Contacts of the helix formed by residues 450 - 465 (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 SER 450 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443S SER* 3.9 6.1 - - - -
449S ARG* 1.3 74.2 - - - +
451S ARG* 1.3 69.3 + - - +
452S LYS* 3.5 19.4 + - - +
453S GLN* 2.5 45.2 + - - +
454S VAL* 3.4 13.2 + - - +
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Residues in contact with ARG 451 (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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419R GLU* 3.9 22.2 + - - -
421R ASN* 5.1 14.4 - - - +
424R ARG* 4.5 19.4 - - - +
429R ILE* 6.0 1.4 - - - +
439S PHE* 4.3 20.0 - - - +
440S ASN* 4.8 18.1 - - - +
443S SER* 3.5 28.8 + - - +
450S SER* 1.3 77.0 + - - +
452S LYS* 1.3 83.2 + - + +
453S GLN 3.1 2.0 - - - -
454S VAL* 2.9 10.4 + - - +
455S LYS* 2.8 28.5 + - - +
52Y A 3.8 32.6 + - - -
53Y C 4.9 9.3 + - - -
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Residues in contact with LYS 452 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424R ARG* 5.1 15.0 - - - +
413S ARG* 5.5 6.7 - - - +
450S SER* 3.7 15.5 - - - +
451S ARG* 1.3 92.9 - - + +
453S GLN* 1.3 62.5 + - + +
455S LYS* 3.2 12.7 - - + +
456S ALA* 2.9 31.5 + - - +
10X T 4.8 0.8 + - - -
11X A 5.0 11.9 - - - +
52Y A 5.3 7.6 + - - -
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Residues in contact with GLN 453 (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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416S TYR 4.8 3.8 + - - -
417S THR* 4.1 33.1 - - + +
420S TRP* 4.0 14.7 + - + +
448S TYR 5.7 0.2 + - - -
449S ARG* 3.2 28.0 - - - +
450S SER* 2.5 45.7 + - - +
452S LYS* 1.3 82.3 - - + +
454S VAL* 1.3 57.3 + - - +
456S ALA* 4.2 0.7 - - - +
457S LYS* 2.9 33.6 + - - +
10X T 4.2 11.5 + - - +
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Residues in contact with VAL 454 (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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420S TRP* 4.0 21.8 - - + -
428S PHE* 3.5 27.5 - - + -
439S PHE* 3.5 20.4 - - + +
442S ILE* 3.7 31.9 - - + +
443S SER* 4.7 5.6 - - - +
446S TYR* 5.1 1.3 - - + -
449S ARG* 5.3 1.1 - - + -
450S SER 3.4 13.7 + - - +
451S ARG* 2.9 11.7 + - - +
453S GLN* 1.3 73.0 - - - +
455S LYS* 1.3 59.8 + - - +
457S LYS* 4.1 5.6 - - - +
458S PHE* 2.9 33.1 + - - +
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Residues in contact with LYS 455 (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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431R ARG* 4.0 17.9 - - - +
439S PHE* 3.5 33.1 - - + -
451S ARG* 2.8 12.2 + - - +
452S LYS* 3.1 20.8 + - + +
454S VAL* 1.3 80.3 - - - +
456S ALA* 1.3 64.8 + - + +
458S PHE* 3.2 2.6 + - - +
459S VAL* 3.0 41.1 + - + +
53Y C 3.2 37.3 - - - +
54Y T 3.8 16.8 + - - -
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Residues in contact with ALA 456 (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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452S LYS 2.9 16.6 + - - +
455S LYS* 1.3 75.8 - - + +
457S LYS* 1.3 64.7 + - - +
459S VAL* 3.0 11.8 + - - +
460S ASN* 2.9 20.8 + - - +
10X T 3.3 31.6 - - - +
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Residues in contact with LYS 457 (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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420S TRP* 3.2 69.3 + - + +
425S MET* 3.2 36.2 - - - +
428S PHE* 5.3 13.9 - - + -
453S GLN 2.9 18.8 + - - +
454S VAL* 4.1 4.3 - - + +
456S ALA* 1.3 75.7 - - - +
458S PHE* 1.3 59.7 + - - +
460S ASN* 2.8 23.0 + - - +
461S GLU* 2.9 28.2 + - + +
9X A 5.3 10.9 + - - +
10X T 5.2 1.0 + - - +
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Residues in contact with PHE 458 (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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431R ARG* 3.8 20.9 - - - -
428S PHE* 3.6 31.8 - + + -
432S LEU* 4.0 18.2 - - + -
437S THR* 4.6 11.7 - - - -
439S PHE* 3.3 28.7 - + + -
454S VAL 2.9 21.4 + - - +
455S LYS 3.4 1.1 - - - +
457S LYS* 1.3 76.2 - - - +
459S VAL* 1.3 63.8 + - + +
461S GLU* 4.4 2.0 - - - +
462S GLU* 2.9 59.1 + - - +
469S ILE* 4.1 28.0 - - + -
473S LEU* 6.1 4.3 - - + -
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Residues in contact with VAL 459 (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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431R ARG* 5.8 2.5 - - - +
455S LYS* 3.0 38.7 + - - +
456S ALA* 3.0 11.5 + - - +
458S PHE* 1.3 81.5 - - + +
460S ASN* 1.3 56.9 + - - +
462S GLU* 3.4 17.3 - - - +
463S LYS* 2.9 30.2 + - + +
54Y T 5.9 8.7 - - - -
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Residues in contact with ASN 460 (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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456S ALA 2.9 11.1 + - - +
457S LYS* 2.8 10.9 + - + +
459S VAL* 1.3 74.7 - - - +
461S GLU* 1.3 61.0 + - + +
463S LYS* 2.7 16.1 + - - +
464S LYS* 2.6 69.5 + - - +
9X A 2.4 46.7 + - - +
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Residues in contact with GLU 461 (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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425S MET* 4.2 17.9 - - + +
428S PHE* 5.6 7.9 - - + -
429S TYR* 5.3 5.4 - - + +
457S LYS* 2.9 35.9 + - + +
458S PHE* 4.4 3.8 - - - +
460S ASN* 1.3 82.2 - - - +
462S GLU* 1.3 56.3 + - - +
464S LYS* 4.4 7.3 - - - +
465S ARG* 2.4 84.7 + - + +
469S ILE* 4.4 9.2 - - + -
9X A 5.0 3.8 + - - -
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Residues in contact with GLU 462 (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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431R ARG* 4.7 5.5 + - - -
436R LYS* 2.2 37.6 + - - +
458S PHE* 2.9 48.6 + - + +
459S VAL* 3.4 19.3 - - - +
461S GLU* 1.3 76.7 - - - +
463S LYS* 1.3 60.4 + - - +
466S PRO* 3.2 26.1 - - + +
469S ILE* 3.7 27.1 - - + +
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Residues in contact with LYS 463 (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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459S VAL* 2.9 16.9 + - + +
460S ASN* 2.7 30.3 + - - +
462S GLU* 1.3 70.3 - - - +
464S LYS* 1.3 82.1 + - - +
466S PRO* 3.4 15.2 - - - +
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Residues in contact with LYS 464 (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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460S ASN* 2.6 54.5 + - - +
461S GLU* 4.6 8.7 - - - +
463S LYS* 1.3 93.2 - - - +
465S ARG* 1.3 67.6 + - + +
466S PRO* 3.2 8.8 - - - +
7X A 5.6 1.1 - - - -
8X C 4.6 13.8 + - - +
9X A 3.8 5.1 + - - -
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Residues in contact with ARG 465 (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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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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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