Contacts of the helix formed by residues 578 - 595 (chain O) in PDB entry 6CNC
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 578 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLN* 5.6 5.2 - - + +
571O THR 5.2 0.2 + - - -
574O TYR* 4.3 4.4 + - - +
575O ASN* 2.6 61.2 + - - +
577O MET* 1.3 74.4 - - - +
579O GLN* 1.3 65.9 - - - +
580O ASN 2.9 0.4 - - - -
581O LEU* 2.9 23.9 + - + +
582O GLU* 3.7 4.0 + - - +
648O TRP* 3.6 24.7 - - + -
651O PHE* 3.2 33.4 + - + -
652O GLN* 4.3 14.1 + - - +
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Residues in contact with GLN 579 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLN* 6.1 0.4 - - - +
543O TYR* 5.6 3.9 - - - -
575O ASN 4.3 1.6 + - - -
576O PHE* 3.0 27.4 + - - +
577O MET* 4.3 3.9 - - - +
578O ARG* 1.3 77.8 - - - +
580O ASN* 1.3 54.2 + - + +
582O GLU* 2.9 11.6 + - - +
583O TRP* 2.5 68.8 + - + +
312P PHE* 3.8 30.7 + - - -
315P TRP* 3.1 45.0 - - + -
316P THR* 4.6 2.9 + - - -
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Residues in contact with ASN 580 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577O MET* 2.7 36.0 + - + +
579O GLN* 1.3 81.2 - - - +
581O LEU* 1.3 63.2 + - - +
583O TRP* 3.2 19.8 + - - +
584O ASN 4.1 1.0 + - - -
585O MET* 4.1 11.5 - - - +
644O LEU* 3.7 28.1 + - - +
647O LEU* 3.3 38.6 - - - +
648O TRP* 4.4 16.1 - - + +
651O PHE* 6.0 0.8 - - - -
41Q LEU* 5.1 4.4 - - - +
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Residues in contact with LEU 581 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O ASP* 4.2 16.6 - - - +
48O LEU* 3.4 34.9 - - + +
49O TYR* 5.5 5.4 - - + +
131O LEU* 5.3 0.4 - - + -
578O ARG* 2.9 15.4 + - + +
580O ASN* 1.3 80.4 - - - +
582O GLU* 1.3 77.7 + - + +
583O TRP 2.8 6.6 + - - -
585O MET* 3.0 37.0 - - - +
586O ALA 3.6 1.9 + - - -
648O TRP* 3.5 41.5 - - + +
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Residues in contact with GLU 582 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O ARG 5.2 1.6 - - - +
43O ASN 2.7 21.8 - - - +
44O PRO* 3.2 11.0 - - + -
45O ASP* 2.5 49.5 + - - +
47O PHE* 3.1 19.1 - - - +
48O LEU* 4.0 4.4 + - - -
578O ARG 4.6 5.8 - - - +
579O GLN* 2.9 9.9 + - - +
581O LEU* 1.3 89.1 - - + +
583O TRP* 1.3 65.3 + - - +
586O ALA* 3.1 16.3 - - - +
315P TRP* 3.9 32.9 - - + +
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Residues in contact with TRP 583 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543O TYR* 6.2 0.4 - + - -
579O GLN* 2.5 56.3 + - + +
580O ASN* 3.3 19.3 - - - +
581O LEU 2.8 4.9 + - - -
582O GLU* 1.3 79.7 - - - +
584O ASN* 1.3 104.7 + - + +
586O ALA* 3.5 7.3 - - - +
587O ASN* 3.7 7.3 + - - -
644O LEU* 4.9 2.5 - - + -
310P VAL* 3.7 10.1 - - + -
311P TYR 2.7 28.7 + - - +
312P PHE* 3.0 28.0 - + - -
313P ASP* 2.8 32.3 + - - -
314P GLU* 4.8 2.8 - - + +
315P TRP* 3.2 35.1 - + + +
316P THR 4.2 2.9 - - - -
41Q LEU* 5.3 1.6 - - + -
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Residues in contact with ASN 584 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580O ASN 4.1 0.4 + - - -
583O TRP* 1.3 107.0 + - + +
585O MET* 1.3 61.5 + - - +
586O ALA 2.9 0.9 - - - -
587O ASN* 2.7 38.6 + - - +
588O LEU* 2.2 47.6 + - + +
644O LEU* 4.1 5.5 - - + +
309P VAL 3.3 13.6 + - - +
310P VAL* 3.0 35.2 - - + +
311P TYR 3.8 0.3 + - - -
314P GLU* 4.2 6.7 + - - +
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Residues in contact with MET 585 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O PHE* 4.8 0.2 - - - -
48O LEU* 3.6 24.9 - - + +
51O GLU* 4.7 1.0 - - - +
131O LEU* 4.6 18.6 - - + -
580O ASN* 4.1 7.3 + - - +
581O LEU* 3.0 41.6 + - - +
584O ASN* 1.3 75.9 - - - +
586O ALA* 1.3 61.4 + - - +
588O LEU* 4.6 4.9 - - - -
589O LEU* 3.6 16.8 - - - +
641O LEU* 4.5 18.4 - - + -
644O LEU* 4.0 14.5 - - + +
645O LEU* 3.7 28.9 - - + +
648O TRP* 3.7 35.9 - - + -
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Residues in contact with ALA 586 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O GLN 5.3 3.6 - - - +
40O ARG* 5.6 3.6 - - - +
43O ASN 5.9 0.4 - - - +
47O PHE* 3.3 32.5 - - + -
48O LEU* 4.7 0.6 - - - +
51O GLU* 3.2 20.3 - - - +
581O LEU 3.6 5.5 + - - -
582O GLU* 3.1 27.1 - - - +
583O TRP 3.5 3.4 - - - +
584O ASN 3.1 0.7 - - - -
