Contacts of the helix formed by residues 486 - 499 (chain L) in PDB entry 3J8B
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 PHE 486 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484L GLN* 3.3 2.5 - - + +
485L GLU* 1.3 76.6 - - + +
487L ARG* 1.3 63.1 + - - +
488L ILE 3.3 2.8 + - - -
489L GLN* 3.4 11.3 + - + +
490L LEU* 3.1 21.4 + - + +
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Residues in contact with ARG 487 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479L LEU 5.1 1.1 - - - +
482L THR* 5.0 8.7 - - - -
484L GLN* 3.4 33.3 + - + +
485L GLU 3.2 1.4 - - - -
486L PHE* 1.3 78.1 - - - +
488L ILE* 1.3 51.7 + - - +
490L LEU* 2.3 5.7 - - - -
491L LEU* 1.1 78.7 + - + +
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Residues in contact with ILE 488 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475L LEU* 4.9 3.4 - - + +
476L ALA* 4.8 12.1 - - + -
479L LEU* 3.3 30.1 + - + +
484L GLN 5.0 0.2 + - - -
485L GLU 4.3 6.8 + - - +
486L PHE 3.3 0.8 - - - -
487L ARG* 1.3 77.4 - - - +
489L GLN* 1.3 60.2 + - - +
491L LEU* 3.3 2.4 - - - +
492L VAL* 2.7 41.0 + - + +
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Residues in contact with GLN 489 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486L PHE* 3.4 12.1 + - + +
488L ILE* 1.3 79.5 - - - +
490L LEU* 1.3 58.8 + - - +
493L PHE* 3.7 16.1 + - - +
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Residues in contact with LEU 490 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486L PHE* 3.1 16.4 + - + +
487L ARG* 2.8 4.7 + - - -
489L GLN* 1.3 79.0 - - + +
491L LEU* 1.4 58.8 + - - +
492L VAL 3.4 0.7 - - - -
493L PHE* 3.6 3.5 + - - +
494L LYS* 2.9 31.2 + - - +
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Residues in contact with LEU 491 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479L LEU* 5.3 4.7 - - + -
482L THR* 5.7 3.6 - - - -
487L ARG* 1.1 88.3 + - + +
488L ILE* 3.3 3.1 - - - +
490L LEU 1.4 45.9 - - - -
492L VAL* 1.3 53.1 + - - +
494L LYS* 3.5 7.2 + - - +
495L HIS* 3.1 27.0 + - - +
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Residues in contact with VAL 492 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475L LEU* 6.3 2.7 - - + -
487L ARG 3.0 0.6 + - - -
488L ILE* 2.7 29.0 + - + +
491L LEU* 1.3 74.5 - - - +
493L PHE* 1.3 63.2 + - - +
495L HIS* 3.2 9.8 + - - +
496L LYS* 3.2 19.1 + - - +
503L THR* 5.0 5.0 - - - -
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Residues in contact with PHE 493 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K THR* 5.2 2.8 - - - -
488L ILE 4.0 1.0 + - - -
489L GLN 3.7 18.1 + - - +
490L LEU* 3.6 5.2 + - - +
491L LEU 3.5 0.2 - - - -
492L VAL* 1.3 78.5 - - - +
494L LYS* 1.3 62.5 + - - +
496L LYS* 3.1 17.3 + - - +
497L MET* 3.2 12.1 + - - +
506L ILE* 5.8 9.2 - - + -
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Residues in contact with LYS 494 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111K THR 4.9 12.3 - - - +
112K CYS* 6.0 3.4 - - + -
490L LEU 2.9 20.2 + - - +
491L LEU* 3.5 9.2 - - - +
493L PHE* 1.3 77.6 - - - +
495L HIS* 1.3 61.1 + - - +
497L MET* 3.1 10.4 + - - +
498L LYS* 3.1 19.8 + - - +
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Residues in contact with HIS 495 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460L ILE* 6.3 3.4 - - + -
491L LEU 3.1 13.8 + - - +
492L VAL* 3.2 13.2 + - - +
494L LYS* 1.3 75.8 - - - +
496L LYS* 1.3 61.4 - - - +
498L LYS* 3.1 10.7 + - - +
499L ASN* 3.0 17.5 + - - -
500L LEU* 4.0 3.7 + - + +
501L VAL* 3.7 20.7 + - + +
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Residues in contact with LYS 496 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K ILE 5.6 0.9 - - - +
149K THR* 4.8 17.0 - - - +
492L VAL 3.2 8.7 + - - +
493L PHE* 3.1 14.0 + - - +
495L HIS* 1.3 79.2 - - - +
497L MET* 1.3 61.3 + - - +
499L ASN* 3.1 15.6 + - - +
501L VAL 3.8 13.8 + - - +
502L TRP* 5.5 0.7 - - - +
503L THR* 4.6 20.4 - - - +
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Residues in contact with MET 497 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K CYS* 5.3 12.8 - - + -
145K VAL* 5.9 6.5 - - + +
148K ILE* 5.9 3.9 - - - +
149K THR* 4.1 19.9 - - - -
493L PHE 3.2 10.4 + - - +
494L LYS* 3.1 14.4 + - - +
496L LYS* 1.3 76.5 - - - +
498L LYS* 1.3 62.3 - - - +
499L ASN* 3.4 3.5 + - - +
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Residues in contact with LYS 498 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494L LYS 3.1 11.0 + - - +
495L HIS* 3.3 13.2 - - - +
497L MET* 1.3 74.8 - - - +
499L ASN* 1.3 69.1 + - - +
500L LEU* 3.2 13.9 + - + +
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Residues in contact with ASN 499 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495L HIS 3.0 8.5 + - - -
496L LYS 3.1 15.1 + - - +
497L MET 4.2 3.1 - - - +
498L LYS* 1.3 81.2 - - - +
500L LEU* 1.3 65.3 + - - +
501L VAL* 3.2 8.2 - - - -
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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