Contacts of the helix formed by residues 507 - 514 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B ILE* 5.0 1.3 - - - -
485B LEU* 3.9 11.3 - - - +
505B GLY 3.3 2.8 - - - -
506B SER* 1.3 79.3 - - - +
508B LYS* 1.3 65.2 + - - +
510B THR* 3.6 5.8 + - - -
511B LEU* 3.3 15.4 + - - +
676B MET* 3.7 13.5 - - - +
679B GLY* 4.9 0.9 - - - -
801B ATP 3.0 30.9 + - - -
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Residues in contact with LYS 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ILE* 3.7 31.9 - - + +
501B VAL* 3.7 23.3 - - - +
502B GLY 2.8 22.6 + - - +
503B ARG 2.8 15.0 + - - -
506B SER* 3.5 8.3 - - - +
507B GLY* 1.3 73.6 - - - +
509B SER* 1.3 64.6 + - - +
511B LEU* 3.1 18.7 + - - +
512B THR* 3.5 12.0 - - - +
631B GLU* 4.4 4.3 - - - -
660B ILE* 3.8 29.4 - - + +
661B ALA 5.1 1.3 - - - -
662B ALA* 5.7 2.7 - - - +
676B MET* 3.8 14.4 - - + +
801B ATP 2.8 44.6 + - - +
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Residues in contact with SER 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B LYS* 1.3 76.8 - - - +
510B THR* 1.3 62.6 + - - +
512B THR* 2.8 27.1 + - - -
513B LYS* 3.1 26.6 + - - +
630B ASP* 3.1 30.0 + - - -
660B ILE* 4.5 2.2 - - - +
801B ATP 3.0 30.1 + - - -
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Residues in contact with THR 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B PHE* 3.6 30.5 - - + -
477B TYR* 2.7 32.2 + - - +
484B ILE* 3.8 19.8 - - + +
485B LEU* 3.9 9.2 - - + -
507B GLY 3.8 5.2 - - - -
508B LYS 3.2 0.2 - - - -
509B SER* 1.3 77.0 - - - +
511B LEU* 1.3 60.7 + - - +
513B LYS* 3.4 13.9 + - + +
514B LEU* 3.6 15.4 + - - +
801B ATP 2.7 29.7 + - - -
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B PHE* 3.5 30.8 - - + -
485B LEU* 4.0 26.4 - - + +
488B ILE* 3.1 31.4 - - + -
490B LEU* 3.9 26.9 - - + -
500B ILE* 3.9 16.8 - - + -
507B GLY 3.3 2.4 + - - +
508B LYS 3.1 12.0 + - - +
510B THR* 1.3 79.2 - - - +
512B THR* 1.3 60.9 + - + +
513B LYS 3.4 0.4 + - - -
514B LEU* 3.9 4.6 + - - +
515B ILE* 3.9 3.8 - - - +
674B ILE* 5.1 3.1 - - + -
676B MET* 3.5 31.0 - - + -
679B GLY 5.8 0.2 - - - +
681B ILE* 5.1 2.2 - - + -
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Residues in contact with THR 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B ILE* 4.6 10.5 - - + -
508B LYS 3.5 14.6 - - - +
509B SER* 2.8 20.6 + - - -
511B LEU* 1.3 74.8 - - - +
513B LYS* 1.3 63.4 + - - +
514B LEU 3.2 2.9 - - - -
515B ILE* 3.3 24.2 + - - +
516B GLN* 3.1 19.1 + - - +
547B VAL* 6.0 1.0 - - - +
628B ILE* 3.9 29.7 - - + +
630B ASP* 4.4 7.0 + - - +
658B ILE* 4.6 6.3 - - + -
660B ILE* 4.0 23.1 - - + -
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Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LEU 5.8 0.4 + - - -
477B TYR* 3.5 23.4 + - - +
509B SER* 3.1 29.6 + - - +
510B THR* 3.4 8.9 + - + +
512B THR* 1.3 77.0 - - - +
514B LEU* 1.3 61.9 + - + +
516B GLN* 3.2 14.5 + - - +
517B ARG 3.2 19.2 + - - -
518B PHE* 3.4 26.2 + - + +
519B TYR* 3.5 40.6 + - + +
801B ATP 4.1 18.2 + - - -
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B PHE* 4.1 12.8 - - + -
473B ILE* 3.7 22.4 - - + -
475B PHE* 3.6 38.6 - - + -
485B LEU* 3.6 26.9 - - + -
510B THR 3.6 13.5 - - - +
511B LEU 4.1 6.1 - - - +
512B THR 3.2 0.6 - - - -
513B LYS* 1.3 76.0 - - - +
515B ILE* 1.3 63.3 + - - +
516B GLN 3.2 0.7 - - - -
517B ARG* 3.3 6.9 + - - +
519B TYR* 3.8 18.2 - - + +
521B PRO* 4.5 8.7 - - + -
526B VAL* 4.0 16.2 - - + +
533B LEU* 3.1 21.8 - - - +
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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