Contacts of the helix formed by residues 383 - 391 (chain L) in PDB entry 6PSU
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 ASN 383 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116L GLU* 5.7 1.6 + - - -
379L MET* 4.1 6.7 - - + +
380L VAL 3.2 2.0 + - - -
381L GLU 3.0 2.0 + - - -
382L ALA* 1.3 81.3 + - - +
384L LEU* 1.3 65.5 + - - +
385L ARG* 3.1 3.4 - - - +
386L LEU* 3.0 32.5 + - - +
387L VAL 3.5 2.4 + - - -
412L LEU* 3.6 28.7 - - + +
427L PHE* 3.3 35.4 - - + -
428L SER* 4.7 1.6 - - - +
431L ALA* 3.7 0.9 - - - +
435L ILE* 4.4 0.5 - - - +
54O T 3.3 33.2 + - - +
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Residues in contact with LEU 384 (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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290J ILE* 5.2 8.7 - - + -
291J ILE* 4.8 10.1 - - + -
101L TYR* 3.2 25.6 - - + +
105L MET* 3.3 28.3 - - + -
108L VAL* 5.8 2.7 - - + -
380L VAL* 3.0 28.5 - - + +
381L GLU* 3.6 18.2 + - - +
383L ASN* 1.3 77.4 - - - +
385L ARG* 1.3 58.0 + - - +
387L VAL* 2.9 14.3 + - + +
388L ILE* 2.9 32.9 + - - +
409L ASN* 3.8 12.1 - - - +
412L LEU* 3.3 17.9 - - + -
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Residues in contact with ARG 385 (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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105L MET* 3.7 25.4 + - + +
106L GLY* 6.0 0.4 + - - -
108L VAL* 4.8 20.9 + - + +
109L GLU* 5.9 1.1 - - - -
110L LEU* 5.7 8.3 - - - +
382L ALA 6.2 1.8 - - - -
383L ASN* 3.1 1.7 - - - -
384L LEU* 1.3 79.1 - - - +
386L LEU* 1.3 59.6 + - - +
389L SER* 3.2 20.4 + - - -
54O T 3.1 37.5 + - + +
55O C 2.2 107.5 + - - +
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Residues in contact with LEU 386 (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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383L ASN* 3.0 28.4 + - - +
385L ARG* 1.3 74.9 - - - +
387L VAL* 1.3 51.3 + - - +
389L SER* 2.1 29.8 + - - +
390L ILE* 2.7 29.0 + - + +
428L SER* 3.4 31.0 - - - +
431L ALA* 3.4 14.1 - - + -
432L THR* 3.3 27.8 - - - +
435L ILE* 4.4 0.9 - - + -
53O T 4.1 23.1 - - + -
54O T 2.7 29.9 + - + +
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Residues in contact with VAL 387 (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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101L TYR* 5.6 1.6 - - + +
383L ASN 3.5 2.8 + - - +
384L LEU* 2.9 34.7 + - + +
386L LEU* 1.3 78.8 - - - +
388L ILE* 1.3 63.1 + - + +
390L ILE* 3.7 7.7 - - - +
391L ALA* 3.0 30.4 + - + +
405L ILE* 4.4 9.9 - - + +
408L GLY* 3.4 42.4 - - - +
409L ASN* 3.9 17.3 - - - +
412L LEU* 4.6 3.4 - - + -
435L ILE* 3.6 19.5 - - + -
439L ILE* 5.4 1.1 - - + -
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Residues in contact with ILE 388 (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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101L TYR* 4.5 10.3 - - + -
102L MET* 4.7 12.8 - - + -
105L MET* 3.4 38.4 - - + -
384L LEU 2.9 15.9 + - - +
387L VAL* 1.3 81.8 - - + +
389L SER* 1.3 59.0 + - - +
391L ALA* 3.9 4.1 + - - +
392L LYS* 3.0 30.5 + - + +
401L PHE* 4.5 21.9 - - + -
405L ILE* 5.3 9.0 - - + -
55O C 4.2 26.9 - - - +
56O C 3.9 21.8 - - - +
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Residues in contact with SER 389 (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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385L ARG 3.2 12.1 + - - -
386L LEU* 2.1 39.8 + - - +
388L ILE* 1.3 77.2 - - - +
390L ILE* 1.3 67.7 + - - +
392L LYS* 3.3 28.4 + - - +
393L LYS* 4.1 12.9 + - - -
53O T 5.0 4.0 - - - +
54O T 4.6 20.2 + - - -
55O C 4.7 7.7 + - - -
56O C 6.1 0.4 - - - -
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Residues in contact with ILE 390 (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 LEU* 2.7 32.7 + - + +
387L VAL 3.2 4.9 + - - +
389L SER* 1.3 77.0 - - - +
391L ALA* 1.3 58.5 + - - +
392L LYS 3.0 5.8 + - - -
393L LYS* 3.6 12.8 + - - +
394L TYR* 4.5 13.1 - - + -
432L THR* 3.3 42.2 - - + +
435L ILE* 3.3 49.1 - - + +
436L ARG* 4.5 14.8 - - + -
439L ILE* 4.9 1.8 - - + -
35P A 4.4 15.2 + - - +
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Residues in contact with ALA 391 (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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387L VAL* 3.0 17.2 + - + +
388L ILE* 4.1 3.1 - - - +
389L SER 3.4 0.2 - - - -
390L ILE* 1.3 74.0 - - - +
392L LYS* 1.3 60.0 + - - +
393L LYS 3.1 7.1 + - - -
394L TYR* 3.6 15.0 + - - +
395L THR* 3.1 18.7 - - - +
401L PHE* 4.9 3.9 - - + -
404L LEU* 3.9 35.3 - - + +
405L ILE* 4.6 11.7 - - + -
439L ILE* 4.8 8.1 - - + -
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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