Contacts of the strand formed by residues 19 - 23 (chain D) in PDB entry 1Y8Q
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 19 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 3.9 2.3 + - - +
18D GLY* 1.3 73.9 - - - -
20D VAL* 1.3 61.8 + - - +
43D HIS* 3.4 18.6 - - + +
45D ASP* 2.8 41.6 + - - +
90D VAL* 4.2 10.8 - - - +
92D TYR* 3.8 6.7 + - - -
108D GLN* 3.4 53.8 + - - +
109D PHE* 3.2 18.9 - - + -
110D ILE* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLY 4.8 0.2 - - - +
19D ARG* 1.3 78.9 - - - +
21D LEU* 1.3 60.2 + - - +
22D VAL* 5.0 0.2 - - + -
36D LEU* 4.3 3.4 - - + -
41D PHE* 3.8 34.1 - - + -
43D HIS 2.9 16.0 + - - +
44D ILE* 3.5 23.1 - - + -
45D ASP 2.8 26.0 + - - +
109D PHE* 3.5 8.2 - - - -
110D ILE* 4.0 8.1 - - + -
111D LEU* 3.4 25.4 - - + +
113D MET* 3.5 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D VAL* 1.3 74.2 - - - +
22D VAL* 1.3 67.4 + - - +
23D VAL* 3.9 16.6 - - + -
45D ASP* 3.4 27.8 - - + +
46D LEU 4.6 0.4 - - - +
47D ILE* 4.3 13.2 - - + -
92D TYR* 5.4 1.1 - - + -
96D ILE* 5.2 1.6 - - + -
105D PHE* 4.0 15.0 - - + -
106D PHE* 3.9 28.0 - - + -
109D PHE* 3.6 35.9 - - + -
111D LEU 3.0 7.3 + - - +
112D VAL* 3.4 10.0 - - + +
113D MET* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 1.3 76.1 - - - +
23D VAL* 1.3 61.2 + - - +
24D GLY 3.5 21.4 + - - +
29D GLY* 4.5 11.9 - - - +
32D LEU* 4.0 24.2 - - + -
33D LEU* 5.2 4.0 - - + +
36D LEU* 3.7 30.1 - - + -
44D ILE* 4.1 13.0 - - + -
45D ASP 2.9 11.6 + - - +
46D LEU* 3.5 13.9 - - + +
47D ILE* 3.2 25.1 + - - +
113D MET* 3.4 9.2 - - + +
115D ALA* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 3.9 25.8 - - + -
22D VAL* 1.3 71.4 - - - +
24D GLY* 1.3 59.7 + - - +
47D ILE* 3.8 12.8 - - + -
96D ILE* 3.4 35.9 - - + -
112D VAL* 4.2 7.4 - - + -
113D MET 2.9 8.9 + - - +
114D ASN* 3.7 19.7 - - - +
115D ALA* 2.8 30.5 + - - -
116D LEU* 3.4 24.3 - - + +
125D VAL* 4.2 7.0 - - + -
801D ATP 4.8 0.7 - - + -
----------------------------------------------------------
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