Contacts of the strand formed by residues 569 - 577 (chain A) 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 GLY 569 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A VAL 3.2 12.3 - - - -
539A LEU* 3.7 7.3 - - - +
549A PRO* 3.9 12.8 - - - -
551A TRP* 3.9 8.2 - - - -
568A PRO* 1.3 78.0 - - - +
570A LEU* 1.3 70.0 + - - +
725A PHE* 3.6 1.3 - - - -
726A CYS 3.1 30.2 + - - -
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Residues in contact with LEU 570 (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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535A GLN 3.7 0.3 - - - +
536A THR* 3.4 5.7 - - - -
537A VAL* 2.8 45.0 + - + +
539A LEU* 3.4 16.4 - - + -
551A TRP* 3.9 5.3 + - - +
569A GLY* 1.3 73.9 - - - +
571A ALA* 1.3 63.4 + - - +
572A VAL* 4.8 3.8 - - + -
600A ILE* 3.6 26.5 - - + -
603A TYR* 3.6 34.8 - - + -
609A PHE* 3.8 22.4 - - + -
724A VAL 3.3 4.5 - - - +
725A PHE* 3.4 36.3 - - + -
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Residues in contact with ALA 571 (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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531A PHE* 5.4 1.0 - - + -
534A PHE* 3.4 25.4 - - + -
535A GLN 3.7 4.5 - - - -
551A TRP* 3.5 33.8 - - + +
560A ILE* 4.9 9.1 - - + +
570A LEU* 1.3 73.4 - - - +
572A VAL* 1.3 58.6 + - - +
573A GLY 4.3 0.2 - - - -
723A GLY* 3.2 2.8 - - - -
724A VAL* 2.9 41.7 + - + +
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Residues in contact with VAL 572 (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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534A PHE* 3.8 4.8 - - - +
535A GLN* 2.8 54.8 + - + +
537A VAL* 4.1 16.4 - - + -
570A LEU* 4.7 4.9 - - + +
571A ALA* 1.3 75.7 - - - +
573A GLY* 1.3 74.6 + - - +
600A ILE* 5.2 1.3 - - + -
603A TYR* 4.2 21.8 - - + -
721A ARG* 3.3 39.8 + - + +
722A LEU 3.4 15.3 - - - +
723A GLY* 4.4 2.5 - - - -
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Residues in contact with GLY 573 (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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530A ASP 5.8 1.3 - - - -
531A PHE* 3.8 22.9 - - - -
533A ALA 3.8 11.4 - - - -
534A PHE* 4.3 0.4 - - - -
572A VAL* 1.3 76.9 - - - +
574A TYR* 1.3 62.2 + - - -
575A THR 3.4 4.7 + - - -
721A ARG* 2.9 26.2 + - - +
722A LEU 2.9 16.1 + - - -
739A TYR* 6.3 0.4 - - - -
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Residues in contact with TYR 574 (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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533A ALA* 3.2 35.3 + - + +
534A PHE 3.4 22.4 + - - -
535A GLN* 3.3 37.3 + - + +
573A GLY* 1.3 71.8 - - - +
575A THR* 1.3 67.3 + - + +
576A ALA* 3.5 2.6 + - - +
721A ARG* 3.9 19.6 + - - +
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Residues in contact with THR 575 (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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526A VAL* 3.7 32.2 - - + +
530A ASP 5.8 0.9 - - - +
573A GLY* 3.4 2.9 - - - +
574A TYR* 1.3 80.8 - - + +
576A ALA* 1.3 63.1 + - - +
577A PHE* 3.3 30.3 - - - -
721A ARG* 3.3 20.3 - - - +
722A LEU 4.0 1.9 + - - -
739A TYR* 4.3 14.9 + - - +
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Residues in contact with ALA 576 (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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441A HIS* 5.7 0.4 - - - +
454A SER* 3.5 26.9 - - - +
455A ALA* 3.6 15.8 - - - +
574A TYR 3.5 2.9 + - - +
575A THR* 1.3 77.7 + - - +
577A PHE* 1.3 72.2 + - - +
720A GLY* 3.4 12.1 - - - +
721A ARG* 3.7 17.0 - - + -
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Residues in contact with PHE 577 (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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454A SER* 3.4 12.6 - - - -
455A ALA* 4.2 6.7 - - - +
520A CYS* 4.4 11.4 - - - -
526A VAL* 5.7 0.4 - - + -
575A THR* 3.3 32.8 - - - -
576A ALA* 1.3 89.9 - - - +
578A ASN* 1.3 69.5 + - - +
579A GLY 4.6 3.1 - - - -
580A VAL* 3.5 32.3 - - + -
719A GLY* 3.5 1.6 - - - -
720A GLY 2.9 34.2 + - - +
722A LEU* 3.7 26.7 - - + -
739A TYR* 3.4 37.0 - + - -
740A ARG 4.3 13.7 - - - -
741A CYS* 4.7 8.3 - - - -
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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