Contacts of the strand formed by residues 26 - 32 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 3.7 23.8 - + + -
21H ILE 3.9 0.3 - - - +
22H LYS* 3.4 5.0 - - - +
23H ALA 2.8 37.8 + - - +
25H ASN* 1.3 84.5 - - + +
27H LEU* 1.3 60.1 + - - +
28H PHE* 3.4 21.7 - + + -
67H TYR* 3.9 1.3 - - - -
73H ILE* 3.7 11.7 - - + -
122H ILE* 3.9 18.6 - - + -
123H ALA 3.5 6.5 - - - -
124H TYR* 4.0 24.7 - + - -
23I ALA* 4.1 15.0 - - + -
24I GLY* 5.3 1.8 - - - -
26I PHE* 4.1 19.3 - + - -
28I PHE* 3.6 34.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ILE* 4.0 16.2 - - + -
20H ALA* 4.0 6.1 - - + -
21H ILE 3.5 22.7 - - - +
22H LYS* 3.8 14.4 - - + -
26H PHE* 1.3 74.5 - - - +
28H PHE* 1.3 62.4 + - - +
29H ILE* 4.0 15.3 + - + +
61H ILE 4.8 1.8 - - - +
62H LEU* 3.6 33.0 - - + -
65H ALA* 3.8 22.2 - - + -
67H TYR* 3.8 23.8 - - + -
121H ALA 4.1 0.2 - - - +
122H ILE* 3.4 9.0 - - - +
123H ALA* 2.9 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 3.9 15.0 - + - -
28G PHE* 6.0 2.5 - + - -
73G ILE* 3.6 33.0 - - + +
74G LYS* 3.8 37.0 - - + -
102G ALA* 3.4 8.5 - - + +
122G ILE* 4.2 19.1 - - + -
20H ALA* 3.1 4.5 - - - -
21H ILE* 2.8 44.4 + - + +
23H ALA* 4.7 2.0 - - + -
26H PHE* 3.4 33.4 - + + -
27H LEU* 1.3 75.3 - - - +
29H ILE* 1.3 61.3 + - - +
121H ALA 4.2 2.2 - - - -
122H ILE* 3.9 31.4 - - + -
28I PHE* 5.6 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LYS* 5.5 4.9 - - - +
102G ALA* 4.2 2.4 - - - +
104G VAL* 4.9 1.7 - - - +
19H GLN 3.6 8.1 - - - +
20H ALA* 3.8 13.2 - - + -
27H LEU* 4.2 9.4 - - + +
28H PHE* 1.3 74.2 - - - +
30H ALA* 1.3 78.5 + - - +
31H GLY 3.7 0.9 + - - -
32H GLN* 4.2 6.5 - - + +
58H ILE* 4.3 19.5 - - + +
61H ILE* 4.0 23.8 - - + -
62H LEU* 3.5 38.4 - - + -
72H VAL* 6.1 0.7 - - + -
119H ILE 5.6 0.2 - - - +
120H GLU* 4.2 5.2 - - - +
121H ALA* 3.1 40.2 + - + +
123H ALA* 5.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G LYS* 6.3 0.4 - - - -
102G ALA* 3.9 3.6 - - - +
103G ARG 3.3 26.7 - - - +
104G VAL* 5.0 0.4 - - - -
17H TYR* 4.1 13.5 - - + -
18H SER 3.3 24.7 - - - +
19H GLN* 2.8 14.5 + - - +
29H ILE* 1.3 82.2 - - - +
31H GLY* 1.3 67.0 + - - +
32H GLN* 2.8 20.6 + - - +
119H ILE 4.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ARG 2.9 16.5 + - - +
104G VAL* 3.6 18.6 - - - +
17H TYR* 5.4 4.3 + - - -
30H ALA* 1.3 74.8 - - - +
32H GLN* 1.3 65.5 + - - -
33H ILE* 4.3 2.1 + - - +
118H GLU* 4.0 19.1 - - - +
119H ILE 3.5 10.3 - - - -
120H GLU* 4.2 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H PRO* 3.6 32.1 + - - +
17H TYR* 5.9 1.6 - - - -
19H GLN* 4.2 5.7 + - - +
29H ILE* 4.2 2.2 - - + +
30H ALA* 2.8 31.7 + - - +
31H GLY* 1.3 80.0 + - - -
33H ILE* 1.3 62.0 + - - +
54H VAL* 3.7 16.2 - - + +
57H ASN* 3.7 11.9 - - + +
58H ILE* 3.9 22.4 - - + -
61H ILE* 3.5 27.8 - - + +
118H GLU* 3.3 7.1 - - - +
119H ILE 2.9 34.2 + - - +
----------------------------------------------------------
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