Contacts of the strand formed by residues 506 - 514 (chain A) in PDB entry 5FZ9
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 TYR 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ILE* 4.0 14.1 - - + +
53A ARG* 3.8 11.8 - - - -
505A SER* 1.3 85.0 + - - +
507A SER* 1.3 61.7 + - - +
580A ILE* 4.4 5.6 - - + -
581A THR* 3.4 17.7 - - - -
582A PHE* 3.6 27.4 - + - -
583A PRO* 3.7 23.6 - - + -
601A ASN* 3.5 3.0 - - - -
602A PHE* 3.0 65.0 + + + +
604A THR* 3.6 30.9 + - + +
606A ASP* 4.1 2.3 + - - +
607A TRP* 4.2 11.9 - - + -
1769A NUK 3.3 23.1 - - - +
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Residues in contact with SER 507 (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 GLU* 3.8 16.8 + - - -
506A TYR* 1.3 75.0 - - - +
508A ILE* 1.3 63.0 + - - +
509A ASN* 5.9 1.0 - - - +
519A TRP* 5.5 3.3 - - - -
579A VAL 4.7 0.4 + - - -
580A ILE* 3.5 6.9 - - - +
581A THR* 2.6 57.3 + - - +
587A HIS* 4.6 1.4 + - - -
599A ALA* 5.9 0.4 - - - -
600A VAL 3.5 6.3 - - - -
602A PHE* 4.0 3.5 - - - -
1756A DMS 3.8 26.0 - - - -
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Residues in contact with ILE 508 (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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49A ILE* 5.3 2.2 - - + -
459A TRP* 3.8 32.3 - - + -
461A LEU* 3.7 20.1 - - + +
464A MET* 4.0 18.2 - - + -
507A SER* 1.3 77.1 - - - +
509A ASN* 1.3 62.6 + - - +
578A PHE* 3.8 22.7 - - + -
579A VAL 3.5 4.7 - - - +
580A ILE* 3.9 19.7 - - + -
599A ALA* 3.2 4.1 - - - +
600A VAL* 3.1 44.8 + - + +
602A PHE* 3.9 17.0 - - + -
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Residues in contact with ASN 509 (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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461A LEU* 4.7 0.2 - - - -
488A TYR* 4.6 8.3 - - - -
507A SER* 5.4 1.8 + - - +
508A ILE* 1.3 73.4 - - - +
510A TYR* 1.3 69.6 + - - +
517A LYS* 4.1 10.2 - - - +
519A TRP* 3.8 36.1 - - + -
573A GLN* 3.2 19.7 + - - +
578A PHE* 3.2 10.7 - - - -
579A VAL 2.9 34.2 + - - +
597A ALA* 3.8 13.3 - - - +
598A GLU 3.5 5.4 - - - -
599A ALA* 3.7 17.5 - - + +
1768A NUK 4.6 3.0 + - - -
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Residues in contact with TYR 510 (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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70A TRP* 3.9 11.2 + + - -
72A PRO* 3.5 23.7 - - + +
438A PHE* 3.4 28.9 - + + -
461A LEU* 4.2 3.5 - - + +
509A ASN* 1.3 77.6 + - - +
511A LEU* 1.3 59.8 + - - +
512A HIS* 3.5 41.0 + + - -
576A GLY* 3.5 39.7 + - - -
577A GLU 3.7 8.7 - - - -
578A PHE* 3.4 43.3 - + + -
597A ALA* 3.3 3.5 - - - +
598A GLU* 2.7 43.8 + - + +
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Residues in contact with LEU 511 (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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510A TYR* 1.3 74.7 - - - +
512A HIS* 1.3 59.7 + - - +
513A TRP 3.9 11.7 - - - +
514A GLY 4.7 2.0 - - - +
515A GLU 3.8 17.7 - - - +
516A PRO* 4.2 1.6 - - + -
517A LYS* 4.2 8.7 - - + +
573A GLN* 3.4 44.0 - - + +
574A CYS* 4.0 7.0 - - - +
575A ALA* 3.6 19.7 - - - +
576A GLY* 2.9 26.9 + - - -
577A GLU 3.4 8.5 + - - +
595A ASN* 4.1 12.1 - - + +
596A PHE 3.4 27.8 - - - +
597A ALA* 3.9 9.9 - - + +
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Residues in contact with HIS 512 (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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72A PRO* 5.7 2.3 - - + +
74A PHE* 3.8 19.1 - + + +
437A GLY* 3.6 24.6 + - - -
438A PHE* 3.8 17.1 - + - -
510A TYR* 3.5 33.5 + + - -
511A LEU* 1.3 74.0 - - - +
513A TRP* 1.3 69.9 + - + +
575A ALA* 4.2 5.6 - - - +
576A GLY* 4.4 2.6 + - - -
596A PHE* 2.8 48.9 + + + +
598A GLU* 2.9 36.8 + - + +
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Residues in contact with TRP 513 (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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74A PHE* 3.1 51.0 - + + -
76A CYS* 5.7 0.7 - - - -
78A VAL* 6.1 2.5 - - + -
379A LEU* 4.4 20.4 - - + -
511A LEU* 3.5 4.6 - - - +
512A HIS* 1.3 85.2 - - + +
514A GLY* 1.3 69.7 + - - +
575A ALA* 3.8 12.8 - - + -
594A PHE* 3.5 47.3 - + - -
595A ASN* 3.5 15.2 - - - +
596A PHE* 3.1 46.7 + + + +
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Residues in contact with GLY 514 (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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511A LEU* 4.7 0.3 - - - +
513A TRP* 1.3 87.6 - - - +
515A GLU* 1.3 68.6 + - - +
516A PRO* 4.1 1.2 - - - +
575A ALA* 4.0 17.3 + - - +
594A PHE 3.5 11.7 - - - -
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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