Contacts of the helix formed by residues 571 - 582 (chain D) in PDB entry 2FGJ
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 SER 571 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557A ARG* 5.0 1.3 - - - +
569D GLY 3.7 2.8 + - - -
570D MET* 1.3 78.6 - - - +
572D VAL* 1.3 65.5 + - - +
573D GLU* 4.0 15.8 - - - -
574D LYS* 3.4 28.9 + - - +
575D VAL* 3.2 19.6 + - - +
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Residues in contact with VAL 572 (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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556A ASN 5.9 2.7 - - - +
557A ARG* 3.5 23.8 - - - +
560D ILE* 4.3 12.8 - - + -
571D SER* 1.3 74.6 - - - +
573D GLU* 1.3 63.7 + - - +
575D VAL* 3.1 7.5 + - - +
576D ILE* 2.8 45.6 + - + +
595D TYR* 6.1 2.2 - - + -
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Residues in contact with GLU 573 (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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571D SER* 4.0 14.7 - - - +
572D VAL* 1.3 83.6 + - - +
574D LYS* 1.3 58.1 + - + +
576D ILE* 3.4 16.5 - - + +
577D TYR* 2.7 34.3 + - - +
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Residues in contact with LYS 574 (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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570D MET* 3.5 35.5 - - + +
571D SER* 3.4 23.9 + - - +
572D VAL 3.2 0.6 - - - -
573D GLU* 1.3 79.8 - - + +
575D VAL* 1.3 63.5 + - - +
577D TYR* 3.6 26.0 + - - +
578D ALA* 3.3 18.0 + - - +
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Residues in contact with VAL 575 (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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557A ARG* 5.0 0.9 - - - +
560D ILE* 3.9 31.9 - - + -
563D ILE* 3.8 32.5 - - + +
564D SER* 3.0 26.0 - - - +
570D MET* 3.6 17.5 - - + +
571D SER 3.2 16.9 + - - +
572D VAL 3.1 6.7 + - - +
574D LYS* 1.3 73.9 - - - +
576D ILE* 1.3 65.3 + - + +
578D ALA* 3.1 8.0 + - - +
579D ALA* 3.1 20.0 + - - +
595D TYR* 4.7 4.9 - - + -
621D VAL* 5.1 0.2 - - - -
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Residues in contact with ILE 576 (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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560D ILE* 6.2 0.2 - - + -
572D VAL* 2.8 39.8 + - + +
573D GLU* 3.4 19.1 - - + +
575D VAL* 1.3 71.9 - - - +
577D TYR* 1.3 58.1 + - - +
579D ALA* 3.0 5.2 + - - +
580D LYS* 2.9 53.8 + - - +
585D HIS* 4.0 15.7 - - + +
595D TYR* 3.7 32.3 + - + +
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Residues in contact with TYR 577 (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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573D GLU 2.7 21.7 + - - +
574D LYS* 3.6 25.6 - - - +
575D VAL 3.2 0.2 - - - -
576D ILE* 1.3 74.4 - - - +
578D ALA* 1.3 58.2 + - - +
580D LYS* 3.3 15.7 + - + +
581D LEU* 3.0 66.7 + - + +
650D LYS* 5.0 14.2 - - - +
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Residues in contact with ALA 578 (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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563D ILE* 4.8 0.7 - - + -
574D LYS 3.3 7.8 + - - +
575D VAL 3.1 9.0 + - - +
577D TYR* 1.3 80.6 - - + +
579D ALA* 1.3 56.8 + - - +
581D LEU* 3.2 14.9 + - + +
582D ALA* 3.0 27.5 + - - +
617D ALA* 3.9 14.8 - - + +
620D LEU* 3.9 12.3 - - + +
621D VAL* 3.9 27.4 - - + +
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Residues in contact with ALA 579 (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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563D ILE* 4.5 7.2 - - + -
575D VAL 3.1 9.6 + - - +
576D ILE 3.0 4.6 + - - +
578D ALA* 1.3 74.7 - - - +
580D LYS* 1.3 57.5 + - - +
582D ALA 3.3 1.2 + - - -
583D GLY 3.0 6.8 + - - -
584D ALA* 2.7 32.8 + - + +
585D HIS 3.8 11.4 - - - +
588D ILE* 4.3 7.6 - - + -
595D TYR* 3.2 33.9 - - + +
617D ALA* 4.1 10.7 - - - +
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Residues in contact with LYS 580 (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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576D ILE* 2.9 35.0 + - + +
577D TYR* 3.3 18.8 + - + +
579D ALA* 1.3 72.8 - - - +
581D LEU* 1.3 68.1 + - + +
583D GLY* 3.2 12.9 + - - +
585D HIS* 3.8 34.8 - - + -
643D VAL* 4.5 2.6 - - - +
647D ASN* 3.6 10.4 + - - -
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Residues in contact with LEU 581 (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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577D TYR* 3.0 66.2 + - + +
578D ALA* 3.2 13.0 + - - +
580D LYS* 1.3 78.7 - - + +
582D ALA* 1.3 59.0 + - - +
583D GLY 3.6 0.5 + - - -
620D LEU* 3.9 24.9 - - + -
644D ILE* 4.0 9.9 - - - -
647D ASN* 3.3 36.4 + - + +
650D LYS* 5.2 14.1 - - + +
651D ILE* 4.0 20.6 - - + +
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Residues in contact with ALA 582 (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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578D ALA 3.0 15.3 + - - +
579D ALA* 3.3 4.0 + - - +
580D LYS 3.2 0.2 - - - -
581D LEU* 1.3 74.6 - - - +
583D GLY* 1.3 61.9 + - - +
584D ALA* 4.4 1.3 - - + +
613D ARG* 3.3 41.1 - - - +
616D ILE* 3.8 12.1 - - + -
617D ALA* 3.6 16.4 - - + +
620D LEU* 4.7 0.7 - - + -
640D SER 4.8 0.3 - - - +
644D ILE* 3.2 25.9 - - - +
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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