Contacts of the strand formed by residues 47 - 52 (chain A) in PDB entry 1T2E
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 ASP 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 2.7 49.2 + - - +
21A ALA 2.8 10.1 + - - +
22A LYS* 4.5 10.3 - - + -
23A ILE* 2.7 33.7 + - - +
46A GLY* 1.3 75.2 - - - -
49A VAL* 1.3 57.0 + - - +
50A VAL* 6.4 0.7 - - + -
77A LYS* 2.7 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE* 3.3 3.6 - - + +
25A LEU* 3.6 31.4 - - + -
37A ALA* 4.1 15.3 - - + +
40A ILE* 3.3 45.5 - - + -
41A VAL* 5.2 1.3 - - + -
46A GLY 3.7 1.8 - - - +
47A ASP* 1.3 77.0 - - - +
50A VAL* 1.3 74.9 + - - +
51A LEU* 4.2 1.8 - - + +
77A LYS 2.8 14.0 + - - +
78A VAL* 3.3 17.3 - - + -
79A SER* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 4.2 19.5 - - + +
23A ILE 2.9 7.5 + - - +
24A VAL* 4.0 29.8 - - + -
25A LEU* 2.7 35.3 + - - +
47A ASP* 6.4 0.4 - - + -
49A VAL* 1.3 81.4 - - - +
51A LEU* 1.3 63.1 + - - +
52A PHE* 4.0 2.7 - - + +
79A SER* 3.2 15.7 - - - +
80A GLY 4.5 0.9 - - - -
81A SER* 3.6 30.3 - - - -
87A ASP* 4.6 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 14.1 - - + -
28A SER* 3.0 36.6 - - - +
32A GLY 3.7 25.4 - - - +
33A GLY* 4.5 3.1 - - - +
37A ALA* 3.8 21.3 - - + -
49A VAL* 4.1 2.0 - - + -
50A VAL* 1.3 73.2 - - - +
52A PHE* 1.3 51.5 + - - +
59A PRO* 3.0 15.5 - - + +
62A LYS* 4.1 13.0 - - + +
63A ALA* 3.7 33.0 - - - +
66A THR* 4.8 0.9 - - - +
78A VAL* 4.0 7.0 - - + -
79A SER 2.8 11.7 + - - +
81A SER 2.7 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A VAL* 4.3 14.8 - - + -
25A LEU 2.9 12.5 + - - +
26A VAL* 3.8 17.3 - - + -
27A GLY 2.8 22.7 + - - -
28A SER* 2.8 10.8 + - - -
50A VAL* 3.5 0.8 + - + -
51A LEU* 1.3 73.3 - - - +
53A ASP* 1.3 69.2 + - - +
54A ILE* 4.7 3.6 - - + -
81A SER* 3.3 28.9 - - - -
83A ASN 3.6 6.7 - - - -
84A THR 3.3 34.3 - - - -
85A TYR* 3.4 40.6 - + - -
87A ASP* 5.6 0.7 - - + -
88A LEU* 6.1 1.8 - - + -
336A NAI 3.3 32.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 2.7 26.1 + - - -
52A PHE* 1.3 80.4 - - - +
54A ILE* 1.3 73.8 + - - +
55A VAL* 3.0 12.3 + - - +
58A MET* 3.5 11.4 - - + +
59A PRO* 3.7 18.8 - - + +
81A SER 3.0 9.1 + - - +
83A ASN* 2.9 24.4 + - - -
336A NAI 2.7 55.9 - - - +
----------------------------------------------------------
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