Contacts of the helix formed by residues 1560 - 1572 (chain B) in PDB entry 2IUK
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 ASP1560 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1267B GLU* 3.2 12.2 + - - +
1269B PHE* 3.1 44.4 + - + +
1271B HIS* 4.5 10.0 + - - -
1279B THR* 5.6 2.5 - - - +
1558B TYR 3.1 1.4 + - - -
1559B ARG* 1.3 78.6 - - + +
1561B THR* 1.3 58.4 + - - +
1562B ILE 3.5 1.8 - - - -
1563B ASN* 2.9 30.5 + - - -
1564B ILE* 3.0 31.4 + - + +
1862B ILE 3.5 1.1 - - - -
1863B SER* 4.2 17.9 - - - +
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Residues in contact with THR1561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530B HIS 4.4 4.3 - - - +
1533B MET* 3.9 21.8 - - + -
1534B GLU* 5.0 4.7 - - - +
1537B ALA* 5.6 1.8 - - + -
1557B HIS 3.9 1.0 + - - -
1558B TYR* 2.8 32.7 + - - -
1560B ASP* 1.3 78.1 - - - +
1562B ILE* 1.3 60.1 + - - +
1564B ILE* 3.3 5.3 - - + +
1565B ASN* 2.9 41.5 + - - +
1862B ILE* 2.9 43.0 + - + +
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Residues in contact with ILE1562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210B TYR* 4.5 6.5 - - + -
1242B VAL* 4.4 7.9 - - + +
1263B VAL* 3.4 20.1 - - + +
1264B PRO* 4.0 9.0 - - + -
1267B GLU* 3.5 45.1 + - + +
1534B GLU* 3.6 32.8 - - + +
1537B ALA* 3.7 28.9 - - + +
1538B ILE* 4.1 22.7 - - + +
1561B THR* 1.3 75.8 - - - +
1563B ASN* 1.3 58.3 + - - +
1565B ASN* 3.8 2.3 - - - +
1566B GLY* 3.1 21.3 + - - -
1569B ARG* 5.1 0.7 + - - -
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Residues in contact with ASN1563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1263B VAL* 3.6 21.5 - - + +
1267B GLU 3.3 18.5 + - - +
1268B ASN* 3.5 33.8 + - - +
1269B PHE 4.0 2.0 + - - +
1279B THR* 4.3 17.6 + - - +
1560B ASP* 2.9 31.8 + - - +
1562B ILE* 1.3 76.5 - - - +
1564B ILE* 1.4 63.0 + - - +
1565B ASN 3.2 1.1 - - - -
1566B GLY* 3.5 1.7 + - - -
1567B LEU* 3.2 21.0 + - - +
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Residues in contact with ILE1564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1279B THR* 4.1 22.0 - - + -
1282B ILE* 4.9 9.6 - - + -
1526B TRP* 4.9 0.2 - - - -
1530B HIS* 3.3 36.6 + - + +
1560B ASP* 3.0 19.7 + - + +
1561B THR* 3.3 25.6 - - - +
1563B ASN* 1.4 71.6 - - - +
1565B ASN* 1.3 60.8 + - - +
1567B LEU* 3.9 6.3 - - + +
1568B ALA* 3.0 26.5 + - - +
1572B LEU* 5.4 0.7 - - - +
1780B LEU* 6.4 0.2 - - + -
1862B ILE* 3.6 13.7 - - + +
1863B SER 3.9 17.7 - - - +
1864B ILE* 4.0 25.8 - - + +
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Residues in contact with ASN1565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B TYR* 5.5 0.2 - - - +
1526B TRP* 3.5 23.6 - - + -
1530B HIS* 2.9 52.8 + - - +
1531B ALA* 4.9 0.4 - - - -
1534B GLU* 3.1 31.3 - - - +
1561B THR* 2.9 26.0 + - - +
1562B ILE 3.8 2.9 - - - +
1563B ASN 3.2 0.8 - - - -
1564B ILE* 1.3 73.8 - - - +
1566B GLY* 1.3 55.4 + - - +
1568B ALA* 3.1 2.9 + - - +
1569B ARG* 2.8 40.2 + - - +
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Residues in contact with GLY1566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261B VAL* 3.6 32.7 - - - +
