Contacts of the strand formed by residues 41 - 48 (chain B) in PDB entry 1T0P
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 41 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LYS* 3.9 21.2 - - - +
264A HIS* 4.3 2.5 - - - -
40B LEU* 1.3 72.7 - - - +
42B LYS* 1.3 58.1 + - - +
56B LEU* 3.3 6.1 - - - +
57B SER* 3.0 50.4 + - - -
58B ASN* 4.3 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 3.0 32.1 + - - -
264A HIS* 3.9 20.5 - - + +
267A THR* 6.0 1.7 - - - +
269A GLU* 4.3 14.2 + - - -
35B ALA* 5.8 0.8 - - - +
36B LEU* 2.7 36.1 + - + +
38B THR* 4.0 14.8 - - + -
40B LEU 3.3 2.4 + - - +
41B SER* 1.3 74.8 - - - +
43B GLU* 1.3 61.8 + - - +
44B LEU 5.8 0.2 - - - +
54B PHE* 4.5 20.2 - - + -
55B ASN 3.5 4.7 - - - -
56B LEU* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 1.3 76.3 - - - +
44B LEU* 1.3 74.6 + - - +
45B VAL* 3.2 18.7 + - + +
54B PHE* 3.3 4.5 - - - -
55B ASN* 2.9 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 1.3 81.2 - - - +
45B VAL* 1.3 59.1 + - - +
46B ALA 3.5 17.3 - - - +
47B SER* 4.7 10.3 - - - +
52B ALA* 4.1 9.2 - - + -
53B ALA 3.4 18.4 - - - +
54B PHE* 3.7 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.7 28.5 - - + -
43B GLU* 3.2 29.8 + - - +
44B LEU* 1.3 74.2 - - - +
46B ALA* 1.3 64.1 + - + +
53B ALA* 3.0 26.1 + - + +
54B PHE* 4.1 2.2 - - - +
55B ASN* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.5 8.3 - - - +
45B VAL* 1.3 82.9 - - + +
47B SER* 1.3 65.2 + - - +
51B TRP* 3.6 20.6 - - + -
53B ALA* 2.8 35.6 + - + +
301B NAG 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.7 12.1 - - - +
46B ALA* 1.3 78.8 - - - +
48B GLY* 1.3 60.0 + - - +
51B TRP* 3.6 24.3 - - - -
52B ALA* 4.4 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 1.3 76.2 - - - +
49B MET* 1.3 63.1 + - - -
50B GLY 3.1 2.8 + - - -
51B TRP* 3.0 38.5 + - - +
----------------------------------------------------------
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