Contacts of the helix formed by residues 1569 - 1582 (chain A) in PDB entry 5XJY
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 SER1569 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ASP* 4.3 6.3 + - - +
414A GLY* 2.7 40.0 + - - -
415A MET* 3.3 10.0 - - - +
418A GLU* 3.5 16.2 + - - -
1567A ASP* 3.3 4.8 + - - -
1568A SER* 1.3 84.5 + - - +
1570A ALA* 1.3 56.2 + - - +
1572A ARG* 3.2 1.9 + - - +
1573A PHE* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A MET* 3.7 21.8 - - + -
418A GLU* 4.3 11.9 - - - +
419A LEU* 5.4 4.0 - - + -
1559A LYS* 5.0 2.0 - - - +
1563A LYS 5.9 0.7 - - - +
1565A ALA* 4.4 14.4 - - + +
1567A ASP* 2.6 18.0 + - - +
1569A SER* 1.3 71.7 - - - +
1571A ASP* 1.3 58.8 + - - +
1573A PHE* 4.4 0.2 - - - -
1574A LEU* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1559A LYS* 2.5 27.3 + - - +
1565A ALA 4.1 2.7 + - - +
1566A LYS* 3.8 35.2 - - - +
1567A ASP* 3.4 20.6 + - - +
1569A SER 3.3 0.4 - - - -
1570A ALA* 1.3 78.3 - - - +
1572A ARG* 1.3 62.5 + - + +
1574A LEU* 4.2 0.3 - - - +
1575A ASN* 2.4 67.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 4.8 11.1 + - - -
411A ASP* 3.1 17.6 - - - +
1567A ASP 4.6 4.3 - - - +
1568A SER* 3.3 24.9 - - - +
1569A SER 3.2 2.2 + - - -
1571A ASP* 1.3 78.6 - - + +
1573A PHE* 1.3 60.1 + - - +
1575A ASN* 4.4 6.5 - - - +
1576A SER* 2.9 32.8 + - - -
2302A NAG 5.1 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL* 4.1 21.8 - - + -
411A ASP* 3.2 30.6 + - + -
412A LEU* 3.7 30.1 - - + -
415A MET* 3.8 33.2 - - + -
1569A SER 2.7 21.5 + - - +
1572A ARG* 1.3 75.5 - - - +
1574A LEU* 1.3 75.9 + - + +
1576A SER* 3.8 1.9 - - - -
1577A LEU* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 5.8 1.6 - - + -
415A MET* 4.7 6.1 - - + -
1555A ILE* 3.3 46.1 - - + +
1558A MET* 5.1 12.6 - - + -
1559A LYS* 4.7 22.4 - - + -
1570A ALA* 2.9 29.8 + - + +
1571A ASP 4.2 1.1 - - - +
1573A PHE* 1.3 94.7 - - + +
1575A ASN* 1.3 61.6 + - - +
1577A LEU* 3.3 13.7 + - + +
1578A GLY 2.9 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1552A ASN* 5.8 1.7 + - - -
1555A ILE* 5.0 5.3 - - - +
1559A LYS* 3.5 14.9 + - - +
1571A ASP* 2.4 46.2 + - - +
1572A ARG* 4.4 7.5 - - - +
1574A LEU* 1.3 75.9 - - - +
1576A SER* 1.3 57.9 + - - +
1578A GLY* 3.2 2.8 + - - +
1579A ARG* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1576 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN 4.6 5.5 + - - -
407A ALA* 3.4 8.1 + - - +
408A VAL* 3.2 32.1 + - - +
411A ASP* 4.4 5.6 - - - -
1572A ARG* 2.9 22.6 + - - -
1573A PHE* 4.0 1.3 - - - -
1575A ASN* 1.3 74.0 - - - +
1577A LEU* 1.3 60.9 + - - +
1579A ARG* 3.5 11.8 + - - +
1580A PHE* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1577 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 6.2 2.2 - - + -
109A ALA* 5.7 4.5 - - + -
113A LEU* 4.0 26.0 - - + -
408A VAL* 3.6 15.4 - - + +
1555A ILE* 4.7 2.5 - - + -
1573A PHE* 2.9 40.0 + - + +
1574A LEU* 3.7 16.6 - - + +
1576A SER* 1.3 73.8 - - - +
1578A GLY* 1.3 60.6 + - - +
1580A PHE* 4.2 6.7 - - + -
1581A MET* 2.9 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1578 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551A VAL* 5.1 2.5 - - - +
1552A ASN* 5.1 11.7 - - - -
1555A ILE* 4.1 20.4 - - - +
1574A LEU 2.9 14.5 + - - -
1575A ASN* 3.2 4.6 + - - -
1577A LEU* 1.3 76.7 - - - +
1579A ARG* 1.3 55.8 + - - +
1581A MET* 3.4 3.8 + - - +
1582A THR* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS* 4.2 31.1 - - - +
404A GLN* 3.8 30.3 + - - +
405A GLU* 4.1 26.4 - - + +
1575A ASN* 3.0 25.7 + - - +
1576A SER* 4.1 10.3 + - - +
1578A GLY* 1.3 75.0 - - - +
1580A PHE* 1.3 60.6 + - - +
1582A THR* 2.9 21.0 + - - +
1583A GLY* 3.0 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 4.1 17.6 - - + +
67A LEU* 5.2 9.0 - - + -
106A PHE* 4.0 35.4 - + - -
405A GLU* 3.1 32.0 - - - +
406A LEU* 4.9 10.3 - - + -
408A VAL* 3.8 28.3 - - + -
409A PHE* 5.4 6.3 - + - -
1576A SER 2.9 19.8 + - - +
1577A LEU* 3.7 12.3 - - + +
1579A ARG* 1.3 77.7 - - - +
1581A MET* 1.3 82.4 + - + +
1583A GLY* 2.8 23.2 + - - +
1584A LEU* 4.0 10.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.7 44.9 - - + +
109A ALA* 4.1 13.5 - - + -
110A ARG* 3.5 44.0 + - - +
113A LEU* 4.4 14.1 - - + -
1548A SER* 6.0 0.2 - - - -
1551A VAL* 3.8 24.0 - - + +
1555A ILE* 6.2 0.2 - - + -
1577A LEU* 2.9 32.9 + - + +
1578A GLY* 3.9 1.8 - - - +
1580A PHE* 1.3 104.7 - - + +
1582A THR* 1.3 60.4 + - - +
1583A GLY 3.1 1.0 + - - -
1584A LEU* 3.9 9.1 + - + -
1585A ASP* 4.9 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLU* 5.0 3.6 + - - +
1548A SER* 3.7 39.7 - - - +
1551A VAL* 4.8 5.2 - - + -
1552A ASN* 5.1 8.5 - - + +
1578A GLY 3.0 15.7 + - - +
1579A ARG* 2.9 20.5 + - - +
1581A MET* 1.3 75.2 - - - +
1583A GLY* 1.3 55.6 + - - +
1584A LEU 3.3 4.9 - - - -
1585A ASP* 2.9 22.8 - - - +
----------------------------------------------------------
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