Contacts of the helix formed by residues 383 - 393 (chain S) in PDB entry 6CNB
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 383 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B VAL* 6.0 4.2 - - - +
89B PRO* 3.3 47.3 - - + +
88P ALA* 4.6 21.1 - - - -
89P GLU* 3.7 23.2 + - - -
116P LEU* 5.2 10.3 - - - +
381S VAL* 3.6 25.3 + - + +
382S ASP* 1.3 77.4 + - - +
384S HIS* 1.3 73.4 + - - +
385S LYS* 3.4 3.8 - - - +
386S ASN* 3.5 33.5 - - + +
387S ALA 3.9 2.3 + - - -
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Residues in contact with HIS 384 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.6 28.0 - - + +
85B SER 4.5 6.5 + - - -
86B ASP* 4.9 13.7 - - - -
87B VAL 4.7 6.4 + - - -
89B PRO* 3.3 40.9 - - + +
382S ASP* 2.8 44.1 + - - +
383S ARG* 1.3 87.3 - - - +
385S LYS* 1.3 64.5 + - + +
386S ASN 3.1 2.0 - - - -
387S ALA* 2.9 17.4 + - - +
388S SER* 2.9 13.8 + - - -
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Residues in contact with LYS 385 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382S ASP* 3.2 30.9 + - + +
383S ARG 3.4 2.0 - - - +
384S HIS* 1.3 77.1 - - - +
386S ASN* 1.3 64.9 + - - +
388S SER* 2.5 27.8 + - - +
389S ILE* 2.9 20.1 + - + +
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Residues in contact with ASN 386 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360S THR* 5.6 9.2 - - - +
383S ARG* 3.5 31.1 - - + +
384S HIS 3.1 0.2 - - - -
385S LYS* 1.3 80.2 - - - +
387S ALA* 1.3 56.8 + - - +
389S ILE* 3.4 13.8 + - - +
390S GLU* 2.9 27.9 + - - +
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Residues in contact with ALA 387 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PRO* 3.5 27.4 - - + +
90B GLU* 3.6 21.8 - - + -
383S ARG 3.9 1.7 + - - +
384S HIS* 2.9 13.8 + - + +
386S ASN* 1.3 75.6 - - - +
388S SER* 1.3 53.1 + - - +
390S GLU* 2.7 9.5 + - - -
391S ASN* 2.3 50.0 + - - +
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Residues in contact with SER 388 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384S HIS 2.9 13.8 + - - -
385S LYS* 2.5 34.5 + - - +
387S ALA* 1.3 71.3 - - - +
389S ILE* 1.3 63.3 + - - +
391S ASN* 3.6 14.0 - - - +
392S GLU* 3.3 31.2 + - - +
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Residues in contact with ILE 389 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385S LYS* 2.9 24.3 + - + +
386S ASN* 3.7 15.7 - - - +
388S SER* 1.3 79.5 + - - +
390S GLU* 1.3 62.1 + - - +
391S ASN 3.5 0.2 + - - -
392S GLU* 3.6 20.1 + - - +
393S TYR* 3.7 11.1 - - + -
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Residues in contact with GLU 390 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU* 2.8 30.1 - - - +
386S ASN 2.9 17.3 + - - +
387S ALA* 2.7 11.7 + - - +
389S ILE* 1.3 72.5 - - - +
391S ASN* 1.3 67.0 + - - +
393S TYR* 3.0 53.4 + - + +
394S LYS* 3.1 33.5 - - - +
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Residues in contact with ASN 391 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLU* 4.3 8.0 - - - +
91B PHE 5.3 2.6 + - - +
92B TYR* 3.7 37.6 + - + +
136B THR* 5.3 2.5 - - - +
142B ILE* 4.7 8.6 - - + +
387S ALA* 2.3 53.2 + - - +
388S SER* 3.6 13.4 - - - +
389S ILE 3.3 0.2 - - - -
390S GLU* 1.3 81.0 - - - +
392S GLU* 1.3 63.4 + - + +
394S LYS* 3.3 37.3 + - + +
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Residues in contact with GLU 392 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B ILE* 5.1 1.7 - - - +
388S SER 3.3 17.5 + - - +
389S ILE* 4.0 13.4 - - - +
390S GLU 3.3 0.8 - - - -
391S ASN* 1.3 77.3 - - + +
393S TYR* 1.3 63.0 + - - +
394S LYS 3.1 10.9 + - - +
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Residues in contact with TYR 393 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ASN* 4.8 2.9 + - - -
389S ILE* 3.7 9.6 - - + -
390S GLU* 3.0 59.8 + - + +
392S GLU* 1.3 74.4 - - - +
394S LYS* 1.3 70.3 + - + +
395S GLU* 3.4 4.2 + - - +
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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
------------------------------------------------------------
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