Contacts of the strand formed by residues 37 - 44 (chain A) in PDB entry 1XTE
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 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 3.4 3.7 - - - -
34A VAL 2.9 33.7 + - - +
35A GLY 3.2 1.4 - - - +
36A ARG* 1.3 84.9 + - - +
38A GLU* 1.3 63.8 + - - +
39A TRP* 4.1 14.3 - - - -
118A HIS 5.4 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.3 48.9 - - + +
32A VAL 3.1 14.1 - - - +
33A SER* 3.2 19.7 + - - +
37A SER* 1.3 78.2 - - - +
39A TRP* 1.3 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.6 6.6 - - - +
32A VAL* 2.9 55.5 + - + +
34A VAL* 3.6 26.2 - - + -
37A SER* 4.1 23.6 - - - -
38A GLU* 1.3 94.1 - - - +
40A PHE* 1.3 63.7 + - - +
41A VAL* 3.6 18.1 - - + +
111A LEU 2.9 20.6 + - - -
112A GLN 3.6 16.2 + - - -
113A MET* 3.9 16.2 - - - -
118A HIS* 3.2 58.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 5.8 0.2 - - + -
29A LYS* 3.6 42.6 - - + -
30A VAL 3.3 4.5 - - - -
31A LEU* 2.9 47.6 - - + -
39A TRP* 1.3 79.2 - - - +
41A VAL* 1.3 68.4 + - - +
42A PHE* 3.7 29.1 - + + -
118A HIS* 4.9 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR 3.6 0.5 - - - +
29A LYS* 3.8 1.4 - - - -
30A VAL* 2.8 44.6 + - + +
32A VAL* 3.9 8.7 - - + -
39A TRP* 3.6 12.6 - - + -
40A PHE* 1.3 81.5 - - - +
42A PHE* 1.4 66.2 + - - +
43A ARG* 3.4 36.3 - - + +
110A PHE 3.5 10.5 - - - +
111A LEU* 3.6 26.5 - - + +
112A GLN* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 5.3 5.2 - - - -
18A HIS* 6.4 1.1 - + - -
27A VAL* 3.7 25.1 - - + -
28A TYR 3.4 2.5 - - - -
29A LYS* 3.9 37.5 - - + -
40A PHE* 3.7 35.2 - + + -
41A VAL* 1.4 75.5 - - - +
43A ARG* 1.3 75.5 + - - +
47A GLU* 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.0 2.6 - - - +
28A TYR* 2.8 40.0 + - - +
30A VAL* 4.7 4.5 - - + -
41A VAL* 3.4 22.2 - - + +
42A PHE* 1.3 82.2 + - - +
44A ARG* 1.3 62.1 + - - +
47A GLU* 2.9 30.2 + - - +
48A PHE* 3.5 22.4 - - + -
109A ALA 3.2 16.8 + - - -
110A PHE* 3.0 59.6 + - + +
112A GLN* 4.0 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.1 28.9 - - - -
26A THR 3.4 20.9 - - - +
27A VAL* 4.2 12.1 - - + -
43A ARG* 1.3 76.6 - - - +
45A TYR* 1.3 67.3 + - - +
46A ALA* 3.6 24.6 - - - +
47A GLU* 2.8 45.1 + - - +
48A PHE* 3.3 13.4 - - - -
----------------------------------------------------------
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