Contacts of the helix formed by residues 507 - 514 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484C ILE* 5.1 1.1 - - - -
485C LEU* 4.0 9.8 - - - +
505C GLY 3.4 1.0 - - - -
506C SER* 1.3 78.9 - - - +
508C LYS* 1.3 67.8 + - - +
510C THR* 3.6 2.5 + - - -
511C LEU* 3.1 24.8 + - - +
676C MET* 3.6 11.9 - - - +
679C GLY* 5.0 0.4 - - - -
802C ATP 3.1 29.2 + - - -
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Residues in contact with LYS 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C ILE* 3.9 26.6 - - + +
501C VAL* 3.7 9.6 - - - -
502C GLY 2.8 39.9 + - - +
503C ARG 3.1 7.5 + - - -
506C SER* 3.6 8.5 - - - +
507C GLY* 1.3 78.5 - - - +
509C SER* 1.3 64.7 + - - +
511C LEU* 3.3 15.8 + - - +
512C THR* 3.4 11.4 + - - +
631C GLU* 4.5 6.5 - - - -
660C ILE* 3.8 34.9 - - + +
661C ALA 5.0 3.8 - - - +
662C ALA* 6.0 1.1 - - - +
676C MET* 4.1 7.0 - - + -
802C ATP 2.6 48.6 + - - +
637D ASP* 5.8 0.2 - - - +
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Residues in contact with SER 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508C LYS* 1.3 76.9 - - - +
510C THR* 1.3 64.3 + - - +
512C THR* 2.6 26.8 + - - -
513C LYS* 3.0 23.9 + - - +
630C ASP* 2.8 26.4 + - - -
660C ILE* 4.1 4.0 - - - +
802C ATP 3.1 33.1 + - - -
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Residues in contact with THR 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C PHE* 3.6 33.9 - - + -
477C TYR* 2.4 37.4 + - + +
484C ILE* 4.2 4.9 - - + -
485C LEU* 3.7 17.0 - - + -
507C GLY 3.8 4.9 - - - -
509C SER* 1.3 74.5 - - - +
511C LEU* 1.3 61.9 + - - +
513C LYS* 3.0 21.4 + - + +
514C LEU* 3.3 13.3 + - - +
802C ATP 2.5 28.8 + - - -
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Residues in contact with LEU 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470C PHE* 3.3 55.8 - - + -
485C LEU* 4.0 8.9 - - + +
488C ILE* 3.7 34.8 - - + -
490C LEU* 4.8 13.9 - - + -
500C ILE* 4.2 23.1 - - + -
507C GLY 3.1 12.1 + - - +
508C LYS 3.3 10.5 - - - +
509C SER 3.2 0.2 - - - -
510C THR* 1.3 76.2 - - - +
512C THR* 1.3 61.0 + - + +
514C LEU* 3.8 4.2 + - - +
515C ILE* 3.8 3.2 - - + +
674C ILE* 4.8 5.4 - - + -
676C MET* 3.8 28.9 - - + -
681C ILE* 5.2 2.0 - - + -
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Residues in contact with THR 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500C ILE* 4.0 17.9 - - + -
508C LYS 3.6 10.5 - - - +
509C SER* 2.6 23.3 + - - -
511C LEU* 1.3 75.5 - - - +
513C LYS* 1.3 65.1 + - - +
514C LEU 3.3 0.4 - - - -
515C ILE* 3.2 25.6 + - + +
516C GLN* 3.3 17.6 + - - +
628C ILE* 3.9 30.0 - - + +
630C ASP* 4.6 3.1 + - - -
658C ILE* 4.2 7.4 - - + -
660C ILE* 3.7 20.5 - - + +
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Residues in contact with LYS 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477C TYR* 3.5 32.0 + - - +
509C SER* 3.0 26.3 + - - +
510C THR* 3.0 12.5 + - - +
512C THR* 1.3 77.2 - - - +
514C LEU* 1.3 56.3 + - - +
515C ILE 3.1 0.2 - - - -
516C GLN* 3.0 31.6 + - - +
517C ARG 3.1 8.8 + - - -
518C PHE* 3.4 47.5 + - + -
802C ATP 4.0 15.2 + - - -
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Residues in contact with LEU 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C PHE* 4.1 14.6 - - + -
473C ILE* 3.8 23.6 - - + -
475C PHE* 3.6 38.6 - - + -
485C LEU* 3.6 27.8 - - + -
510C THR 3.3 9.8 + - - +
511C LEU 4.0 7.0 - - - +
512C THR 3.3 0.4 - - - -
513C LYS* 1.3 75.9 - - - +
515C ILE* 1.3 60.2 + - - +
516C GLN 3.3 0.2 - - - -
517C ARG* 3.7 9.9 + - - +
518C PHE* 4.1 10.8 - - + -
519C TYR 4.1 10.2 - - - +
521C PRO* 4.7 9.0 - - + -
526C VAL* 3.6 17.8 - - + +
533C LEU* 3.5 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