Contacts of the strand formed by residues 29 - 33 (chain A) in PDB entry 2DJ0
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 TRP 29 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 4.2 15.5 - - + -
12A PHE* 3.4 40.2 - + - -
20A GLU* 3.4 21.0 + - + +
21A LEU* 3.4 31.6 - - + -
24A ASP* 3.0 40.4 + - + +
27A VAL* 3.7 11.1 + - - +
28A THR* 1.3 86.4 - - - +
30A ILE* 1.3 62.1 + - - +
31A VAL* 4.0 3.6 - - + -
61A ASN* 3.0 53.4 + - + -
62A PHE 3.5 19.7 - - - -
63A GLY 4.5 0.7 - - - -
93A LEU* 4.1 0.5 - - - -
94A PHE* 3.1 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TRP* 1.3 72.6 - - - +
31A VAL* 1.3 61.5 + - - +
48A TYR* 3.1 7.6 + - + +
60A LEU* 5.0 6.0 - - + +
61A ASN 3.3 18.4 + - - +
62A PHE* 3.6 36.3 - - + -
63A GLY 3.0 19.5 + - - -
91A LEU* 4.0 32.5 - - + -
92A ILE 3.6 12.1 - - - +
93A LEU* 4.8 8.7 - - + -
122A VAL* 5.5 1.3 - - + -
126A PHE* 4.6 16.8 - - + -
128A LEU* 4.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.6 20.9 - - + -
17A ILE* 4.7 11.7 - - + -
21A LEU* 5.0 6.7 - - + -
29A TRP* 4.8 5.2 - - + +
30A ILE* 1.3 77.5 - - - +
32A GLU* 1.3 62.1 + - - +
33A PHE* 3.5 21.0 - - + -
63A GLY* 3.6 3.6 - - - -
64A LYS 4.1 7.9 - - - +
65A VAL* 3.4 40.2 - - + +
90A THR 3.9 0.2 - - - +
91A LEU* 3.9 2.9 - - - -
92A ILE 3.5 27.1 + - - -
94A PHE* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE 4.1 0.4 + - - -
31A VAL* 1.3 72.2 - - - +
33A PHE* 1.3 64.8 + - - +
34A PHE* 3.4 16.5 + - + +
41A CYS* 4.2 18.7 - - - -
44A PHE* 3.4 23.5 - - - -
45A ALA* 6.1 0.2 - - - -
48A TYR* 2.8 43.2 - - + +
63A GLY 3.2 7.7 + - - -
64A LYS* 3.8 17.2 - - + -
65A VAL 3.4 19.1 + - - -
89A PRO* 4.3 11.7 - - + +
90A THR 3.3 10.1 - - - +
91A LEU* 3.6 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.6 2.0 - - + -
31A VAL* 3.5 26.7 - - + -
32A GLU* 1.3 70.0 - - - +
34A PHE* 1.3 58.5 + - - +
65A VAL* 3.3 32.8 - - + -
67A VAL* 3.4 24.2 - - + -
73A VAL* 4.0 6.7 - - + -
77A TYR* 3.4 43.7 - + - -
79A VAL* 4.6 9.6 - - + -
88A LEU* 2.9 16.4 - - - +
90A THR* 2.8 45.6 + - + +
92A ILE* 3.1 34.1 - - + -
94A PHE* 4.6 2.5 - + - -
----------------------------------------------------------
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