Contacts of the strand formed by residues 526 - 531 (chain D) in PDB entry 5FM8
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 526 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518D CYS* 3.8 24.2 - - - -
520D GLU 3.5 3.4 - - - -
521D ALA* 3.9 12.1 - - + -
522D ASN 4.2 2.9 - - - +
525D TYR* 1.3 78.5 - - - +
527D ILE* 1.3 63.9 + - - +
528D ILE* 3.7 16.3 + - + -
569D PHE 3.5 1.6 - - - +
571D VAL* 2.8 38.3 + - + +
574D LEU* 3.6 20.4 - - + -
580D TYR* 4.5 8.3 - - + -
582D PHE* 3.9 27.8 - - + -
602D VAL* 3.7 27.4 - - + +
604D ALA* 4.5 7.2 - - - -
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Residues in contact with ILE 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B TYR* 3.2 49.8 - - + +
518D CYS* 3.4 5.5 - - - -
519D LEU* 2.8 48.4 + - + -
520D GLU* 2.8 47.6 + - + +
525D TYR* 3.4 28.7 - - + -
526D ILE* 1.3 73.2 - - - +
528D ILE* 1.3 66.6 + - - +
568D ARG* 4.5 4.0 - - + -
569D PHE 3.5 5.8 - - - +
570D PRO* 4.3 11.2 - - + -
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Residues in contact with ILE 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D VAL* 4.1 20.6 - - + -
517D LYS 3.1 13.7 - - - +
518D CYS* 4.4 4.3 - - + +
519D LEU* 4.7 0.7 - - - -
526D ILE* 3.9 14.8 - - + +
527D ILE* 1.3 83.3 - - - +
529D SER* 1.3 60.6 + - - +
530D TRP* 3.8 12.1 - - + -
546D ILE* 3.6 36.8 - - + -
568D ARG* 3.0 6.3 - - - -
569D PHE* 2.9 43.0 + - + +
571D VAL* 4.4 4.0 - - + -
582D PHE* 3.9 33.7 - - + -
584D VAL* 4.2 3.4 - - + -
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Residues in contact with SER 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515D ASP 4.4 0.8 + - - -
516D VAL* 3.3 5.9 - - - +
517D LYS* 2.8 42.0 + - - +
519D LEU* 3.4 34.5 - - - +
528D ILE* 1.3 73.9 - - - +
530D TRP* 1.3 69.5 + - - +
567D ALA 3.1 17.0 - - - -
568D ARG* 4.7 0.9 - - - -
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Residues in contact with TRP 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D PRO* 3.8 13.9 - - + -
514D LEU 3.6 12.1 - - - +
515D ASP 3.7 6.1 - - - -
516D VAL* 4.0 16.2 - - + -
528D ILE* 3.8 19.7 - - + -
529D SER* 1.3 85.0 - - - +
531D LYS* 1.3 81.0 + - - +
532D GLN 4.3 0.9 - - - +
544D TYR* 3.4 43.9 - + + -
546D ILE* 3.8 31.4 - - + -
564D VAL* 4.4 1.3 - - + -
566D PHE 3.1 26.9 - - - -
567D ALA* 3.6 31.9 + - + +
568D ARG 4.0 2.5 - - - -
569D PHE* 4.1 9.0 - - + -
584D VAL* 3.8 19.5 - - + -
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Residues in contact with LYS 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D PRO* 3.5 7.4 - - - +
514D LEU* 2.8 41.8 + - + +
515D ASP* 2.9 33.8 + - + +
517D LYS* 5.7 4.2 - - - +
530D TRP* 1.3 83.2 - - - +
532D GLN* 1.3 73.1 + - + +
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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