Contacts of the helix formed by residues 465 - 475 (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 465 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425S MET* 3.6 12.3 - - - +
429S TYR* 3.2 25.2 + - - -
461S GLU* 2.4 59.8 + - + +
464S LYS* 1.3 79.8 - - + +
466S PRO* 1.3 65.0 - - - +
467S ILE* 3.2 4.3 + - + -
468S LEU* 3.5 38.1 + - + +
469S ILE* 3.7 8.0 + - - +
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Residues in contact with PRO 466 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462S GLU* 3.2 22.2 - - + +
463S LYS* 3.4 9.2 - - - +
464S LYS 3.2 12.6 - - - +
465S ARG* 1.3 86.0 - - - +
467S ILE* 1.3 66.4 + - + +
468S LEU 3.4 0.2 - - - -
469S ILE* 3.1 9.7 + - + +
470S GLU* 2.9 37.1 + - + +
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Residues in contact with ILE 467 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465S ARG* 3.2 1.7 - - - -
466S PRO* 1.3 84.4 - - + +
468S LEU* 1.3 68.0 + - + +
470S GLU* 2.8 33.0 + - + +
471S LEU* 2.9 14.2 + - + +
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Residues in contact with LEU 468 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429S TYR* 3.2 44.2 - - + +
465S ARG* 3.5 43.0 + - + +
466S PRO 3.4 0.4 - - - -
467S ILE* 1.3 82.4 - - + +
469S ILE* 1.3 60.0 + - + +
471S LEU* 3.6 7.4 + - - +
472S ALA* 2.9 28.1 + - - +
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Residues in contact with ILE 469 (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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433R ARG* 5.1 2.3 - - + -
428S PHE* 5.3 2.0 - - + -
429S TYR* 5.5 3.4 - - + -
432S LEU* 4.2 18.4 - - + -
458S PHE* 4.1 35.7 - - + -
461S GLU* 4.7 7.4 - - + -
462S GLU* 3.7 40.6 - - + +
465S ARG 3.7 8.1 - - - +
466S PRO* 3.1 8.3 + - + +
467S ILE 3.1 0.4 - - - -
468S LEU* 1.3 78.6 - - + +
470S GLU* 1.3 65.2 + - - +
472S ALA* 4.0 3.1 - - + -
473S LEU* 2.9 43.4 + - + +
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Residues in contact with GLU 470 (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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433R ARG* 3.1 43.2 + - - +
466S PRO* 2.9 25.1 + - + +
467S ILE* 2.8 28.8 + - + +
469S ILE* 1.3 81.0 - - - +
471S LEU* 1.3 54.2 + - - +
474S ARG* 2.4 53.5 + - + +
475S SER* 4.7 0.2 + - - -
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Residues in contact with LEU 471 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433S SER* 4.5 6.5 - - - +
467S ILE* 2.9 11.3 + - + +
468S LEU* 4.0 7.6 - - - +
470S GLU* 1.3 76.5 - - - +
472S ALA* 1.3 59.1 + - - +
475S SER* 2.7 57.4 + - - +
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Residues in contact with ALA 472 (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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429S TYR* 4.7 5.8 - - + +
432S LEU* 3.5 38.1 - - + -
433S SER* 2.8 36.7 + - - +
468S LEU 2.9 19.7 + - - +
469S ILE* 3.4 7.2 + - + +
471S LEU* 1.3 79.3 - - - +
473S LEU* 1.3 58.8 + - + +
475S SER 2.9 10.4 - - - +
476S LYS* 3.4 0.7 - - - +
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Residues in contact with LEU 473 (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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416R ARG* 4.6 17.0 + - + +
417R ASN* 4.9 17.9 - - - +
431R ARG* 6.4 1.1 - - - -
433R ARG* 3.6 40.2 - - + +
432S LEU* 4.6 4.5 - - + +
436S GLY* 5.1 11.4 - - - -
437S THR* 5.3 3.6 - - - +
458S PHE* 6.1 4.0 - - + -
469S ILE* 2.9 26.5 + - + +
472S ALA* 1.3 72.8 - - + +
474S ARG* 1.3 64.8 + - - +
476S LYS* 3.2 30.4 - - + +
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Residues in contact with ARG 474 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416R ARG* 5.5 0.9 + - - -
433R ARG* 4.1 35.1 - - - +
609R GLU* 6.0 1.3 - - - +
469S ILE 3.9 0.2 + - - -
470S GLU* 2.4 51.6 + - - +
473S LEU* 1.3 81.0 - - - +
475S SER* 1.3 61.5 + - - +
476S LYS* 3.6 6.1 + - - +
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Residues in contact with SER 475 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433S SER* 3.3 7.6 + - - -
470S GLU 4.7 0.3 + - - -
471S LEU* 2.7 50.0 + - - +
472S ALA 2.9 12.0 - - - +
474S ARG* 1.3 77.5 - - - +
476S LYS* 1.3 59.2 + - - +
477S LEU 4.1 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
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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