.9 - - - -
580C VAL* 3.4 5.0 - - - +
581C ASP* 2.8 59.1 + - + +
583C GLU* 3.0 30.5 + - - +
685C PHE* 4.9 4.0 - - - -
738C ARG* 4.7 11.7 + - - +
739C TYR* 1.3 77.7 + - - +
741C CYS* 1.3 70.4 + - - +
742C ASN 3.4 0.2 + - - -
1F NAG 2.9 43.0 + - + +
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Residues in contact with CYS 741 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519C VAL 3.2 10.1 + - - +
520C CYS* 2.1 51.5 - - + -
521C PRO* 5.1 5.7 - - + +
522C GLU* 6.6 0.2 - - + -
523C ASN* 5.6 2.7 - - - -
526C VAL* 4.8 1.6 - - - -
577C PHE* 4.4 13.5 - - - -
578C ASN 6.2 0.4 - - - -
579C GLY 3.9 7.6 - - - +
740C ARG* 1.3 78.6 - - - +
742C ASN* 1.3 63.1 + - - +
743C ASP* 4.2 3.8 - - - +
1F NAG 5.2 2.1 - - - +
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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