Contacts of the strand formed by residues 20 - 26 (chain F) in PDB entry 1Y62
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 GLU 20 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 4.4 1.6 - - + -
52A ASP* 3.6 28.2 - - + +
55A ARG* 4.4 3.4 + - - +
18F LYS* 4.1 19.1 - - + +
19F ALA* 1.3 79.3 - - - +
21F LYS* 1.3 68.4 + - - +
22F ARG* 3.5 20.8 + - - +
36F ASP* 3.5 10.2 - - - +
37F TYR* 3.1 33.6 + - + +
39F GLY* 3.2 27.0 - - - -
104F SO4 2.8 41.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 4.6 7.3 + - - +
55A ARG* 3.3 31.2 - - - +
20F GLU* 1.3 74.5 - - - +
22F ARG* 1.3 74.1 + - - +
34F ARG* 4.2 46.7 - - + +
35F PHE 3.4 8.7 - - - +
36F ASP* 3.1 28.5 + - - +
48F ARG* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 5.7 2.2 - - - +
52A ASP* 4.9 3.0 + - - -
20F GLU* 3.5 35.1 + - - +
21F LYS* 1.3 79.9 + - - +
23F ILE* 1.3 66.2 + - - +
34F ARG* 3.2 6.1 - - - -
35F PHE* 2.9 52.3 + - + -
37F TYR* 3.5 35.4 - - + -
39F GLY* 5.0 1.2 + - - -
46F ASN* 3.4 24.8 + - - +
47F PHE 3.7 10.5 - - - -
48F ARG* 3.0 44.1 - - - +
104F SO4 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ARG* 1.3 73.1 - - - +
24F TYR* 1.3 64.0 + - - +
32F CYS* 3.6 29.8 - - + +
33F LEU* 3.2 11.7 - - - +
34F ARG* 3.4 37.5 - - + +
35F PHE* 3.9 1.3 - - - -
46F ASN* 3.5 2.6 - - - -
47F PHE* 2.7 57.3 + - + +
48F ARG 4.4 5.8 - - - +
49F ARG 4.3 0.7 - - - -
50F THR* 3.7 35.2 - - + +
53F CYS* 3.7 12.6 - - + -
112F SO4 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LEU 4.7 1.1 - - - -
10F PRO* 5.1 0.9 - - + -
11F ALA* 3.9 27.8 - - + -
23F ILE* 1.3 72.8 - - - +
25F TYR* 1.3 76.2 + - - +
26F ASN* 3.1 36.3 + - + +
32F CYS* 3.4 1.0 - - - -
33F LEU* 2.9 52.7 + - + +
34F ARG 3.9 17.7 - - - -
35F PHE* 3.6 26.5 - + + -
45F ASN* 3.3 35.0 - - - +
47F PHE* 4.5 0.2 - - - -
53F CYS* 3.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F CYS* 3.5 31.0 - - + +
9F LEU 4.3 1.9 - - - +
24F TYR* 1.3 76.4 - - - +
26F ASN* 1.3 57.8 + - - +
27F SER* 3.5 23.4 + - - -
30F LYS* 3.3 27.2 - - - +
31F GLN* 3.6 23.3 - - - -
32F CYS* 3.7 17.9 - - - -
45F ASN* 2.8 34.4 + - - +
53F CYS* 3.7 7.0 - - - -
57F CYS* 3.4 44.9 + - + -
58F LEU* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 3.1 35.0 + - + +
25F TYR* 1.3 71.9 - - - +
27F SER* 1.3 56.3 + - - +
28F ALA* 3.3 11.6 + - - +
29F ARG* 2.9 48.2 + - + +
30F LYS 2.8 22.3 + - - -
31F GLN 3.0 21.3 + - - +
33F LEU* 4.1 10.2 - - + +
----------------------------------------------------------
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