Contacts of the helix formed by residues 394 - 403 (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 TYR 394 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384L GLU* 6.1 4.0 - - + -
387L HIS* 6.0 6.3 - - + -
391L ARG* 4.6 4.6 + - + +
393L LYS* 1.3 78.2 - - + +
395L GLY* 1.3 62.1 + - - +
396L ASP 3.3 1.1 - - - -
397L LYS* 3.2 7.3 + - - +
398L MET* 2.9 27.5 + - - +
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Residues in contact with GLY 395 (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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384L GLU* 5.5 10.8 - - - +
391L ARG 4.2 10.9 + - - -
392L GLU* 4.0 2.6 + - - -
394L TYR* 1.3 75.3 - - - +
396L ASP* 1.3 60.9 + - - +
398L MET* 3.2 9.9 + - - +
399L LEU* 2.9 27.7 + - - +
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Residues in contact with ASP 396 (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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392L GLU* 2.5 36.4 + - + +
393L LYS 4.8 0.7 - - - +
395L GLY* 1.3 74.8 - - - +
397L LYS* 1.3 62.9 + - - +
399L LEU* 3.2 9.0 + - - +
400L ARG* 3.1 22.9 + - - +
412L LEU* 5.8 5.4 - - + -
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Residues in contact with LYS 397 (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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393L LYS 3.8 13.8 + - - +
394L TYR* 3.2 12.2 + - - +
396L ASP* 1.3 78.6 - - - +
398L MET* 1.3 61.5 + - - +
400L ARG* 3.3 7.8 + - - +
401L MET* 3.1 22.9 + - - +
412L LEU* 5.2 12.3 - - + +
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Residues in contact with MET 398 (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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381L ARG 5.4 3.8 - - - +
382L ILE* 5.4 15.5 - - + -
383L ASP 6.1 0.2 - - - +
394L TYR 2.9 13.4 + - - +
395L GLY* 3.4 12.3 - - - +
397L LYS* 1.3 78.0 - - - +
399L LEU* 1.3 61.4 + - - +
401L MET* 3.4 8.0 + - - +
402L GLN* 3.1 21.5 + - - +
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Residues in contact with LEU 399 (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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395L GLY 2.9 12.7 + - - +
396L ASP* 3.2 11.9 + - - +
398L MET* 1.3 76.5 - - - +
400L ARG* 1.3 57.9 + - - +
402L GLN* 3.1 9.7 + - - +
403L LYS* 2.8 28.5 + - - +
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Residues in contact with ARG 400 (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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396L ASP 3.1 13.5 + - - +
397L LYS* 3.6 10.5 - - - +
399L LEU* 1.3 73.8 - - - +
401L MET* 1.3 65.4 + - - +
403L LYS* 3.3 9.1 + - - +
404L GLY* 3.2 17.3 + - - -
405L ASP 4.1 8.3 + - - +
408L VAL* 4.1 15.0 - - + +
409L TYR* 4.1 32.4 - - + +
412L LEU* 5.3 3.8 - - + -
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Residues in contact with MET 401 (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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397L LYS 3.1 12.8 + - - +
398L MET* 3.6 10.8 - - - +
400L ARG* 1.3 76.0 - - - +
402L GLN* 1.3 62.1 + - - +
404L GLY* 3.3 12.7 + - - -
409L TYR* 6.3 0.4 - - - -
455L ALA* 6.0 6.5 - - + -
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Residues in contact with GLN 402 (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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398L MET 3.1 13.9 + - - +
399L LEU* 3.1 13.0 + - - +
401L MET* 1.3 78.5 - - - +
403L LYS* 1.3 61.5 + - - +
404L GLY* 3.4 1.2 + - - -
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Residues in contact with LYS 403 (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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399L LEU 2.8 13.1 + - - +
400L ARG* 3.5 13.7 - - - +
401L MET 3.2 0.2 - - - -
402L GLN* 1.3 78.8 - - - +
404L GLY* 1.3 58.9 + - - +
405L ASP* 3.2 16.7 + - + +
408L VAL* 5.5 3.8 - - + -
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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