Contacts of the helix formed by residues 1588 - 1598 (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 TYR1588 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1442B TYR* 4.1 18.0 - + + -
1445B ARG* 3.4 72.9 + - + -
1446B ILE* 4.1 5.4 - - + -
1448B SER* 4.6 0.6 + - - -
1449B LEU 6.0 1.8 - - - -
1585B PRO* 3.7 21.5 - - - +
1586B GLY 3.1 0.6 - - - -
1587B LYS* 1.3 113.3 + - + +
1589B SER* 1.3 60.3 + - - +
1590B ILE 3.7 0.9 - - - -
1591B GLU* 3.7 25.3 + - - +
1592B MET* 3.1 23.9 + - - +
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Residues in contact with SER1589 (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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1522B LEU* 3.2 37.0 - - - +
1579B ILE* 4.4 6.7 + - - -
1580B GLU* 4.3 12.2 - - - -
1583B PHE* 4.2 3.6 + - - +
1585B PRO* 3.5 18.1 - - - +
1586B GLY* 2.8 33.9 + - - -
1587B LYS 3.2 2.2 - - - -
1588B TYR* 1.3 75.0 - - - +
1590B ILE* 1.3 68.5 + - - +
1592B MET* 3.3 13.5 - - - +
1593B SER 3.5 1.6 + - - -
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Residues in contact with ILE1590 (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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1218B LEU* 4.0 15.9 - - + -
1230B LEU* 3.5 22.5 - - + +
1238B TYR* 3.9 13.9 - - + +
1522B LEU* 4.0 19.1 - - + -
1526B TRP* 4.9 6.3 - - + -
1573B ILE* 3.5 57.4 - - + +
1579B ILE* 5.0 2.2 - - + -
1580B GLU* 5.2 4.9 - - + +
1587B LYS 4.7 2.0 + - - +
1588B TYR 3.7 0.2 - - - -
1589B SER* 1.3 74.6 - - - +
1591B GLU* 1.3 66.0 + - - +
1592B MET 3.1 1.8 - - - -
1593B SER* 2.5 31.4 + - - +
1594B SER 3.1 4.3 + - - -
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Residues in contact with GLU1591 (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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1228B PRO* 4.0 35.5 - - + +
1230B LEU* 3.9 13.4 - - + +
1236B TYR* 3.7 26.1 + - + -
1442B TYR* 3.0 26.1 + - - -
1587B LYS 5.0 3.2 + - - +
1588B TYR* 3.7 37.1 - - - +
1590B ILE* 1.3 76.7 - - - +
1592B MET* 1.3 59.8 + - - +
1594B SER* 3.2 16.3 - - - -
1595B SER* 3.2 4.5 + - - -
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Residues in contact with MET1592 (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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1438B ALA* 3.7 27.4 - - + +
1439B PHE* 3.9 33.4 - - + -
1442B TYR* 3.3 40.4 + - + -
1446B ILE* 5.9 0.9 - - - -
1519B TYR* 5.1 7.2 - - + -
1522B LEU* 5.0 6.5 - - + -
1523B VAL* 5.4 5.2 - - + -
1585B PRO* 4.0 24.5 - - + -
1588B TYR 3.1 13.2 + - - +
1589B SER* 3.3 13.5 - - - +
1590B ILE 3.1 0.2 - - - -
1591B GLU* 1.3 74.8 - - - +
1593B SER* 1.3 63.1 + - - +
1595B SER* 3.2 4.0 + - - -
1596B VAL* 3.1 28.8 + - + +
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Residues in contact with SER1593 (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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1238B TYR* 2.7 29.0 + - - -
1522B LEU* 3.8 27.1 - - - +
1523B VAL* 4.5 10.8 - - - -
1526B TRP* 4.6 2.2 - - - -
1527B LEU* 3.8 12.4 - - - +
1589B SER 3.5 4.9 + - - -
1590B ILE* 2.5 30.8 + - - +
1592B MET* 1.3 74.9 - - - +
1594B SER* 1.3 54.3 + - - +
1596B VAL* 3.4 1.9 + - - +
1597B TYR* 2.9 28.6 + - - +
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Residues in contact with SER1594 (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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1230B LEU* 3.7 19.6 - - - +
1235B ILE 4.7 0.9 + - - -
1236B TYR* 3.5 12.4 - - - -
1237B PRO* 2.7 47.7 + - - +
1238B TYR* 3.5 9.8 - - - -
1590B ILE 3.1 6.6 + - - -
1591B GLU* 3.2 12.3 - - - -
1593B SER* 1.3 74.9 + - - +
1595B SER* 1.3 63.5 + - - +
1597B TYR* 3.3 14.8 + - - +
1598B LYS* 3.5 4.3 + - - +
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Residues in contact with SER1595 (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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1235B ILE 5.7 0.9 + - - -
1442B TYR* 2.8 35.1 + - - -
1591B GLU 3.2 1.4 + - - -
1592B MET 3.2 9.3 + - - -
1594B SER* 1.3 78.2 + - - +
1596B VAL* 1.3 64.2 + - - +
1598B LYS* 3.2 38.9 + - - +
1599B ASN* 4.3 4.2 + - - +
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Residues in contact with VAL1596 (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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1438B ALA* 4.7 15.0 - - + +
1519B TYR* 4.3 19.3 - - + +
1523B VAL* 3.4 43.5 - - + -
1527B LEU* 4.5 2.4 - - + +
1528B ASN* 5.8 0.2 - - - +
1592B MET* 3.1 20.4 + - + +
1593B SER 3.4 4.2 + - - +
1595B SER* 1.3 77.9 - - - +
1597B TYR* 1.3 56.0 + - - +
1599B ASN* 3.0 30.0 + - + +
1600B TRP* 3.5 7.1 + - - +
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Residues in contact with TYR1597 (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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1237B PRO* 3.5 28.7 - - + +
1238B TYR* 3.5 31.9 + - + -
1239B PRO* 3.7 14.1 - - + -
1527B LEU* 3.8 24.0 - - + +
1532B VAL* 4.4 1.8 - - + -
1593B SER 2.9 15.4 + - - +
1594B SER* 3.3 13.2 - - - +
1595B SER 3.2 0.2 - - - -
1596B VAL* 1.3 72.1 - - - +
1598B LYS* 1.3 63.5 + - - +
1599B ASN 3.0 2.0 - - - -
1600B TRP* 2.9 30.0 + + + +
1683B HIS* 2.9 37.5 + + - +
1685B ASP* 4.7 2.5 - - + -
1686B LEU* 3.6 39.2 - - + +
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Residues in contact with LYS1598 (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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1234B SER 4.0 16.1 + - - +
1235B ILE* 3.7 25.9 + - - +
1237B PRO* 3.6 22.7 - - + -
1594B SER 3.5 1.5 + - - +
1595B SER* 3.2 29.7 + - - +
1597B TYR* 1.3 77.8 - - - +
1599B ASN* 1.3 65.4 + - - +
1600B TRP 3.9 1.2 + - - +
1686B LEU* 4.3 15.6 - - - +
1689B LYS* 4.3 14.4 + - - -
1691B TRP* 4.9 1.6 - - - -
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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