Contacts of the strand formed by residues 1567 - 1574 (chain A) in PDB entry 2IG0
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 GLU1567 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1562A ARG 3.7 0.3 - - - +
1563A LYS* 3.3 8.6 - - - -
1564A GLU 3.0 32.6 + - - +
1565A SER* 3.0 13.4 - - - +
1566A GLY* 1.3 82.8 - - - +
1568A LEU* 1.3 62.0 + - - +
1569A TYR* 3.5 26.8 + - + +
1582A LYS* 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536A ASP* 4.3 0.9 - - - +
1537A PRO* 3.6 33.4 - - + -
1561A HIS* 4.2 14.1 - - + +
1562A ARG 3.5 15.3 - - - +
1563A LYS* 4.1 16.3 - - + +
1566A GLY 4.3 0.4 + - - -
1567A GLU* 1.3 74.0 - - - +
1569A TYR* 1.3 75.4 + - - +
1570A TYR* 3.6 23.1 - - + +
1582A LYS* 4.1 0.7 - - - +
1583A ARG* 3.3 69.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1561A HIS* 3.4 5.0 - - - -
1562A ARG* 2.9 46.6 + - + +
1564A GLU* 4.0 24.8 + - + -
1567A GLU* 3.5 41.6 + - + +
1568A LEU* 1.3 78.8 - - - +
1570A TYR* 1.3 63.3 + - - +
1580A TRP* 3.5 28.6 - + + -
1581A TYR 3.3 14.1 - - - +
1582A LYS* 3.9 39.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537A PRO* 3.5 6.3 - - + +
1538A ILE* 2.8 62.4 + - + +
1558A VAL* 3.9 18.2 - - + -
1560A GLY 3.6 2.5 - - - -
1561A HIS* 3.8 18.2 - - - -
1568A LEU* 3.6 23.3 - - + +
1569A TYR* 1.3 76.0 - - - +
1571A SER* 1.3 59.2 + - - +
1572A ILE* 3.7 18.1 + - + -
1579A LYS 3.7 0.9 - - - +
1580A TRP* 3.3 7.1 - - - -
1581A TYR* 2.8 36.5 + - - +
1583A ARG* 4.0 27.2 + - + +
1586A VAL* 3.6 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1558A VAL* 3.6 3.1 - - - -
1559A LYS* 2.8 32.9 + - - +
1560A GLY* 3.0 22.2 + - - +
1570A TYR* 1.3 71.3 - - - +
1572A ILE* 1.3 58.0 + - - +
1578A ARG* 3.6 32.1 + - - +
1579A LYS 3.6 5.6 + - - -
1580A TRP* 3.7 33.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544A VAL* 3.7 26.5 - - + -
1546A ALA* 4.6 8.7 - - + -
1556A GLY* 3.7 28.5 - - - -
1557A VAL 3.5 1.1 - - - -
1558A VAL* 3.8 16.8 - - + -
1570A TYR* 3.7 27.1 - - + -
1571A SER* 1.3 76.6 + - - +
1573A GLU* 1.3 65.3 + - - +
1574A LYS* 3.9 2.7 + - + +
1577A GLN 3.5 1.4 - - - +
1578A ARG* 3.3 2.5 - - - -
1579A LYS* 2.9 34.4 + - - +
1581A TYR* 3.4 36.7 - - + -
1586A VAL* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A SO4 3.5 18.0 + - - -
1556A GLY* 3.2 6.0 - - - -
1557A VAL* 2.9 35.1 + - + +
1559A LYS* 3.9 29.3 - - + +
1571A SER 4.3 0.4 + - - -
1572A ILE* 1.3 74.3 - - - +
1574A LYS* 1.3 62.8 + - - +
1575A GLU 5.1 0.2 - - - +
1576A GLY* 3.8 31.6 + - - +
1577A GLN 3.1 13.7 - - - +
1578A ARG* 3.2 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1554A SER* 3.5 35.0 - - - +
1555A ALA 3.7 16.4 - - - +
1556A GLY* 4.8 1.6 - - - -
1572A ILE* 3.9 3.6 + - + +
1573A GLU* 1.3 75.1 - - - +
1575A GLU* 1.3 109.3 + - + +
1576A GLY 3.2 0.4 - - - -
1577A GLN* 2.9 21.4 + - - +
----------------------------------------------------------
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