Contacts of the helix formed by residues 421 - 435 (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 THR 421 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419S PRO 3.9 2.2 + - - -
420S TRP* 1.3 77.1 - - - +
422S VAL* 1.3 67.1 + - - +
423S GLU* 3.9 15.5 + - + +
424S GLU* 3.4 34.3 + - + +
425S MET* 2.8 27.0 + - - +
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Residues in contact with VAL 422 (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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421S THR* 1.3 80.6 + - - +
423S GLU* 1.3 54.7 + - + +
425S MET* 2.7 17.3 + - + -
426S ILE* 2.4 57.6 + - + +
429S TYR* 5.4 4.5 - - + -
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Residues in contact with GLU 423 (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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421S THR* 3.5 12.1 + - + +
422S VAL* 1.3 78.5 - - + +
424S GLU* 1.3 60.0 + - - +
426S ILE* 3.1 33.2 + - + +
427S LYS* 3.7 15.8 + - - +
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Residues in contact with GLU 424 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419S PRO 4.1 0.9 - - - +
420S TRP* 3.2 29.1 - - + -
421S THR* 3.4 32.8 + - + +
422S VAL 3.2 0.4 - - - -
423S GLU* 1.3 78.3 - - - +
425S MET* 1.3 58.3 + - - +
427S LYS* 5.8 0.2 - - - -
428S PHE* 3.9 1.6 + - - +
446S TYR* 2.2 50.4 + - + -
448S TYR* 4.6 3.8 - - - -
449S ARG* 2.4 50.1 + - - +
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Residues in contact with MET 425 (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* 4.5 11.4 - - + +
421S THR 2.8 18.3 + - - +
422S VAL* 2.7 25.0 + - + +
424S GLU* 1.3 72.8 - - - +
426S ILE* 1.3 57.0 + - - +
427S LYS 3.4 0.2 - - - -
428S PHE* 3.0 18.5 + - + +
429S TYR* 2.8 65.3 + - + -
457S LYS* 3.2 40.2 - - - +
461S GLU* 4.2 11.2 - - + +
465S ARG* 3.6 17.9 - - - +
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Residues in contact with ILE 426 (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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422S VAL* 2.4 46.6 + - + +
423S GLU* 3.1 31.0 - - + +
425S MET* 1.3 67.1 - - - +
427S LYS* 1.3 59.4 + - + +
429S TYR* 2.9 20.2 + - + +
430S LYS* 2.7 48.8 + - - +
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Residues in contact with LYS 427 (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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423S GLU 3.7 11.6 + - - +
424S GLU* 5.8 0.4 - - - -
426S ILE* 1.3 81.0 - - + +
428S PHE* 1.3 60.1 + - - +
430S LYS* 3.3 27.7 - - + +
431S ALA* 3.2 21.7 + - - +
445S LEU* 4.5 9.6 - - + +
446S TYR* 3.0 31.1 - - + +
486S CYS* 5.0 18.4 - - - -
489S LYS* 5.1 10.9 - - - +
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Residues in contact with PHE 428 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420S TRP* 5.9 3.1 - + + -
424S GLU 4.1 4.3 - - - +
425S MET* 3.0 31.5 + - + +
427S LYS* 1.3 74.7 - - - +
429S TYR* 1.3 70.3 + + - +
430S LYS 3.2 0.2 + - - -
431S ALA* 3.3 4.2 + - - +
432S LEU* 3.1 46.9 + - + +
439S PHE* 5.3 0.4 - + - -
442S ILE* 3.5 36.6 - - + -
446S TYR* 3.5 11.9 + + + -
454S VAL* 3.5 25.6 - - + -
457S LYS* 5.3 15.3 - - + -
458S PHE* 3.6 40.8 - + + -
461S GLU* 5.6 8.3 - - + -
469S ILE* 5.3 3.4 - - + -
