Contacts of the helix formed by residues 400 - 418 (chain L) in PDB entry 6PSS
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 GLN 400 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271J ARG* 3.9 21.7 - - - +
275J ARG* 2.4 35.5 + - - +
316J ILE* 3.4 46.3 - - - +
398L GLY 4.1 0.8 + - - +
399L LEU* 1.3 83.4 - - - +
401L PHE* 1.3 65.9 + - - +
402L LEU* 3.4 5.5 - - + +
403L ASP* 3.2 21.5 + - - +
404L LEU* 3.3 13.3 + - - +
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Residues in contact with PHE 401 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L VAL* 4.3 20.6 - - + -
102L MET* 4.2 13.2 - - + -
388L ILE* 4.4 3.6 - - + -
391L ALA* 3.9 27.6 - - + -
392L LYS* 3.4 35.0 - - + -
395L THR* 3.7 25.9 - - + +
400L GLN* 1.3 75.1 - - - +
402L LEU* 1.3 66.5 + - + +
403L ASP 3.3 0.5 + - - -
404L LEU* 3.5 8.9 + - + +
405L ILE* 3.4 43.2 + - + +
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Residues in contact with LEU 402 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275J ARG* 4.8 5.8 - - - +
294J ASN* 3.7 23.1 - - - +
298J MET* 3.6 28.4 - - + +
97L PRO* 4.1 16.4 - - + +
98L VAL* 3.7 35.4 - - + +
101L TYR* 4.2 14.8 - - + -
102L MET* 6.2 0.2 - - + -
400L GLN* 3.4 4.4 - - + +
401L PHE* 1.3 86.3 - - + +
403L ASP* 1.3 60.4 + - - +
405L ILE* 3.9 10.5 - - + +
406L GLN* 3.1 32.4 + - - +
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Residues in contact with ASP 403 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271J ARG* 4.7 8.0 + - - +
274J ASN* 5.4 3.6 - - - +
275J ARG* 3.3 35.9 + - - +
278J ARG* 3.3 32.4 + - - +
298J MET* 3.4 5.2 - - - +
399L LEU* 3.8 30.2 - - + +
400L GLN* 3.2 15.5 + - - +
401L PHE 3.2 1.0 - - - -
402L LEU* 1.3 77.4 - - - +
404L LEU* 1.3 64.1 + - - +
407L GLU* 3.2 30.2 + - - +
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Residues in contact with LEU 404 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391L ALA* 4.1 16.4 - - + +
394L TYR* 3.3 19.1 - - + +
395L THR* 3.7 28.7 - - + +
399L LEU* 4.0 13.7 - - + +
400L GLN 3.3 18.3 + - - +
401L PHE* 3.8 15.7 - - + +
402L LEU 3.5 0.2 - - - -
403L ASP* 1.3 78.7 - - - +
405L ILE* 1.3 61.1 + - - +
407L GLU* 3.6 3.1 + - - -
408L GLY 3.2 14.2 + - - -
439L ILE* 3.3 34.1 - - + +
443L ILE* 3.7 31.6 - - + -
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Residues in contact with ILE 405 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294J ASN* 5.5 0.2 - - - +
101L TYR* 3.6 42.6 - - + +
102L MET* 4.9 0.9 - - + -
387L VAL* 4.0 6.5 - - + +
388L ILE* 4.6 20.2 - - + -
391L ALA* 3.7 20.0 - - + -
401L PHE* 3.4 49.3 + - + +
402L LEU* 3.9 12.1 - - + +
403L ASP 3.2 0.4 - - - -
404L LEU* 1.3 78.5 - - - +
406L GLN* 1.3 58.5 + - + +
408L GLY* 2.7 19.8 + - - -
409L ASN* 2.9 25.3 + - - +
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Residues in contact with GLN 406 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J ARG* 3.4 23.8 - - - +
282J LEU* 3.4 26.5 - - - +
291J ILE* 3.2 37.0 + - - +
294J ASN* 2.4 37.2 + - - +
295J GLU* 3.4 15.3 - - - +
