Contacts of the strand formed by residues 60 - 65 (chain M) in PDB entry 3QSU
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 ILE 60 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K TYR* 3.2 21.1 - - + -
58K HIS* 2.8 27.5 + - - -
24M VAL* 3.8 22.9 - - + -
25M PHE 3.7 7.9 - - - +
26M PHE* 4.5 1.6 - - + +
27M LEU* 4.2 2.5 - - - -
44M VAL* 4.8 7.4 - - + -
55M ILE* 3.7 23.3 - - + -
56M TYR 3.7 13.7 - - - +
57M LYS* 2.8 16.3 + - - +
58M HIS 3.4 0.2 - - - -
59M ALA* 1.3 79.6 - - - +
61M SER* 1.3 62.0 - - - +
62M THR 3.5 24.2 - - - +
63M TYR* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K PHE* 3.1 20.8 - - - -
28K ASN* 5.4 3.1 - - - -
30K PHE* 6.1 0.3 - - - -
55K ILE* 3.6 5.2 - - - +
56K TYR* 3.0 27.6 + - - +
59K ALA* 3.6 17.7 - - - +
25M PHE* 2.8 20.5 + - - +
26M PHE 4.0 15.9 - - - -
27M LEU* 4.0 5.3 - - - +
59M ALA 3.9 2.0 + - - -
60M ILE* 1.3 74.8 - - - +
62M THR* 1.3 71.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K PHE* 3.5 17.2 - - - -
32K MET* 4.3 5.1 - - + +
53K HIS* 3.9 20.6 - - + -
54K LEU 3.3 9.9 - - - +
55K ILE* 3.9 5.2 - - + +
56K TYR* 5.6 0.2 - - - -
23M THR 3.7 0.5 - - - +
24M VAL* 3.6 2.9 - - - -
25M PHE* 2.9 40.1 + - + +
60M ILE* 3.5 7.3 - - - +
61M SER* 1.3 94.4 + - - +
63M TYR* 1.3 77.5 + - - +
64M THR* 3.4 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52K GLN 3.8 0.5 - - - +
53K HIS* 3.3 5.2 - - - -
54K LEU* 2.9 68.2 + - + +
56K TYR* 2.9 39.4 + + - -
8M GLN* 5.3 0.2 - - - -
12M LEU* 3.9 20.7 - - + +
15M PHE* 4.2 19.6 - + + -
22M VAL* 3.9 24.2 - - + -
23M THR 3.4 4.3 - - - -
24M VAL* 4.2 11.7 - - + -
36M ILE* 4.6 5.2 - - + -
44M VAL* 3.4 26.0 - - + +
57M LYS* 4.3 0.2 - - - +
60M ILE* 3.7 24.0 - - + +
62M THR* 1.3 73.4 - - - +
64M THR* 1.3 62.2 + - - +
65M VAL* 4.2 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LYS* 4.0 21.5 - - + +
52K GLN 3.5 4.3 - - - +
53K HIS* 3.1 36.2 - - + +
79K ZN 3.8 8.3 - - - -
21M GLU 4.2 0.7 - - - +
22M VAL* 3.8 1.6 - - - +
23M THR* 2.8 48.5 + - - +
25M PHE* 3.8 16.6 - - + -
62M THR* 3.4 7.6 - - - +
63M TYR* 1.3 74.7 - - - +
65M VAL* 1.3 67.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LYS* 3.4 18.3 - - - +
52K GLN* 3.0 47.4 + - + +
15M PHE* 3.6 36.3 - - + -
20M THR* 3.4 26.7 - - + -
21M GLU 4.2 6.3 - - - +
22M VAL* 4.2 13.0 - - + -
63M TYR 5.1 0.9 - - - +
64M THR* 1.3 84.6 - - - +
----------------------------------------------------------
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