Contacts of the strand formed by residues 45 - 53 (chain A) in PDB entry 3TGX
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 SER 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 5.0 6.3 - - - -
30A LEU* 3.3 10.5 - - - -
31A THR* 3.5 18.7 + - - +
43A ALA* 3.5 7.2 - - - +
44A THR* 1.3 91.3 + - - +
46A CYS* 1.3 65.0 + - - +
64A MET* 3.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 3.6 5.7 - - - +
30A LEU* 3.0 46.6 + - - +
45A SER* 1.3 78.9 - - - +
47A SER* 1.3 59.4 + - - +
48A LEU* 4.6 0.2 - - - -
62A CYS* 2.0 54.7 - - + -
63A HIS 5.0 3.1 - - - +
64A MET* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 3.6 10.3 - - - -
29A THR* 4.3 9.9 - - - +
46A CYS* 1.3 74.0 - - - +
48A LEU* 1.3 62.0 + - - +
49A HIS* 3.2 31.3 + - - -
62A CYS* 3.6 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL 4.1 3.8 - - - +
16A CYS* 4.0 18.4 - - + -
26A SER 4.8 1.7 - - - +
27A THR* 5.2 0.9 - - - -
28A LEU* 2.9 51.1 + - + +
30A LEU* 3.9 24.9 - - + +
46A CYS 3.9 0.2 + - - -
47A SER* 1.3 74.3 - - - +
49A HIS* 1.3 67.8 + - - +
60A TYR* 3.9 21.7 - - + +
61A THR* 3.4 28.3 - - - +
62A CYS* 3.6 18.6 - - + +
77A VAL* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 6.2 0.4 - - - -
47A SER* 3.2 44.1 + - - -
48A LEU* 1.3 76.4 + - - +
50A ARG* 1.3 69.2 + - - +
51A SER* 3.0 5.9 + - - -
60A TYR* 3.5 7.0 - - - -
61A THR* 3.1 29.1 + - - +
62A CYS* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.9 11.2 - - - +
23A LEU 3.0 23.4 + - - -
24A HIS* 4.3 0.4 - - - +
25A PRO* 3.2 42.2 - - + +
49A HIS* 1.3 71.6 - - - +
51A SER* 1.3 60.6 + - - +
52A ALA* 4.1 12.8 - - - +
53A HIS* 3.0 40.6 + - - +
58A ALA* 3.8 22.7 - - + -
59A THR 3.4 6.7 - - - +
60A TYR* 3.4 25.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS 3.0 3.2 + - - -
50A ARG* 1.3 75.6 - - - +
52A ALA* 1.3 67.0 + - - +
59A THR* 2.8 20.1 + - - +
61A THR* 3.3 35.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ARG* 3.6 2.9 - - - +
51A SER* 1.3 86.4 + - - +
53A HIS* 1.3 64.0 + - - +
58A ALA* 3.5 0.7 - - - +
59A THR* 2.6 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.8 13.6 - - - +
23A LEU 5.8 0.8 + - - -
50A ARG* 3.0 38.7 + - - -
52A ALA* 1.3 80.8 - - - +
54A ASN* 1.3 83.9 + - - +
57A HIS 3.2 15.9 - - - +
58A ALA* 3.5 13.5 - - + +
59A THR* 5.7 0.4 - - - -
----------------------------------------------------------
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