Contacts of the helix formed by residues 529 - 537 (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 LYS 529 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528O MET* 1.3 94.2 - - + +
530O GLU* 1.3 67.3 + - - +
531O LYS* 4.0 23.6 - - + +
532O ASP* 2.8 28.0 + - + +
533O ILE* 3.5 2.9 + - - +
171P ASP 5.2 6.1 + - - -
172P ILE* 5.6 15.2 - - + +
173P GLU* 4.0 25.8 + - - +
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Residues in contact with GLU 530 (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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307A ILE 5.1 1.6 - - - +
308A SER* 3.2 12.1 + - - -
523O ASN* 4.8 13.7 + - - +
528O MET 3.3 5.4 + - - -
529O LYS* 1.3 71.4 - - - +
531O LYS* 1.3 66.8 + - + +
533O ILE* 3.0 9.2 + - - +
534O ARG* 2.5 77.2 + - + +
142P PHE* 5.9 2.6 - - - -
31X G 5.4 4.8 + - - -
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Residues in contact with LYS 531 (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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305A LYS* 3.2 26.5 - - - +
306A GLY* 4.6 19.2 - - - -
307A ILE 5.3 2.2 - - - +
529O LYS* 3.0 24.7 - - + -
530O GLU* 1.3 80.7 - - + +
532O ASP* 1.3 58.5 + - - +
534O ARG* 5.1 1.6 - - - -
535O SER* 3.7 6.6 + - - -
30X T 3.4 23.2 + - - -
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Residues in contact with ASP 532 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503O SER* 3.6 15.6 + - - -
528O MET* 3.3 43.1 - - + +
529O LYS* 2.8 8.1 + - + +
531O LYS* 1.3 77.5 - - - +
533O ILE* 1.3 66.5 + - - +
535O SER* 2.8 16.6 + - - -
536O THR* 2.9 26.0 + - - +
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Residues in contact with ILE 533 (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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506O ARG* 5.1 5.4 - - - +
507O LEU* 3.9 20.6 - - + -
519O GLU* 5.3 2.7 - - + +
522O ILE* 5.0 15.7 - - + +
523O ASN* 5.0 12.3 - - + +
526O ALA* 5.8 1.6 - - + -
527O LEU* 5.1 4.7 - - - +
528O MET* 4.5 23.1 - - + +
529O LYS 4.1 9.6 - - - +
530O GLU* 3.0 11.3 + - - +
532O ASP* 1.3 76.8 - - + +
534O ARG* 1.3 80.3 + - - +
535O SER 2.9 1.0 + - - -
536O THR* 3.9 5.6 - - + -
537O LEU* 2.7 58.1 + - + +
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Residues in contact with ARG 534 (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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303A LEU* 4.1 6.6 - - - +
305A LYS 3.8 8.5 - - - +
306A GLY 3.3 23.1 - - - +
307A ILE* 3.3 14.1 - - + +
308A SER* 2.7 33.1 + - - +
309A ILE* 3.5 11.6 - - - +
519O GLU* 3.2 38.7 + - - +
523O ASN* 6.3 0.8 - - - +
530O GLU* 2.5 50.9 + - + +
531O LYS* 4.5 1.3 - - - +
533O ILE* 1.3 102.6 - - - +
535O SER* 1.3 59.1 + - - +
537O LEU* 5.2 4.3 - - - +
538O ALA* 3.2 25.9 - - + +
566O PHE* 6.1 0.4 - - - -
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Residues in contact with SER 535 (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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303A LEU 4.6 1.1 - - - -
304A ASP 2.9 26.2 + - - -
305A LYS* 3.0 19.0 + - - +
531O LYS 3.7 5.0 + - - -
532O ASP* 2.8 13.5 + - - -
534O ARG* 1.3 75.9 - - - +
536O THR* 1.3 53.8 + - - -
537O LEU 2.8 10.6 + - - -
538O ALA 3.1 0.5 + - - -
539O SER* 2.6 39.1 + - - +
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Residues in contact with THR 536 (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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500O LEU* 4.7 4.5 + - - +
503O SER* 3.4 17.5 - - - +
504O ALA* 3.0 37.4 + - - +
507O LEU* 3.6 26.9 - - + +
532O ASP* 2.9 32.9 + - - +
533O ILE* 3.9 7.0 - - + -
535O SER* 1.3 75.4 - - - +
537O LEU* 1.3 58.6 + - - +
539O SER* 4.7 4.0 - - - -
540O LEU* 3.7 16.0 + - - +
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Residues in contact with LEU 537 (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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309A ILE* 5.3 6.7 - - + -
507O LEU* 4.3 21.8 - - + -
511O ILE* 5.3 4.9 - - + -
519O GLU* 5.5 0.9 - - + -
522O ILE* 5.2 9.9 - - + -
533O ILE* 2.7 34.2 + - + +
534O ARG* 6.1 3.8 - - - +
536O THR* 1.3 78.3 - - - +
538O ALA* 1.3 65.2 + - + +
539O SER 3.2 1.1 - - - -
540O LEU* 2.7 26.6 + - - +
541O ILE* 3.0 13.6 + - + +
546O VAL* 5.1 15.1 - - + +
566O PHE* 3.4 49.8 - - + -
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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