Contacts of the helix formed by residues 403 - 416 (chain A) 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 LEU 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A TRP* 5.3 11.0 - - + +
398A PHE* 6.1 0.4 - - - -
399A ASN 2.9 21.7 + - - +
400A PRO* 3.7 9.0 + - + +
402A LYS* 1.3 77.7 - - - +
404A CYS* 1.3 57.4 + - - +
406A ARG* 3.3 6.8 + - - +
407A VAL* 2.9 32.8 + - - +
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Residues in contact with CYS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A PRO 4.6 5.8 + - - +
401A LEU 6.4 0.4 - - - -
402A LYS 3.3 0.4 - - - -
403A LEU* 1.3 78.5 - - - +
405A GLU* 1.3 56.6 + - - +
407A VAL* 3.6 5.4 + - - +
408A THR* 3.0 28.1 + - - -
458A LEU 5.1 9.6 - - - +
460A PRO* 5.7 11.0 - - + -
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Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A LYS* 3.3 14.3 + - + +
403A LEU 3.2 0.4 - - - -
404A CYS* 1.3 76.0 - - - +
406A ARG* 1.3 66.0 + - - +
408A THR* 2.9 17.0 + - - -
409A LYS* 3.0 15.3 + - - +
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A TRP* 4.8 16.6 - - + -
402A LYS* 3.2 14.7 + - + +
403A LEU* 3.7 7.0 - - - +
405A GLU* 1.3 79.1 - - - +
407A VAL* 1.3 61.1 + - - +
409A LYS* 3.2 8.0 + - - +
410A VAL* 3.0 25.3 + - - +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU 2.9 18.9 + - - +
404A CYS* 3.9 5.4 - - - +
406A ARG* 1.3 75.8 - - - +
408A THR* 1.3 56.6 + - - +
410A VAL* 4.4 5.8 - - - -
411A LEU* 2.9 35.1 + - + +
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Residues in contact with THR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A CYS 3.0 15.0 + - - -
405A GLU* 2.9 13.0 + - - -
407A VAL* 1.3 77.1 - - - +
409A LYS* 1.3 60.4 + - - +
411A LEU* 3.9 8.5 + - - +
412A ASN* 4.0 11.6 + - - +
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Residues in contact with LYS 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A GLU 3.0 13.9 + - - +
406A ARG* 3.8 5.8 - - - +
408A THR* 1.3 76.9 - - - +
410A VAL* 1.3 61.7 + - - +
412A ASN* 4.3 10.4 + - - +
413A TRP* 4.6 4.9 + - - +
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Residues in contact with VAL 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLU* 5.0 16.0 - - + +
389A ASP* 5.9 6.1 - - + -
390A LEU* 6.1 4.3 - - + +
406A ARG 3.0 17.6 + - - +
407A VAL* 4.0 6.1 - - - +
409A LYS* 1.3 78.4 - - - +
411A LEU* 1.3 63.8 + - - +
412A ASN 3.3 0.9 - - - -
413A TRP* 3.5 18.3 + - - +
414A VAL* 3.7 6.9 + - - +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A VAL* 2.9 18.2 + - + +
408A THR* 4.3 5.6 - - - +
409A LYS 3.5 0.2 - - - -
410A VAL* 1.3 76.6 - - - +
412A ASN* 1.3 62.9 + - - +
413A TRP 3.3 0.2 - - - -
414A VAL* 3.8 7.5 + - - +
415A ARG* 3.6 19.8 + - - +
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Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A THR 4.0 11.1 + - - +
409A LYS* 4.4 7.9 - - - +
410A VAL 3.3 0.4 - - - -
411A LEU* 1.3 77.6 - - - +
413A TRP* 1.3 64.3 + - - +
415A ARG* 3.4 7.1 + - - +
416A GLU* 3.3 21.0 + - - +
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Residues in contact with TRP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLU* 5.1 11.0 - - + -
409A LYS 4.6 4.4 + - - +
410A VAL* 3.5 13.4 + - - +
411A LEU 3.3 0.6 - - - -
412A ASN* 1.3 79.8 - - - +
414A VAL* 1.3 62.0 + - - +
416A GLU* 3.4 7.5 + - - +
417A GLN* 3.4 20.1 + - - +
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLU* 5.6 8.0 - - + +
410A VAL 3.7 8.6 + - - +
411A LEU* 4.1 9.6 - - - +
412A ASN 3.3 0.2 - - - -
413A TRP* 1.3 76.3 - - - +
415A ARG* 1.3 64.8 + - - +
417A GLN* 3.4 6.6 + - - +
420A LYS* 4.5 12.6 - - + -
421A GLU* 3.2 26.2 + - - +
424A LEU* 4.6 19.3 - - + -
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Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LEU 3.6 11.0 + - - +
412A ASN* 3.4 9.4 + - - +
413A TRP 3.3 0.6 - - - -
414A VAL* 1.3 79.7 - - - +
416A GLU* 1.3 64.2 + - - +
417A GLN 3.4 5.9 + - - +
421A GLU* 3.7 11.3 - - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A ASN 3.3 10.4 + - - +
413A TRP* 3.7 9.9 - - - +
414A VAL 3.3 0.6 - - - -
415A ARG* 1.3 80.1 - - - +
417A GLN* 1.3 62.0 + - - +
418A PRO* 3.5 2.3 - - - +
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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