Contacts of the helix formed by residues 1538 - 1553 (chain B) in PDB entry 1XTB
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 ASP1538 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.8 16.6 - - + -
30A ASP* 6.1 0.4 - - - +
56A LYS* 4.6 0.8 - - - -
433A GLU* 4.1 10.0 + - - +
436A MET* 3.4 33.3 - - + +
1537B HIS* 1.3 82.9 - - - +
1539B SER* 1.3 63.4 + - - +
1540B SER* 2.8 20.3 + - - -
1541B THR* 2.5 44.7 + - - -
1542B ASN* 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.5 15.8 + - - +
32A ASP 4.4 1.6 + - - -
33A LYS* 3.7 23.5 + - - -
35A ARG* 3.9 4.3 - - - +
36A PHE* 3.2 36.6 + - - +
1537B HIS 3.8 0.6 + - - -
1538B ASP* 1.3 73.7 - - - +
1540B SER* 1.3 58.8 + - - +
1542B ASN* 3.6 9.2 - - - +
1543B GLY* 2.8 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.4 11.6 - - - -
36A PHE* 3.9 6.7 - - - -
53A ASP* 2.7 20.8 + - - +
55A SER* 3.3 20.5 + - - -
56A LYS* 2.6 30.4 + - - +
1538B ASP* 2.8 19.8 + - - -
1539B SER* 1.3 72.9 + - - +
1541B THR* 1.3 63.9 + - - -
1543B GLY* 3.1 1.7 + - - -
1544B LEU* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LYS* 4.2 6.1 + - - -
429A LEU* 4.8 8.0 + - + +
433A GLU* 3.7 21.6 - - + +
1524B ILE* 4.3 11.2 - - + -
1537B HIS* 3.5 36.1 - - + +
1538B ASP* 2.5 36.0 + - - -
1540B SER* 1.3 73.7 + - - +
1542B ASN* 1.3 62.4 + - - +
1544B LEU* 3.8 9.5 - - - +
1545B ILE* 3.1 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1534B VAL* 3.5 24.9 + - - +
1535B THR* 3.3 16.6 - - - +
1536B SER 3.8 2.8 - - - +
1537B HIS* 2.9 50.0 - - - +
1538B ASP 3.0 16.6 + - - +
1539B SER* 3.6 8.4 - - - +
1541B THR* 1.3 76.2 - - - +
1543B GLY* 1.3 57.3 + - - +
1545B ILE* 3.3 6.3 + - - +
1546B ASN* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.6 34.1 - - - -
1539B SER 2.8 17.4 + - - -
1540B SER 3.6 0.9 - - - -
1542B ASN* 1.3 70.3 - - - +
1544B LEU* 1.3 66.4 + - - +
1546B ASN* 3.4 7.5 + - - +
1547B PHE* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 4.4 0.4 - - + -
51A LEU* 3.8 24.0 - - + -
53A ASP* 3.5 19.7 - - + +
56A LYS* 3.5 28.9 - - - +
428A PHE* 4.8 1.3 - - + -
429A LEU* 3.6 25.1 - - + -
432A THR* 4.6 2.9 - - - +
475A SER* 3.7 29.6 - - - +
477A VAL* 3.9 14.8 - - + +
1540B SER 2.9 16.8 + - - +
1541B THR* 3.8 2.9 - - - +
1543B GLY* 1.3 74.8 - - - +
1545B ILE* 1.3 65.0 + - - +
1547B PHE* 3.2 3.8 + - - +
1548B ILE* 3.0 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1545 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 3.6 21.1 - - + -
1524B ILE* 4.2 18.2 - - + -
1527B GLU* 4.3 4.3 - - + +
1528B LEU* 4.1 15.3 - - + -
1534B VAL* 3.7 33.0 - - + -
1537B HIS* 4.2 15.5 - - + -
1541B THR* 3.1 37.6 + - + +
1542B ASN* 3.6 4.3 - - - +
1544B LEU* 1.3 76.3 - - - +
1546B ASN* 1.3 65.2 + - - +
1548B ILE* 3.2 12.3 + - - +
1549B LYS* 3.0 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1546 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1533B PRO* 3.1 23.7 - - + +
