Contacts of the helix formed by residues 60 - 67 (chain K) in PDB entry 5ANC
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 60 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K THR* 3.0 20.0 + - - +
58K ASP* 3.8 13.4 + - + +
59K SER* 1.3 81.7 - - - +
61K GLU* 1.3 63.4 + - - +
62K ASP* 3.0 38.6 + - - +
63K GLU* 3.8 21.4 - - + +
64K GLN* 3.6 13.7 - - - +
69K THR* 3.8 38.3 + - - +
3358N G 4.1 11.5 + - - +
3366N G 5.2 10.7 + - - -
3367N G 3.8 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K THR* 5.3 2.4 - - - +
60K ARG* 1.3 71.5 - - - +
62K ASP* 1.3 60.5 + - - +
63K GLU 3.2 1.6 - - - -
64K GLN* 3.2 12.0 + - - +
65K ILE* 2.9 33.3 + - + +
147K LYS* 3.8 14.1 + - - -
154K GLU* 5.4 2.9 - - - +
237K ALA 3.2 23.5 - - - +
238K ILE* 3.7 19.7 - - - +
3358N G 5.4 4.3 - - - -
3359N U 3.7 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 62 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K ARG* 3.0 37.9 + - - +
61K GLU* 1.3 76.4 - - - +
63K GLU* 1.3 52.8 + - + +
65K ILE* 3.2 7.5 + - - +
66K ARG 2.8 37.9 + - - +
67K GLY* 4.2 2.7 - - - -
69K THR* 5.8 0.7 - - - +
3358N G 3.7 10.2 + - - +
3359N U 3.1 27.0 + - - +
3360N A 5.1 0.9 + - - -
3361N C 4.4 1.9 + - - -
3362N G 4.3 11.1 - - - +
3365N A 4.6 7.5 + - - -
3366N G 3.6 23.3 - - - +
3367N G 3.5 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K ASP* 3.0 20.9 - - - +
30K HIS* 3.1 17.9 + - - -
31K GLY 5.4 0.9 - - - +
32K LYS* 3.9 13.5 + - - +
33K THR* 4.1 11.0 + - - -
58K ASP 4.7 2.7 - - - +
60K ARG* 3.8 25.2 + - + +
62K ASP* 1.3 78.9 - - + +
64K GLN* 1.3 68.2 + - - +
66K ARG* 3.2 0.5 - - - -
67K GLY* 3.1 35.7 + - - +
68K ILE 3.0 22.0 - - - +
69K THR* 3.5 13.7 - - - +
71K LYS* 3.2 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 64 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K HIS* 3.3 19.1 + - - -
31K GLY* 3.7 21.9 + - - +
33K THR* 3.6 22.1 + - + -
34K THR* 3.0 33.3 - - - +
60K ARG 3.6 14.8 - - - +
61K GLU* 3.2 16.8 + - - +
63K GLU* 1.3 80.0 - - - +
65K ILE* 1.3 65.1 + - + +
147K LYS* 3.8 43.7 - - - +
150K ARG* 3.5 18.1 + - - +
237K ALA 5.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K HIS* 4.8 0.7 - - - -
61K GLU* 2.9 20.2 + - + +
62K ASP* 3.2 11.6 + - - +
64K GLN* 1.3 80.6 - - + +
66K ARG* 1.3 65.1 + - - +
120K VAL* 4.9 10.4 - - - +
147K LYS* 6.2 0.9 - - - +
150K ARG* 5.2 10.5 + - - +
154K GLU* 3.6 36.3 - - - +
3359N U 4.4 9.6 - - - +
3360N A 3.7 32.3 - - - +
3362N G 3.6 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 66 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27K HIS* 3.6 13.1 + - - -
28K VAL* 3.5 22.8 - - - +
30K HIS* 4.0 9.9 - - + +
62K ASP* 2.8 7.7 + - - +
63K GLU 3.2 7.0 - - - -
65K ILE* 1.3 81.2 - - - +
67K GLY* 1.3 59.3 + - - +
68K ILE* 4.9 0.2 - - - +
119K ALA* 3.6 14.8 - - - +
120K VAL* 4.2 22.2 - - + -
121K GLU* 3.8 20.0 + - - +
126K GLN* 2.9 32.1 + - - +
3362N G 3.1 16.1 + - - +
3363N A 2.6 39.7 + - - -
3364N G 2.8 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K VAL* 4.3 6.7 - - - +
29K ASP 4.3 3.8 - - - +
30K HIS* 4.4 5.0 + - - -
62K ASP* 4.0 3.8 - - - -
63K GLU* 3.1 34.2 + - - +
66K ARG* 1.3 77.5 - - - +
68K ILE* 1.3 68.7 + - - +
69K THR* 4.7 0.4 - - - -
3364N G 3.8 7.9 - - - -
3365N A 3.6 11.7 - - - -
----------------------------------------------------------
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