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Residues in contact with TYR 429 (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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422S VAL* 5.4 2.2 - - + -
425S MET* 2.8 67.5 + - + -
426S ILE* 2.9 24.4 + - + +
428S PHE* 1.3 76.5 - + - +
430S LYS* 1.3 64.7 - - - +
432S LEU* 3.2 33.3 - - + +
433S SER* 3.3 9.4 + - - -
461S GLU* 4.7 6.0 + - + +
465S ARG* 3.2 10.9 + - - -
468S LEU* 3.2 48.5 - - + +
469S ILE* 5.5 3.1 - - + -
472S ALA* 4.7 3.1 - - + +
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Residues in contact with LYS 430 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426S ILE* 2.7 30.0 + - + +
427S LYS* 3.3 35.4 - - + +
428S PHE 3.1 0.2 - - - -
429S TYR* 1.3 71.1 - - - +
431S ALA* 1.3 65.1 + - - +
433S SER* 2.8 18.7 + - - -
434S MET* 2.9 17.1 + - + +
482S ASP* 3.1 33.5 + - - +
486S CYS* 5.2 3.1 - - - -
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Residues in contact with ALA 431 (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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427S LYS 3.2 4.1 + - - +
428S PHE 3.3 6.0 + - - +
430S LYS* 1.3 77.2 - - - +
432S LEU* 1.3 62.5 + - - +
434S MET* 3.5 3.6 - - - -
435S TRP* 3.0 52.4 + - + +
436S GLY 3.8 8.7 + - - +
441S LEU* 6.1 0.2 - - + -
442S ILE* 4.0 17.0 - - + -
445S LEU* 3.6 23.1 - - + -
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Residues in contact with LEU 432 (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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428S PHE* 3.1 57.8 + - + +
429S TYR* 3.2 27.6 - - + +
430S LYS 2.9 1.2 + - - -
431S ALA* 1.3 77.2 - - - +
433S SER* 1.3 49.3 + - - +
436S GLY* 4.2 14.1 + - - +
437S THR* 6.1 1.6 - - - -
442S ILE* 4.7 6.5 - - + -
458S PHE* 4.0 18.4 - - + -
469S ILE* 4.2 11.4 - - + -
472S ALA* 3.5 31.7 - - + +
473S LEU* 4.6 3.6 - - - +
476S LYS* 2.3 29.5 + - - -
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Residues in contact with SER 433 (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 3.3 5.3 + - - -
430S LYS* 2.8 10.6 + - - -
432S LEU* 1.3 70.7 - - - +
434S MET* 1.3 58.5 + - - +
471S LEU* 3.9 7.6 + - - +
472S ALA* 2.8 32.1 + - - -
475S SER 3.3 10.8 + - - -
476S LYS* 3.2 20.8 - - - +
477S LEU* 3.3 39.9 + - - +
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Residues in contact with MET 434 (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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430S LYS* 2.9 32.3 + - - +
431S ALA* 3.2 3.3 + - - +
433S SER* 1.3 80.5 - - - +
435S TRP* 1.3 88.3 + - + +
476S LYS* 3.8 4.2 + - - -
477S LEU* 3.6 28.9 - - + -
479S PRO* 3.2 49.8 - - + +
480S ASN 4.4 0.9 - - - +
482S ASP* 3.5 24.9 - - + +
483S GLU* 3.3 33.0 - - - +
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Residues in contact with TRP 435 (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* 4.4 13.0 - - - +
619R ALA* 6.2 1.1 - - + -
622R LEU* 5.1 0.2 - - - +
623R LYS* 3.3 49.4 + - + +
626R ILE* 5.0 13.9 - - + +
431S ALA* 3.0 39.4 + - + +
434S MET* 1.3 104.7 - - + +
436S GLY* 1.3 59.6 + - - +
438S ASP* 6.1 2.2 - - + -
441S LEU* 3.6 33.0 - - + +
445S LEU* 4.4 13.2 - - + -
476S LYS* 3.6 10.6 + - - -
479S PRO* 5.4 2.5 - - + -
482S ASP* 4.6 5.4 - - - -
483S GLU* 3.7 56.9 + - + +
486S CYS* 4.7 12.1 - - + -
487S GLU* 5.1 2.0 - - - -
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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