Contacts of the helix formed by residues 403 - 416 (chain L) in PDB entry 6QX2
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 THR 403 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434J THR* 4.3 4.8 - - - +
436J LEU* 4.1 22.0 - - + -
401L SER* 3.8 3.3 - - - -
402L ASP* 1.3 85.7 - - + +
404L ASP* 1.3 64.6 + - - +
405L LYS* 3.5 11.0 + - - +
406L VAL* 3.3 27.3 + - + +
407L ALA* 3.2 20.8 + - - +
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Residues in contact with ASP 404 (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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431J ARG* 1.8 62.7 + - - +
434J THR* 3.5 23.0 + - - +
437J GLU* 5.5 1.4 - - - +
403L THR* 1.3 71.0 - - - +
405L LYS* 1.3 54.8 + - - +
407L ALA* 3.3 7.2 + - - +
408L MET* 2.9 39.6 + - + +
426L LEU* 4.0 5.0 - - + +
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Residues in contact with LYS 405 (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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403L THR* 3.3 9.5 - - - +
404L ASP* 1.3 77.6 - - - +
406L VAL* 1.3 63.6 + - + +
408L MET* 3.4 9.3 - - - +
409L GLU* 3.2 48.2 + - - +
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Residues in contact with VAL 406 (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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400L GLU 5.5 0.4 - - - +
401L SER* 4.0 17.7 - - - -
402L ASP* 4.3 14.6 - - + +
403L THR* 3.3 29.4 + - + +
405L LYS* 1.3 77.9 - - + +
407L ALA* 1.3 52.9 + - - +
409L GLU* 3.2 16.1 + - - +
410L SER* 2.8 47.3 + - - +
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Residues in contact with ALA 407 (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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434J THR* 4.7 5.2 - - + -
397L THR 5.1 0.4 - - - -
398L ILE* 4.6 10.3 - - + -
401L SER* 3.2 27.5 + - - +
403L THR 3.2 8.4 + - - +
404L ASP* 3.5 10.8 - - - +
406L VAL* 1.3 77.4 - - - +
408L MET* 1.3 55.2 + - - +
410L SER* 3.4 1.7 + - - -
411L LEU* 2.9 38.7 + - - +
426L LEU* 4.2 21.1 - - + -
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Residues in contact with MET 408 (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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404L ASP* 2.9 21.6 + - + +
405L LYS* 3.4 12.3 - - - +
407L ALA* 1.3 75.6 - - - +
409L GLU* 1.3 61.9 + - + +
411L LEU* 3.9 2.1 - - - +
412L GLN* 3.1 39.3 + - - +
419L GLU* 3.4 39.0 - - + +
422L ALA* 3.7 7.4 - - + +
423L GLN* 3.2 56.8 - - + +
426L LEU* 3.6 15.0 - - + +
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Residues in contact with GLU 409 (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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405L LYS* 3.2 39.8 - - + +
406L VAL* 3.2 14.8 + - - +
408L MET* 1.3 73.5 - - + +
410L SER* 1.3 59.9 - - - +
412L GLN* 3.3 11.0 + - - +
413L GLN* 3.0 33.2 + - - +
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Residues in contact with SER 410 (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 THR* 3.6 21.8 - - - -
400L GLU* 5.5 3.8 - - - +
401L SER* 3.9 9.0 + - - -
406L VAL* 2.8 26.2 + - - +
407L ALA 3.8 2.7 - - - -
409L GLU* 1.3 76.4 - - - +
411L LEU* 1.3 55.6 + - - +
413L GLN* 3.9 8.9 - - - +
414L ARG* 2.9 35.0 + - - +
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Residues in contact with LEU 411 (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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394L ILE* 3.9 35.4 - - + +
397L THR* 3.9 23.6 - - + -
398L ILE* 4.1 15.5 - - + -
407L ALA 2.9 23.2 + - - +
408L MET 3.9 3.6 - - - +
410L SER* 1.3 72.6 - - - +
412L GLN* 1.3 66.0 + - - +
415L PHE* 3.1 35.7 + - + +
417L LEU* 3.6 14.7 - - + +
422L ALA* 4.3 15.9 - - + +
425L ILE* 4.5 8.7 - - + -
426L LEU* 4.1 26.2 - - + -
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Residues in contact with GLN 412 (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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408L MET* 3.1 34.6 + - - +
409L GLU* 3.5 9.3 + - - +
411L LEU* 1.3 76.1 - - - +
413L GLN* 1.3 55.8 + - - +
416L LYS* 3.0 25.6 + - - -
417L LEU* 3.2 29.5 + - - +
418L SER* 3.7 10.5 - - - +
419L GLU* 3.7 33.6 - - - +
422L ALA* 4.1 4.7 - - + -
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Residues in contact with GLN 413 (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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409L GLU 3.0 18.6 + - - +
410L SER* 4.0 7.7 - - - +
412L GLN* 1.3 77.6 - - - +
414L ARG* 1.3 65.7 - - - +
416L LYS* 3.9 4.9 + - - +
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Residues in contact with ARG 414 (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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393L GLU* 2.6 50.1 + - - +
396L SER* 4.9 4.2 - - - -
397L THR* 2.8 31.7 + - - +
400L GLU* 5.1 7.0 + - - -
410L SER 2.9 19.8 + - - +
413L GLN* 1.3 82.0 - - + +
415L PHE* 1.3 83.6 + - + +
416L LYS 3.7 0.2 - - - -
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Residues in contact with PHE 415 (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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386L ILE* 4.3 25.0 - - + +
390L HIS* 4.1 23.8 - + + -
393L GLU* 3.8 21.1 - - + -
394L ILE* 3.8 33.2 - - + -
397L THR* 3.7 9.6 - - - -
411L LEU* 3.1 25.4 + - + +
414L ARG* 1.3 116.2 - - + +
416L LYS* 1.3 71.1 + - - +
417L LEU* 3.3 21.2 + - + +
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Residues in contact with LYS 416 (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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386L ILE* 5.8 1.2 - - - +
412L GLN 3.0 12.6 + - - -
413L GLN 3.9 3.8 + - - +
414L ARG 3.7 2.0 - - - -
415L PHE* 1.3 79.5 - - - +
417L LEU* 1.3 61.1 + - - +
421L GLN* 4.8 1.4 - - - +
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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