585O MET* 1.3 79.0 - - - +
587O ASN* 1.3 69.7 + - - +
590O PHE* 3.2 10.6 + - - -
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Residues in contact with ASN 587 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O SER* 4.9 9.1 + - - -
39O GLN* 4.4 14.6 + - - +
40O ARG* 5.0 12.3 - - - +
583O TRP 3.7 7.0 + - - -
584O ASN* 2.7 35.0 + - - +
586O ALA* 1.3 80.1 - - - +
588O LEU* 1.3 66.3 + - - +
590O PHE* 2.9 15.4 + - - +
591O LYS* 2.8 37.0 + - - +
314P GLU* 4.1 21.6 + - - +
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Residues in contact with LEU 588 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584O ASN* 2.2 37.4 + - + +
585O MET* 4.6 1.8 - - - +
587O ASN* 1.3 68.1 - - - +
589O LEU* 1.3 54.6 + - - +
591O LYS* 3.1 13.7 - - + +
592O LYS* 3.0 22.0 + - - +
637O VAL* 3.3 35.6 - - + +
640O ARG* 3.6 27.1 - - + +
641O LEU* 3.3 49.4 - - + +
644O LEU* 4.8 13.0 - - + -
308P GLU* 5.2 6.7 - - + -
309P VAL 5.7 3.1 - - - +
310P VAL* 5.0 8.1 - - + -
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Residues in contact with LEU 589 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LEU* 5.0 1.3 - - + +
51O GLU* 3.0 33.7 - - + +
52O LEU* 3.6 42.2 - - + +
55O ALA* 3.9 13.2 - - + -
584O ASN 3.7 0.8 + - - -
585O MET* 3.6 17.7 - - - +
586O ALA 3.5 1.4 + - - -
587O ASN 3.1 0.8 - - - -
588O LEU* 1.3 75.1 - - - +
590O PHE* 1.3 67.0 + - - +
592O LYS* 3.2 34.6 - - + +
593O GLU* 2.9 19.2 + - - +
638O PHE* 5.7 0.2 - - + -
641O LEU* 5.6 13.2 - - + -
58Q TYR* 6.1 0.4 - - - +
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Residues in contact with PHE 590 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O GLN* 2.9 51.8 - - + +
47O PHE* 3.1 39.3 - + - -
51O GLU* 2.7 30.1 + - + -
54O LYS* 6.0 6.3 - - + -
586O ALA 3.2 16.0 + - - -
587O ASN* 2.9 10.6 + - - +
589O LEU* 1.3 72.6 - - - +
591O LYS* 1.3 60.7 + - + +
593O GLU* 2.4 28.6 + - + +
594O LYS* 2.5 35.3 + - + -
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Residues in contact with LYS 591 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587O ASN* 2.8 33.9 + - - +
588O LEU* 3.1 12.8 - - - +
590O PHE* 1.3 74.0 - - + +
592O LYS* 1.3 61.7 + - - +
594O LYS* 5.2 2.5 - - - -
595O LEU* 3.2 27.4 + - - +
633O ARG* 3.4 18.6 + - - +
637O VAL* 4.1 7.2 - - + -
307P LYS* 3.3 45.1 + - - +
308P GLU* 3.4 29.2 - - + +
309P VAL 5.3 0.2 - - - +
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Residues in contact with LYS 592 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55O ALA* 4.6 6.4 + - - -
588O LEU 3.0 11.9 + - - +
589O LEU* 3.2 30.1 - - + +
590O PHE 2.8 0.6 + - - -
591O LYS* 1.3 78.3 - - - +
593O GLU* 1.3 79.8 + - - +
596O LYS* 2.9 43.0 + - + +
633O ARG* 5.3 0.2 - - - +
634O GLU* 3.8 19.1 + - - +
637O VAL* 4.4 11.6 - - + +
638O PHE* 3.3 39.7 - - + -
58Q TYR* 5.7 1.1 - - - -
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Residues in contact with GLU 593 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O GLU* 4.0 7.0 - - + +
54O LYS* 5.1 1.8 - - + +
55O ALA* 3.2 41.5 - - + +
589O LEU 2.9 15.5 + - - +
590O PHE* 2.4 19.8 + - + +
592O LYS* 1.3 95.9 + - - +
594O LYS* 1.3 54.4 + - + +
595O LEU 3.1 4.0 - - - -
596O LYS* 2.5 41.0 + - - +
597O GLN* 2.7 17.0 + - - +
66Q LYS* 5.9 0.9 + - - -
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Residues in contact with LYS 594 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O GLN* 4.5 8.1 - - - +
590O PHE* 2.5 45.7 + - + +
591O LYS* 5.1 1.6 - - - +
593O GLU* 1.3 76.7 - - + +
595O LEU* 1.3 55.1 + - - +
597O GLN* 2.8 34.0 + - - +
598O GLU* 4.8 4.2 + - - +
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Residues in contact with LEU 595 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591O LYS* 3.2 18.5 + - - +
592O LYS 4.5 1.8 - - - +
593O GLU 2.9 1.0 + - - -
594O LYS* 1.3 73.6 - - - +
596O LYS* 1.3 62.1 + - - +
597O GLN 2.9 5.8 - - - -
598O GLU* 2.8 49.0 + - + +
599O ASN* 4.1 1.2 + - - +
630O VAL* 3.6 26.4 - - + +
633O ARG* 3.4 51.6 - - + +
634O GLU* 3.9 10.5 - - - +
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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
------------------------------------------------------------
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