Contacts of the helix formed by residues 45 - 53 (chain K) in PDB entry 1Y69
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 45 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LYS* 4.1 21.4 - - - +
43K ILE 3.8 0.2 + - - -
44K LYS* 1.3 71.8 - - - +
46K ASN* 1.3 60.4 + - - +
47K GLN 3.0 5.3 + - - -
48K ILE* 3.7 15.1 + - - +
49K GLU* 4.1 15.2 + - - +
71K PRO* 3.6 22.4 - - - -
93K TYR* 4.1 6.6 - - - +
94K TRP* 2.8 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24630 G 2.8 52.8 + - - +
24640 G 5.8 0.7 - - - +
44K LYS* 3.0 7.0 - - + +
45K SER* 1.3 80.3 + - - +
47K GLN* 1.3 57.4 + - + +
49K GLU* 5.6 2.0 - - - -
50K ALA* 3.4 8.3 + - - +
92K GLU* 4.5 4.1 + - - +
93K TYR* 3.8 34.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24630 G 3.6 25.8 - - - +
24640 G 3.8 15.0 + - - -
42K TRP 3.9 4.4 + - - +
43K ILE* 3.6 16.5 - - + +
44K LYS* 2.9 57.7 + - - +
46K ASN* 1.3 82.0 - - + +
48K ILE* 1.3 65.2 + - + +
49K GLU 3.3 1.6 - - - -
50K ALA* 3.4 6.8 - - - +
51K CYS* 2.8 35.5 + - - +
125K LYS* 4.8 3.8 - - + +
126K LEU* 4.0 20.0 - - + +
127K PRO* 4.3 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LYS* 5.7 5.8 - - - +
43K ILE* 3.8 13.2 - - + +
44K LYS 3.5 18.6 - - - +
45K SER* 3.7 13.0 + - - +
47K GLN* 1.3 76.7 - - - +
49K GLU* 1.3 61.0 + - + +
51K CYS* 3.1 12.7 - - - -
52K ARG* 3.0 45.5 + - - +
67K ILE* 4.2 24.0 - - + +
69K ILE* 3.2 45.8 - - + +
70K PHE* 6.1 0.2 - - - -
71K PRO* 4.9 7.0 - - + -
96K SER* 5.7 0.2 - - - +
105K PHE* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LYS* 3.4 46.5 + - + +
45K SER 4.1 9.3 + - - +
46K ASN* 5.6 2.5 - - - -
48K ILE* 1.3 76.7 - - + +
50K ALA* 1.3 64.1 + - - +
52K ARG* 2.6 58.6 + - - +
53K ILE* 3.4 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24620 C 2.8 44.9 - - + +
24630 G 3.8 10.3 - - - +
46K ASN 3.4 23.2 + - - +
47K GLN* 3.2 9.0 + - - +
49K GLU* 1.3 79.6 - - - +
51K CYS* 1.3 58.0 + - - +
53K ILE* 2.9 26.4 - - - +
54K VAL* 3.7 1.9 - - - +
125K LYS* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 51 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24620 C 5.4 0.2 - - - -
47K GLN* 2.8 30.7 + - - +
48K ILE* 3.1 19.7 - - - -
50K ALA* 1.3 75.5 - - + +
52K ARG* 1.3 64.5 + - - +
53K ILE 3.4 0.2 - - - -
54K VAL* 3.2 11.7 + - - +
55K MET* 3.1 30.9 + - + +
105K PHE* 4.1 28.3 - - - -
122K ALA* 4.0 21.1 - - + -
125K LYS* 5.0 14.8 - - + +
126K LEU* 6.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LYS* 4.4 11.1 - - - +
48K ILE* 3.0 29.3 + - - +
49K GLU* 2.6 46.9 + - - +
50K ALA 3.3 0.6 - - - -
51K CYS* 1.3 77.7 - - - +
53K ILE* 1.3 65.2 + - + +
54K VAL 3.2 0.7 + - - -
55K MET* 3.2 19.4 + - + +
56K SER* 2.8 23.8 + - - +
65K ILE* 5.4 5.1 - - + +
67K ILE* 4.4 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24610 G 3.1 39.7 - - + +
24620 C 4.3 9.4 - - - +
49K GLU 3.4 14.6 - - - +
50K ALA* 2.9 29.4 - - - +
52K ARG* 1.3 77.2 - - + +
54K VAL* 1.3 59.7 + - - +
56K SER* 3.7 8.6 - - - -
57K ARG* 3.2 32.4 + - + +
----------------------------------------------------------
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