298J MET* 3.7 4.3 - - - -
101L TYR* 4.6 3.4 + - - -
402L LEU 3.1 15.7 + - - +
403L ASP 3.6 0.2 + - - -
404L LEU 3.4 0.2 - - - -
405L ILE* 1.3 75.9 - - + +
407L GLU* 1.3 60.0 + - - +
409L ASN* 4.1 11.7 + - - +
410L ILE* 3.3 27.9 + - - +
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Residues in contact with GLU 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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278J ARG* 2.9 30.4 + - - +
281J ARG* 3.2 29.3 + - - -
399L LEU* 6.0 1.1 - - + -
403L ASP 3.2 18.8 + - - +
404L LEU* 4.1 4.9 - - - +
405L ILE 3.2 0.6 - - - -
406L GLN* 1.3 75.7 - - - +
408L GLY* 1.3 64.2 + - - +
409L ASN 3.5 0.2 - - - -
410L ILE* 3.6 10.8 + - - +
411L GLY 3.4 13.7 + - - -
438L ALA* 3.5 23.8 - - - +
439L ILE* 4.8 2.5 - - - -
442L SER* 2.8 37.6 + - - +
446L GLN* 4.2 9.0 - - - +
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Residues in contact with GLY 408 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387L VAL* 3.8 16.6 - - - -
404L LEU 3.2 9.1 + - - -
405L ILE 2.7 10.8 + - - -
407L GLU* 1.3 76.5 - - - +
409L ASN* 1.3 53.4 + - - -
410L ILE 3.1 0.2 - - - -
411L GLY* 3.2 2.8 + - - -
412L LEU* 2.8 33.7 + - - +
435L ILE* 3.8 21.3 - - - +
438L ALA* 5.1 0.2 - - - -
439L ILE* 4.3 2.9 - - - -
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Residues in contact with ASN 409 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282J LEU* 6.1 0.2 - - + -
291J ILE* 3.4 35.7 - - + +
101L TYR* 3.0 26.1 + - - -
380L VAL* 5.7 0.9 - - + -
384L LEU* 3.7 12.8 - - + +
387L VAL* 3.3 19.6 - - - +
405L ILE* 2.9 19.9 + - - +
406L GLN* 4.0 13.5 + - - +
408L GLY* 1.3 72.4 - - - +
410L ILE* 1.3 60.1 + - + +
412L LEU* 3.7 14.3 - - + +
413L MET* 3.0 34.6 + - - +
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Residues in contact with ILE 410 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J ARG* 3.7 20.0 - - + +
281J ARG* 3.4 37.7 - - + +
282J LEU* 4.2 23.3 - - + -
285J LEU* 5.4 3.6 - - + -
406L GLN 3.3 16.9 + - - +
407L GLU* 3.7 15.9 - - - +
408L GLY 3.1 0.6 - - - -
409L ASN* 1.3 77.3 - - - +
411L GLY* 1.3 63.9 + - - +
413L MET* 3.3 12.2 + - + +
414L LYS* 3.1 53.4 + - + +
438L ALA* 5.7 2.5 - - + -
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Residues in contact with GLY 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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407L GLU 3.4 6.8 + - - -
408L GLY 3.2 6.0 + - - -
410L ILE* 1.3 79.5 - - - +
412L LEU* 1.3 54.6 + - - +
414L LYS* 3.4 8.9 - - - +
415L ALA* 2.5 37.2 + - - +
434L TRP* 4.0 18.9 - - - +
435L ILE* 5.1 1.1 - - - -
438L ALA* 4.4 13.7 - - - +
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Residues in contact with LEU 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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380L VAL* 3.6 36.8 - - + +
383L ASN* 4.0 15.7 - - + +
384L LEU* 3.9 13.0 - - + -
386L LEU* 5.0 1.1 - - + -
387L VAL* 3.8 27.1 - - + -
408L GLY 2.8 21.0 + - - +
409L ASN* 3.7 9.0 - - - -
411L GLY* 1.3 73.4 - - - +
413L MET* 1.3 60.1 + - - +
