Contacts of the helix formed by residues 507 - 514 (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 GLY 507 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484D ILE* 5.0 3.4 - - - -
485D LEU* 4.1 8.8 - - - +
505D GLY 3.4 0.6 - - - -
506D SER* 1.3 77.4 - - - +
508D LYS* 1.3 66.1 + - - +
510D THR* 3.3 5.5 + - - -
511D LEU* 3.1 19.1 + - - +
676D MET* 3.2 13.5 - - - +
803D ATP 3.1 31.4 + - - -
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Residues in contact with LYS 508 (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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500D ILE* 3.4 42.8 - - + +
501D VAL* 3.5 19.7 - - - +
502D GLY 2.8 12.0 + - - +
503D ARG 2.8 29.5 + - - -
506D SER* 3.8 8.1 - - - +
507D GLY* 1.3 79.2 - - - +
509D SER* 1.3 63.2 + - - +
511D LEU* 3.4 15.0 - - - +
512D THR* 3.6 5.0 + - - +
631D GLU* 4.3 6.5 - - - -
660D ILE* 3.6 35.7 - - + +
661D ALA 4.9 4.5 - - - -
662D ALA* 5.9 0.9 - - - +
676D MET* 3.4 10.7 - - + +
803D ATP 2.8 30.4 + - - +
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Residues in contact with SER 509 (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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508D LYS* 1.3 75.5 - - - +
510D THR* 1.3 66.2 + - - +
512D THR* 2.5 27.5 + - - -
513D LYS* 3.0 23.2 + - - +
630D ASP* 3.1 28.6 + - - -
660D ILE* 3.9 2.8 - - - +
803D ATP 2.7 36.9 + - - -
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Residues in contact with THR 510 (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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475D PHE* 3.9 22.2 - - + -
477D TYR* 2.6 44.9 + - + +
484D ILE* 4.5 5.6 - - + -
485D LEU* 4.2 13.7 - - + -
507D GLY* 3.3 7.4 + - - -
509D SER* 1.3 74.7 - - - +
511D LEU* 1.3 64.1 + - - +
513D LYS* 3.0 18.6 + - + +
514D LEU* 3.2 14.2 + - + +
519D TYR* 6.3 0.4 - - + -
803D ATP 2.7 30.0 + - - -
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Residues in contact with LEU 511 (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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470D PHE* 3.4 53.4 - - + -
485D LEU* 3.8 21.0 - - + +
488D ILE* 3.8 24.7 - - + -
490D LEU* 4.6 14.6 - - + -
500D ILE* 4.3 19.1 - - + -
507D GLY 3.1 10.8 + - - +
508D LYS 3.4 11.0 - - - +
510D THR* 1.3 78.1 - - - +
512D THR* 1.3 61.1 + - + +
514D LEU* 3.5 7.0 + - - +
515D ILE* 3.6 4.0 - - + +
674D ILE* 5.3 2.7 - - + -
676D MET* 3.8 26.2 - - + -
681D ILE* 5.3 4.5 - - + -
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Residues in contact with THR 512 (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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500D ILE* 4.3 14.4 - - + -
508D LYS 3.6 3.8 + - - +
509D SER* 2.5 23.4 + - - -
511D LEU* 1.3 73.0 - - - +
513D LYS* 1.3 64.6 + - - +
514D LEU 3.2 2.0 - - - -
515D ILE* 3.2 25.6 + - + +
516D GLN* 3.3 24.3 + - - +
628D ILE* 4.2 27.4 - - + +
630D ASP* 4.3 4.0 + - - -
658D ILE* 4.4 8.1 - - + -
660D ILE* 3.7 25.5 - - + +
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Residues in contact with LYS 513 (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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477D TYR* 3.0 28.9 + - - +
509D SER* 3.0 29.4 + - - +
510D THR* 3.0 14.9 + - + +
512D THR* 1.3 76.9 - - - +
514D LEU* 1.3 60.8 + - + +
516D GLN* 3.7 11.1 + - - +
517D ARG 3.4 2.9 + - - -
518D PHE* 3.0 46.5 + - + +
519D TYR* 4.1 24.7 + - + +
803D ATP 3.7 22.2 + - - -
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Residues in contact with LEU 514 (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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470D PHE* 4.0 15.0 - - + -
473D ILE* 4.4 18.4 - - + -
475D PHE* 4.0 40.8 - - + -
485D LEU* 3.4 29.2 - - + -
510D THR* 3.2 12.3 + - + +
511D LEU 3.7 5.6 - - - +
512D THR 3.2 0.4 - - - -
513D LYS* 1.3 78.4 - - + +
515D ILE* 1.3 64.5 + - - +
517D ARG* 3.4 11.4 + - - +
519D TYR* 4.1 19.0 - - + +
521D PRO* 5.0 6.5 - - + -
526D VAL* 3.8 18.3 - - + +
533D LEU* 3.4 15.4 - - - +
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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