Contacts of the helix formed by residues 523 - 531 (chain D) in PDB entry 1FSJ
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 THR 523 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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423D LEU 5.5 0.9 - - - +
426D ALA* 3.1 13.2 + - + -
427D GLY* 3.6 18.9 - - - +
487D THR* 4.3 6.1 - - + -
488D PRO* 5.4 1.8 - - + -
491D GLN* 2.8 44.5 + - + +
499D TYR* 4.1 12.8 - - + -
500D GLU* 5.0 0.7 - - - -
522D THR* 1.3 77.0 - - - +
524D PRO* 1.4 75.4 - - - +
525D LYS 3.7 0.3 + - - -
526D ARG* 3.2 16.6 + - - +
527D HIS* 2.9 22.1 + - - +
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Residues in contact with PRO 524 (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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487D THR* 3.5 11.7 - - + +
491D GLN 3.4 14.8 - - - +
492D GLN* 4.4 0.2 - - - -
493D VAL* 3.9 10.1 - - + +
496D ARG* 3.3 44.0 - - + +
497D LYS* 4.2 1.1 - - - -
498D VAL 3.3 28.0 - - - +
500D GLU* 3.8 16.6 - - - +
523D THR* 1.4 84.2 - - - +
525D LYS* 1.3 63.0 + - - +
528D ILE* 2.9 31.4 + - + +
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Residues in contact with LYS 525 (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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325C LYS* 3.9 3.3 - - - +
329C ASP* 2.8 33.2 + - - -
490D ASN 5.1 3.4 - - - +
491D GLN* 3.0 48.4 + - - +
492D GLN 5.0 0.7 - - - +
493D VAL* 3.6 22.1 - - + +
523D THR 3.2 0.4 - - - -
524D PRO* 1.3 77.7 - - - +
526D ARG* 1.3 61.8 + - - +
528D ILE* 4.1 1.4 - - - +
529D ASP* 2.7 58.6 + - - +
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Residues in contact with ARG 526 (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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426D ALA 3.7 13.2 - - - +
427D GLY 3.6 16.8 - - - +
428D LYS 3.5 20.2 - - - +
429D ASP* 2.9 47.2 + - - +
431D GLY 4.9 0.2 - - - +
491D GLN* 4.3 0.6 + - - -
522D THR* 4.6 4.7 - - + -
523D THR* 3.2 18.5 + - - +
525D LYS* 1.3 80.2 - - - +
527D HIS* 1.3 59.7 + - - +
529D ASP* 3.2 24.3 + - - +
530D ILE* 2.9 57.9 + - + +
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Residues in contact with HIS 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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134B LYS* 3.7 19.0 + - - -
496D ARG* 4.4 1.8 - - - +
500D GLU* 2.8 32.9 + - + +
501D LEU 3.9 12.6 - - - -
502D HIS* 3.2 16.8 + + + -
522D THR* 3.4 16.8 - - - +
523D THR 2.9 11.7 + - - +
524D PRO 4.0 1.1 - - - +
526D ARG* 1.3 74.0 - - - +
528D ILE* 1.3 65.7 + - - +
530D ILE* 3.3 7.6 + - + +
531D HIS* 3.1 35.3 + + - +
534D LYS* 4.0 1.1 - - - +
803D PO4 3.5 12.8 - - - -
903D ZN 2.2 36.1 - - - -
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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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108B SER* 3.8 18.8 - - - +
493D VAL* 3.8 31.9 - - + +
496D ARG* 3.5 45.5 - - - +
524D PRO* 2.9 21.1 + - + +
525D LYS* 4.2 3.1 - - - +
527D HIS* 1.3 78.5 - - - +
529D ASP* 1.3 60.5 + - - +
531D HIS 3.4 1.0 + - - -
532D ARG 2.9 8.5 + - - -
533D GLY* 2.9 51.1 + - - -
534D LYS* 3.7 6.3 - - - +
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Residues in contact with ASP 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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325C LYS* 2.7 31.1 + - - -
329C ASP* 4.1 1.9 - - - +
525D LYS* 2.7 46.6 + - - +
526D ARG* 3.2 24.2 + - - +
528D ILE* 1.3 79.7 - - - +
530D ILE* 1.3 65.9 + - - +
532D ARG* 3.1 24.8 + - - +
533D GLY 5.0 0.2 - - - +
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Residues in contact with ILE 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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132B ARG* 3.7 22.4 - - + +
429D ASP 4.2 7.4 - - - +
430D SER 5.4 2.9 - - - -
502D HIS* 3.6 45.8 - - + +
522D THR* 4.4 10.1 - - + -
526D ARG* 2.9 58.2 + - + +
527D HIS* 3.6 7.4 - - - +
528D ILE 3.3 0.4 - - - -
529D ASP* 1.3 77.6 - - - +
531D HIS* 1.3 69.2 + - + +
532D ARG* 3.5 3.5 + - - +
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Residues in contact with HIS 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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131B HIS* 2.9 47.4 + - - +
132B ARG 3.1 18.1 + - - -
133B GLY* 4.4 2.0 - - - -
134B LYS* 3.6 30.7 - - + +
502D HIS* 3.4 11.5 + + - -
503D HIS 5.3 0.4 - - - -
506D PRO* 5.3 4.7 - - + -
527D HIS* 3.1 28.8 + + - +
528D ILE 3.4 0.4 - - - -
530D ILE* 1.3 78.1 - - + +
532D ARG* 1.3 67.7 + - - +
533D GLY 3.2 3.2 + - - -
534D LYS* 3.3 18.1 + - - +
803D PO4 3.7 7.4 + - - -
903D ZN 2.1 37.0 - - - -
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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