Contacts of the helix formed by residues 501 - 511 (chain B) in PDB entry 2FJN
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 MET 501 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497B LYS 5.8 0.4 - - - +
498B LEU* 4.7 16.4 - - + +
499B GLU 3.1 0.6 - - - -
500B PHE* 1.3 78.9 - - - +
502B GLU* 1.3 68.3 + - + +
503B MET 3.4 0.2 - - - -
504B GLU* 3.7 11.8 + - - +
505B LYS* 3.1 26.4 + - - +
508B GLU* 5.4 0.2 - - - +
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Residues in contact with GLU 502 (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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498B LEU* 4.1 16.2 - - + +
499B GLU* 3.6 5.7 + - - +
501B MET* 1.3 80.9 - - + +
503B MET* 1.3 59.4 + - - +
504B GLU 3.1 2.5 - - - -
505B LYS* 2.9 36.8 + - - +
506B GLU* 2.9 17.0 + - - +
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Residues in contact with MET 503 (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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499B GLU* 3.0 20.5 + - + +
500B PHE* 3.4 41.5 - - + -
502B GLU* 1.3 78.7 - - - +
504B GLU* 1.3 59.4 + - - +
506B GLU* 3.9 6.1 + - - +
507B PHE 3.6 11.8 + - - -
735B MET* 3.4 33.9 - - + -
741B PRO* 4.8 1.1 - - - -
742B SER* 4.5 23.6 - - - -
775B ILE* 3.6 51.0 - - + +
778B ALA* 3.8 2.0 - - + -
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Residues in contact with GLU 504 (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 PHE 2.7 26.1 - - - +
501B MET* 3.7 12.0 + - - +
502B GLU 3.1 0.2 - - - -
503B MET* 1.3 75.0 - - - +
505B LYS* 1.3 60.6 + - - +
507B PHE* 3.3 8.0 + - - +
508B GLU* 2.9 43.1 + - + +
775B ILE* 3.9 22.2 - - + +
776B GLU* 5.3 0.5 - - - +
779B LYS* 3.1 21.6 - - - +
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Residues in contact with LYS 505 (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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501B MET 3.1 20.4 + - - +
502B GLU* 2.9 31.4 + - + +
504B GLU* 1.3 76.2 - - - +
506B GLU* 1.3 67.5 + - - +
508B GLU* 2.9 32.2 + - + +
509B GLN* 2.9 13.5 + - - +
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Residues in contact with GLU 506 (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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502B GLU 2.9 12.7 + - - +
503B MET* 4.1 7.0 - - - +
505B LYS* 1.3 75.0 - - - +
507B PHE* 1.3 58.0 + - - +
509B GLN* 3.2 8.4 + - + +
510B ILE* 2.8 61.5 + - + +
742B SER 5.8 0.2 - - - +
771B TYR* 5.7 2.6 - - - -
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Residues in contact with PHE 507 (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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503B MET 3.6 3.7 + - - +
504B GLU* 3.3 10.9 + - + +
505B LYS 3.0 0.6 - - - -
506B GLU* 1.3 76.0 - - - +
508B GLU* 1.3 68.2 + - + +
510B ILE* 3.2 7.3 + - - +
511B ASP* 2.8 58.2 + - - +
516B TRP* 3.6 33.4 - + - -
768B ARG* 4.0 17.3 - - + -
771B TYR* 3.9 17.9 - + + -
772B LEU* 3.4 36.3 - - + -
775B ILE* 3.6 33.0 - - + -
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Residues in contact with GLU 508 (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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501B MET 5.4 0.2 - - - +
504B GLU* 2.9 35.0 + - + +
505B LYS* 2.9 29.7 + - + +
507B PHE* 1.3 83.3 - - + +
509B GLN* 1.3 62.3 + - - +
511B ASP* 3.4 18.9 + - - +
512B LYS* 4.0 11.6 + - - -
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Residues in contact with GLN 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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616A LYS* 5.8 2.1 + - - -
505B LYS 2.9 11.5 + - - +
506B GLU* 3.4 12.3 - - + +
508B GLU* 1.3 73.8 - - - +
510B ILE* 1.3 70.6 + - - +
511B ASP 3.0 8.2 + - - -
512B LYS* 3.2 31.3 - - - +
515B SER* 4.7 0.7 + - - -
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Residues in contact with ILE 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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506B GLU* 2.8 52.5 + - + +
507B PHE* 3.5 6.1 - - - +
509B GLN* 1.3 84.6 - - - +
511B ASP* 1.3 56.0 + - - +
512B LYS 2.8 13.1 + - - -
515B SER* 3.2 21.7 - - - -
516B TRP* 3.6 22.4 - - + -
519B ILE* 3.7 31.6 - - + -
771B TYR* 5.2 10.5 - - + -
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Residues in contact with ASP 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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507B PHE* 2.8 42.3 + - - +
508B GLU* 3.4 13.7 - - - +
509B GLN 3.0 3.0 - - - -
510B ILE* 1.3 75.2 - - - +
512B LYS* 1.3 69.0 + - - +
513B SER 4.4 0.3 + - - -
516B TRP* 3.0 12.1 + - - +
768B ARG* 3.0 32.9 + - - -
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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