Contacts of the helix formed by residues 397 - 409 (chain I) in PDB entry 6LTJ
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 ARG 397 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385I LEU 4.9 2.0 + - - -
388I LEU* 3.4 34.7 + - - +
396I LEU* 1.3 77.0 - - - +
398I THR* 1.3 63.3 + - + +
400I ALA* 3.2 7.3 + - - +
401I THR* 3.0 41.7 + - + +
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Residues in contact with THR 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396I LEU 4.2 6.0 + - - +
397I ARG* 1.3 77.8 - - + +
399I LYS* 1.3 70.1 + - - +
401I THR* 3.2 8.9 - - - +
402I ILE* 2.9 37.9 + - - +
603O GLU* 4.6 16.6 - - - +
604O GLN* 5.3 15.3 + - + +
607O LEU* 4.4 13.5 - - + -
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Residues in contact with LYS 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396I LEU* 3.6 29.1 + - + +
398I THR* 1.3 87.7 + - - +
400I ALA* 1.3 63.1 + - - +
402I ILE* 3.2 16.9 - - + +
403I GLU* 2.9 26.4 + - - +
603O GLU* 5.5 12.6 - - + -
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Residues in contact with ALA 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381I ARG* 5.8 2.2 - - - +
385I LEU* 3.8 14.5 - - + +
388I LEU* 3.7 31.9 - - + -
396I LEU 3.3 11.1 + - - +
397I ARG* 3.2 13.8 + - - +
399I LYS* 1.3 78.8 - - - +
401I THR* 1.3 58.3 + - - +
403I GLU* 3.4 4.5 + - - +
404I LEU* 2.9 28.4 + - - +
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Residues in contact with THR 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397I ARG* 3.0 31.8 + - + +
398I THR* 3.2 22.0 - - + +
400I ALA* 1.3 74.5 - - - +
402I ILE* 1.3 61.6 + - - +
404I LEU* 3.3 12.7 + - - +
405I LYS* 3.0 46.5 + - - +
607O LEU* 3.6 19.4 - - + +
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Residues in contact with ILE 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398I THR* 2.9 20.7 + - - +
399I LYS* 3.2 21.8 - - + +
401I THR* 1.3 77.2 - - - +
403I GLU* 1.3 61.4 + - + +
405I LYS* 4.6 1.8 - - - -
406I ALA* 2.9 27.1 + - - +
603O GLU* 4.1 22.2 - - + +
606O THR* 4.7 13.9 - - + -
607O LEU* 3.6 44.6 - - + +
610O LEU* 3.2 21.8 - - + +
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Residues in contact with GLU 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381I ARG* 3.0 46.5 + - - +
385I LEU* 3.6 11.2 - - + -
399I LYS 2.9 18.5 + - - +
400I ALA* 3.7 4.9 - - - +
402I ILE* 1.3 77.9 - - + +
404I LEU* 1.3 60.1 + - - +
406I ALA* 3.3 6.5 + - + +
407I LEU* 2.9 44.0 + - + +
648O TYR* 4.8 1.9 + - - -
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Residues in contact with LEU 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382I ILE* 3.8 26.9 - - + +
385I LEU* 3.6 36.9 - - + +
386I GLU* 4.5 5.8 - - + +
400I ALA 2.9 17.4 + - - +
401I THR* 3.3 13.9 + - - +
403I GLU* 1.3 76.4 - - - +
405I LYS* 1.3 61.8 + - + +
407I LEU* 3.3 4.3 + - - +
408I ARG* 3.0 61.5 + - - +
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Residues in contact with LYS 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401I THR* 3.0 35.8 + - - +
402I ILE* 3.9 5.2 - - - +
404I LEU* 1.3 83.1 - - + +
406I ALA* 1.3 58.2 + - - +
408I ARG* 3.3 5.1 + - - +
409I LEU* 2.9 33.1 + - + +
607O LEU* 4.6 14.4 - - + -
610O LEU* 3.9 28.5 - - + -
611O GLU* 2.5 28.7 + - - +
614O GLU* 2.3 48.8 + - - +
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Residues in contact with ALA 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402I ILE 2.9 18.3 + - - +
403I GLU* 3.6 7.9 - - - +
405I LYS* 1.3 73.9 - - - +
407I LEU* 1.3 67.2 + - + +
409I LEU* 3.0 2.2 + - - -
410I LEU 2.9 20.1 + - - -
610O LEU* 3.9 13.6 - - + +
642O LEU* 4.9 4.5 - - + -
644O ILE* 3.3 39.8 - - + +
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Residues in contact with LEU 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378I ILE* 4.4 16.1 - - + +
381I ARG* 3.5 37.7 - - + -
382I ILE* 3.6 34.0 - - + +
385I LEU* 4.2 9.6 - - + -
403I GLU* 2.9 29.2 + - + +
404I LEU 3.3 3.1 + - - +
406I ALA* 1.3 76.8 - - + +
408I ARG* 1.3 61.6 + - - +
410I LEU* 3.5 13.2 + - + +
411I ASN 5.1 0.2 + - - -
644O ILE* 3.6 31.0 - - + +
648O TYR* 3.9 15.3 - - + +
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Residues in contact with ARG 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382I ILE* 4.1 20.8 - - + +
383I GLN* 5.8 0.2 - - - +
386I GLU* 3.5 39.2 + - - +
404I LEU* 3.0 48.2 + - + +
405I LYS* 3.6 8.3 - - - +
406I ALA 3.1 0.2 - - - -
407I LEU* 1.3 77.9 - - - +
409I LEU* 1.3 64.3 + - + +
410I LEU 3.2 3.2 + - - -
411I ASN* 4.2 9.0 + - - +
614O GLU* 4.4 15.9 - - + +
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Residues in contact with LEU 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405I LYS 2.9 17.6 + - - +
406I ALA* 3.0 6.7 + - - +
408I ARG* 1.3 78.8 - - + +
410I LEU* 1.3 59.7 + - - +
411I ASN 3.3 2.2 - - - -
412I PHE* 3.2 19.1 + - + -
413I GLN* 2.9 28.8 + - - +
610O LEU* 4.0 14.1 - - + +
613O LEU* 3.5 36.8 - - + +
614O GLU* 4.0 30.7 - - + +
617O LYS* 6.1 4.7 - - + -
639O PHE* 3.9 12.9 - - + -
644O ILE* 4.4 0.7 - - - -
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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