Contacts of the strand formed by residues 26 - 32 (chain F) in PDB entry 2DYY
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 PHE 26 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ALA* 3.6 23.3 - - + -
24D GLY* 5.6 1.3 - - - -
26D PHE* 4.0 28.9 - + + -
28D PHE* 3.8 11.7 - + - -
26E PHE* 4.0 17.5 - + - -
21F ILE 4.0 0.3 - - - +
22F LYS* 3.6 3.5 - - - +
23F ALA* 2.9 34.6 + - - +
24F GLY 3.3 0.8 - - - -
25F ASN* 1.3 84.6 - - + +
27F LEU* 1.3 60.2 + - - +
28F PHE* 3.7 22.2 + + + -
67F TYR* 3.9 2.1 + - - -
73F ILE* 3.6 28.0 - - + -
122F ILE* 4.1 9.2 - - + -
123F ALA 3.1 13.7 - - - -
124F TYR* 3.8 22.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 3.7 24.5 - - + -
20F ALA* 4.0 9.6 - - + -
21F ILE 3.4 16.6 - - - +
22F LYS* 4.2 5.2 - - + -
26F PHE* 1.3 74.2 - - - +
28F PHE* 1.3 60.9 + - - +
29F ILE* 3.7 20.8 + - + +
61F ILE 4.8 1.1 - - - +
62F LEU* 3.8 31.6 - - + -
65F ALA* 3.9 24.2 - - + -
67F TYR* 3.6 22.2 - - + -
122F ILE* 3.4 6.6 - - - -
123F ALA* 2.8 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PHE* 5.8 3.8 - + - -
26E PHE* 3.8 18.4 - + - -
28E PHE* 5.8 4.7 - + - -
73E ILE* 3.6 34.3 - - + +
74E LYS* 3.7 35.0 - - + -
102E ALA* 4.0 2.9 - - + +
122E ILE* 4.1 19.1 - - + -
20F ALA* 3.1 3.4 - - - -
21F ILE* 2.9 42.5 + - + +
23F ALA* 4.5 1.8 - - + -
26F PHE* 3.7 31.0 - + + -
27F LEU* 1.3 73.2 - - - +
29F ILE* 1.3 62.6 + - - +
30F ALA 3.9 0.2 + - - -
121F ALA 4.0 2.0 - - - -
122F ILE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E LYS* 5.6 4.9 - - - +
102E ALA* 4.4 1.6 - - - -
104E VAL* 4.9 1.4 - - - +
19F GLN 3.8 9.4 - - - +
20F ALA* 3.9 1.1 - - + -
27F LEU* 4.0 21.8 - - + +
28F PHE* 1.3 73.9 - - - +
30F ALA* 1.3 80.3 + - - +
32F GLN* 4.1 16.4 - - + +
58F ILE* 4.0 25.8 - - + +
61F ILE* 4.0 18.4 - - + -
62F LEU* 3.9 29.8 - - + -
72F VAL* 6.1 0.2 - - + -
119F ILE 5.3 0.7 - - - +
120F GLU* 4.1 5.9 - - - +
121F ALA* 3.1 38.7 + - + +
122F ILE* 6.3 0.2 - - - -
123F ALA* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E LYS* 6.4 0.2 - - - -
102E ALA* 3.9 11.8 - - + +
103E ARG 3.6 20.2 - - - +
104E VAL* 4.4 1.8 - - - -
13F PRO* 6.3 3.8 - - + -
17F TYR* 6.4 0.2 - - + -
18F SER 3.3 26.0 - - - +
19F GLN* 2.9 14.9 + - - +
29F ILE* 1.3 91.2 - - - +
31F GLY* 1.3 68.2 + - - +
32F GLN* 3.3 11.2 + - - +
119F ILE 3.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ARG 3.0 16.3 + - - +
104E VAL* 3.7 14.3 - - - +
30F ALA* 1.3 73.2 - - - +
32F GLN* 1.3 66.0 + - - -
33F ILE* 4.0 3.6 + - - +
118F GLU* 3.8 25.4 - - - +
119F ILE 3.5 9.4 - - - -
120F GLU* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ALA* 4.8 0.2 - - - +
11F PRO* 4.1 17.7 + - - +
19F GLN* 4.0 8.9 + - - +
29F ILE* 4.1 5.4 - - + -
30F ALA* 3.3 27.0 + - - +
31F GLY* 1.3 80.5 + - - -
33F ILE* 1.3 63.1 + - - +
54F VAL* 3.3 24.4 - - + +
57F ASN* 3.7 21.9 + - + +
58F ILE* 3.9 19.7 - - + -
61F ILE* 3.5 27.0 - - + +
118F GLU* 3.3 6.3 - - - -
119F ILE 2.8 35.9 + - - +
----------------------------------------------------------
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