1534B VAL 2.9 38.3 + - - -
1535B THR* 5.6 0.8 - - - +
1542B ASN* 2.9 26.4 + - - +
1543B GLY* 3.9 6.7 - - - +
1545B ILE* 1.3 77.6 - - - +
1547B PHE* 1.3 64.9 + - - +
1549B LYS* 3.3 7.6 + - - +
1550B GLN* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1547 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 4.1 16.2 - - + -
49A HIS* 3.7 25.6 - - + -
51A LEU* 3.5 39.5 - - + -
409A VAL* 4.2 5.2 - - + -
477A VAL* 3.5 44.4 - - + -
478A PHE* 4.6 1.3 - - - -
479A THR* 5.0 0.2 - - - -
1543B GLY 3.0 14.2 + - - +
1544B LEU 3.5 8.3 - - - +
1546B ASN* 1.3 76.4 - - - +
1548B ILE* 1.3 58.3 + - - +
1550B GLN* 3.2 16.0 + - - +
1551B GLN* 2.8 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1548 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ILE* 5.9 0.2 - - + -
409A VAL* 3.5 27.7 - - + +
425A LEU* 4.0 39.5 - - + -
428A PHE* 5.4 3.1 - - + -
429A LEU* 4.0 35.4 - - + -
477A VAL* 4.4 12.1 - - + -
1528B LEU* 5.0 6.7 - - + -
1544B LEU* 3.0 16.1 + - + +
1545B ILE* 3.3 7.9 - - - +
1547B PHE* 1.3 78.1 - - + +
1549B LYS* 1.3 58.3 + - - +
1552B ARG* 2.8 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1527B GLU 2.9 28.3 + - - -
1528B LEU* 3.6 9.9 - - + +
1530B GLY* 2.8 33.1 + - - +
1531B SER* 3.9 14.3 + - - +
1532B SER* 2.6 31.0 + - - +
1533B PRO* 4.8 0.7 - - + -
1534B VAL* 4.0 4.3 - - - +
1545B ILE* 3.0 30.6 + - + +
1546B ASN* 3.7 11.4 - - - +
1548B ILE* 1.3 76.9 - - + +
1550B GLN* 1.3 62.6 + - - +
1552B ARG* 3.6 34.6 + - - +
1553B GLU* 4.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 5.9 1.0 - - - +
49A HIS* 5.0 7.3 + - - -
1546B ASN 3.0 16.8 + - - +
1547B PHE* 3.2 17.0 + - - +
1549B LYS* 1.3 79.9 - - - +
1551B GLN* 1.3 86.5 + - - +
1552B ARG 3.4 0.7 + - - -
1553B GLU* 3.7 10.7 + - - +
1554B ALA* 3.9 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1551 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLY* 5.3 0.4 - - - -
49A HIS* 3.6 27.7 + - - -
409A VAL* 3.9 21.2 - - + +
410A GLN* 2.9 24.9 + - - -
479A THR* 2.5 32.0 + - + +
1547B PHE* 2.8 42.6 + - + +
1550B GLN* 1.3 96.2 + - - +
1552B ARG* 1.3 60.8 + - - +
1553B GLU 3.2 2.2 - - - -
1554B ALA* 3.2 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 3.9 9.6 - - + -
410A GLN* 3.8 15.1 + - - +
425A LEU* 6.2 0.4 - - - +
1528B LEU* 2.6 38.7 + - - +
1529B ASP* 3.6 8.9 + - - +
1530B GLY 3.4 14.1 + - - -
1531B SER* 4.9 3.2 - - - +
1548B ILE* 2.8 27.3 + - + +
1549B LYS* 3.6 32.6 + - - +
1550B GLN 3.2 0.2 - - - -
1551B GLN* 1.3 79.0 - - - +
1553B GLU* 1.3 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1549B LYS 4.3 3.8 + - - +
1550B GLN 3.7 7.9 + - - +
1551B GLN 3.2 0.4 - - - -
1552B ARG* 1.3 79.4 - - + +
1554B ALA* 1.3 65.4 + - - +
1555B LYS* 3.3 6.8 + - - +
----------------------------------------------------------
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