415L ALA* 3.9 4.7 - - - +
416L VAL* 3.3 25.7 + - + +
427L PHE* 4.0 26.5 - - + -
431L ALA* 4.4 8.3 - - + -
435L ILE* 4.6 6.2 - - + +
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Residues in contact with MET 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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282J LEU* 3.9 20.4 - - + -
285J LEU* 3.8 32.1 - - + +
287J ALA* 3.6 29.4 - - + -
288J PRO* 3.9 7.6 - - + -
291J ILE* 4.0 4.7 - - + -
376L LYS* 4.3 11.5 + - + +
380L VAL* 3.8 28.5 - - + -
409L ASN 3.0 24.0 + - - +
410L ILE* 3.6 13.5 - - + +
411L GLY 3.3 0.2 - - - -
412L LEU* 1.3 76.0 - - - +
414L LYS* 1.3 61.1 + - + +
416L VAL* 3.6 4.0 + - - +
417L ASP* 3.5 18.2 + - - +
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Residues in contact with LYS 414 (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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281J ARG* 4.1 15.2 - - - +
285J LEU* 3.8 33.8 - - - +
410L ILE* 3.1 39.1 + - + +
411L GLY* 3.0 11.0 + - - +
413L MET* 1.3 76.8 - - + +
415L ALA* 1.3 65.5 + - - +
417L ASP* 3.5 7.8 + - + +
418L LYS* 3.4 20.3 + - - +
434L TRP* 4.6 19.5 - - + -
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Residues in contact with ALA 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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411L GLY 2.5 20.9 + - - +
412L LEU* 3.9 5.4 - - - +
413L MET 3.3 0.2 - - - -
414L LYS* 1.3 71.9 - - - +
416L VAL* 1.3 59.4 + - - +
418L LYS 3.4 2.3 + - - -
419L PHE* 2.9 29.8 + - - +
427L PHE* 4.2 4.7 - - + -
430L TYR* 4.0 3.8 - - + -
431L ALA* 3.9 24.7 - - + +
434L TRP* 3.6 34.5 - - + +
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Residues in contact with VAL 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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123L ILE* 4.5 13.7 - - + +
376L LYS* 3.7 41.2 - - + +
379L MET* 4.5 17.5 - - + -
380L VAL* 4.1 16.6 - - + +
412L LEU* 3.3 19.1 + - + +
413L MET 3.9 4.9 - - - +
414L LYS 3.3 0.4 - - - -
415L ALA* 1.3 78.3 - - - +
417L ASP* 1.3 61.2 + - - +
419L PHE* 3.3 21.8 + - + +
427L PHE* 3.6 22.0 - - + -
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Residues in contact with ASP 417 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263L PRO* 5.7 4.7 - - - +
376L LYS* 3.1 26.5 + - - +
413L MET 3.5 9.0 + - - +
414L LYS* 3.9 10.1 - - + +
415L ALA 3.3 0.4 - - - -
416L VAL* 1.3 80.1 - - - +
418L LYS* 1.3 60.9 + - - +
419L PHE 3.5 2.0 + - - +
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Residues in contact with LYS 418 (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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414L LYS 3.4 11.7 + - - +
415L ALA 3.4 5.5 + - - +
416L VAL 3.2 0.4 - - - -
417L ASP* 1.3 79.4 - - - +
419L PHE* 1.3 63.4 + - - +
420L GLU* 3.6 19.2 + - - +
430L TYR* 3.2 27.5 + - - +
434L TRP* 3.9 20.2 - - + -
48O G 3.3 42.6 + - - +
49O C 3.2 31.7 + - - -
50O A 5.8 0.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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