1263B VAL* 5.0 4.9 - - - -
1562B ILE 3.1 17.8 + - - -
1563B ASN 3.5 1.8 + - - -
1564B ILE 3.4 0.2 - - - -
1565B ASN* 1.3 72.6 - - - +
1567B LEU* 1.3 64.5 + - - +
1569B ARG* 3.1 15.1 + - - +
1570B GLN* 3.1 18.5 + - - +
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Residues in contact with LEU1567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261B VAL* 5.0 3.8 - - - +
1279B THR* 4.3 24.0 - - + +
1282B ILE* 3.4 43.1 - - + -
1283B LYS* 4.1 31.4 - - + +
1563B ASN 3.2 16.0 + - - +
1564B ILE* 4.1 9.2 - - + +
1566B GLY* 1.3 73.8 - - - +
1568B ALA* 1.3 61.7 + - - +
1570B GLN* 4.5 4.9 - - + +
1571B SER* 2.9 41.3 + - - +
1572B LEU* 4.6 3.1 - - + -
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Residues in contact with ALA1568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526B TRP* 3.8 22.7 - - + -
1564B ILE 3.0 20.8 + - - +
1565B ASN 3.1 5.8 + - - +
1567B LEU* 1.3 75.8 - - - +
1569B ARG* 1.3 58.8 + - - +
1572B LEU* 3.1 37.5 + - + -
1573B ILE* 2.9 33.4 + - + +
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Residues in contact with ARG1569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B TYR* 3.4 32.3 + - + -
1217B ASP* 2.9 43.0 + - - +
1218B LEU* 3.9 13.2 - - + +
1241B ARG* 3.5 33.7 - - - +
1242B VAL* 4.0 9.5 + - - +
1244B THR* 3.8 22.0 - - - +
1261B VAL* 4.0 14.3 - - - +
1262B TYR 4.9 0.4 + - - -
1526B TRP* 5.2 1.3 - - + -
1534B GLU* 3.9 17.6 + - - -
1562B ILE 5.1 0.4 + - - -
1565B ASN* 2.8 19.9 + - - +
1566B GLY* 3.1 19.8 + - - +
1568B ALA* 1.3 76.6 - - - +
1570B GLN* 1.3 64.5 + - - +
1573B ILE* 3.7 13.0 - - + -
1574B ASN* 3.2 21.9 - - - +
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Residues in contact with GLN1570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1217B ASP* 4.4 12.3 + - - +
1246B ARG* 3.0 29.7 + - - +
1258B PRO* 3.9 12.6 - - - +
1259B GLY 3.6 35.6 + - - +
1261B VAL* 3.3 25.0 - - + +
1566B GLY 3.1 13.4 + - - +
1567B LEU* 4.0 6.3 - - + +
1569B ARG* 1.3 84.6 + - - +
1571B SER* 1.3 62.6 + - - +
1574B ASN* 3.3 18.5 + - - +
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Residues in contact with SER1571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282B ILE* 4.5 6.7 - - - -
1283B LYS* 4.7 5.2 - - - +
1286B SER* 4.4 26.5 + - - -
1567B LEU* 2.9 38.2 + - - +
1568B ALA 3.6 0.2 + - - -
1570B GLN* 1.3 82.3 + - - +
1572B LEU* 1.3 56.3 + - - +
1574B ASN* 3.2 16.3 + - - +
1577B GLY* 3.7 2.1 - - - -
1578B ILE* 3.5 20.4 + - - +
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Residues in contact with LEU1572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282B ILE* 3.7 30.7 - - + -
1526B TRP* 6.1 1.6 - - + -
1564B ILE 5.4 0.9 - - - +
1567B LEU* 4.6 5.4 - - + -
1568B ALA* 3.1 30.5 + - + +
1571B SER* 1.3 74.9 - - - +
1573B ILE* 1.3 65.1 + - + +
1574B ASN* 3.5 1.5 - - - +
1577B GLY* 3.7 3.6 - - - -
1578B ILE* 3.4 29.0 + - + +
1579B ILE* 2.9 45.5 + - + +
1580B GLU 4.2 1.6 + - - -
1776B VAL* 3.9 14.4 - - + -
1780B LEU* 4.8 18.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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