Contacts of the helix formed by residues 518 - 526 (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 SER 518 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 5.3 4.2 - - - +
208A ASN* 5.2 8.3 + - - +
517O VAL* 1.3 76.2 - - - +
519O GLU* 1.3 71.0 + - - +
520O LYS* 4.1 10.3 + - - +
521O ILE* 3.0 25.5 + - - +
522O ILE* 3.0 19.3 + - - +
563O VAL* 6.4 0.2 - - - -
564O PHE 3.6 20.0 - - - -
565O LEU* 4.4 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 519 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 5.3 0.2 + - - -
309A ILE* 3.5 23.0 - - + +
310A ASN* 5.1 5.7 - - - +
517O VAL 4.1 1.2 + - - -
518O SER* 1.3 67.7 - - - +
520O LYS* 1.3 62.2 + - - +
522O ILE* 3.5 14.6 - - + +
523O ASN* 2.7 34.0 + - - +
533O ILE* 5.3 4.0 - - + +
534O ARG* 3.2 39.7 + - - +
537O LEU* 5.5 0.4 - - + -
564O PHE* 3.7 19.0 + - - +
566O PHE* 4.2 21.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 520 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ASN* 5.2 14.8 + - - +
518O SER* 3.1 8.2 + - - +
519O GLU* 1.3 89.7 - - - +
521O ILE* 1.3 68.6 + - + +
523O ASN* 3.1 21.0 + - - +
524O SER* 3.3 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 521 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLU 4.9 5.2 - - - +
204A VAL* 5.4 5.2 - - + -
207A HIS* 3.2 52.5 - - + +
208A ASN* 5.6 7.2 - - + -
514O ASN* 5.7 0.9 - - - +
517O VAL* 3.5 22.4 - - + -
518O SER* 3.0 24.9 + - - +
520O LYS* 1.3 88.5 - - + +
522O ILE* 1.3 62.8 + - - +
523O ASN 3.2 0.7 - - - -
524O SER* 3.3 13.3 - - - +
525O THR* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 522 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507O LEU* 4.9 13.0 - - + -
510O CYS* 4.1 20.9 - - + -
511O ILE* 3.7 17.0 - - + -
514O ASN* 4.8 1.1 - - - +
517O VAL* 3.5 37.2 - - + +
518O SER 3.0 18.3 + - - +
519O GLU* 3.5 15.9 - - - +
521O ILE* 1.3 73.8 - - - +
523O ASN* 1.3 57.7 + - - +
524O SER 2.9 5.2 + - - -
525O THR* 4.7 0.7 - - - +
526O ALA* 2.8 41.9 + - + +
533O ILE* 5.0 18.7 - - + +
537O LEU* 5.2 6.1 - - + -
566O PHE* 5.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 523 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519O GLU 2.7 16.1 + - - +
520O LYS* 3.1 15.1 + - - +
522O ILE* 1.3 73.2 - - - +
524O SER* 1.3 56.3 + - - +
526O ALA 2.9 11.2 - - - +
527O LEU* 4.0 6.4 - - - +
528O MET 3.1 28.5 + - - +
530O GLU* 4.8 12.4 + - - +
533O ILE* 5.0 11.0 - - + +
534O ARG* 6.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 524 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520O LYS* 3.3 12.3 + - - +
521O ILE* 3.1 18.0 + - - +
522O ILE 2.9 2.2 - - - -
523O ASN* 1.3 77.4 - - - +
525O THR* 1.3 66.2 + - - +
526O ALA 2.8 10.7 - - - +
527O LEU* 4.5 5.5 - - - +
242P SER* 5.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 525 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A HIS* 5.8 1.6 + - - -
510O CYS* 4.1 9.2 - - - -
514O ASN* 5.5 2.2 - - - +
521O ILE* 2.9 18.6 + - - +
522O ILE* 5.2 1.1 - - - -
524O SER* 1.3 76.1 - - - +
526O ALA* 1.3 60.5 + - - +
527O LEU* 4.6 2.6 - - - +
242P SER* 4.8 16.4 - - - +
245P GLU* 4.7 10.5 - - + +
246P VAL* 4.0 15.2 - - - +
249P TYR* 3.4 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 526 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506O ARG* 3.5 24.0 - - - +
507O LEU* 4.8 8.7 - - + -
510O CYS* 4.6 17.6 - - + -
522O ILE* 2.8 34.2 + - + +
523O ASN 2.9 5.2 - - - +
524O SER 2.8 15.8 - - - +
525O THR* 1.3 80.0 - - - +
527O LEU* 1.3 62.6 + - - +
533O ILE* 5.8 2.2 - - + -
246P VAL* 4.8 0.7 - - - -
249P TYR* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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