Contacts of the helix formed by residues 1577 - 1583 (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 GLY1577 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1571B SER 3.7 4.0 - - - -
1572B LEU 3.7 2.7 - - - -
1574B ASN* 3.1 32.7 + - - -
1575B ALA 3.5 0.2 - - - -
1576B ASP* 1.3 81.9 - - - +
1578B ILE* 1.3 66.3 + - - -
1579B ILE 3.5 2.2 - - - -
1580B GLU* 3.4 2.8 + - - +
1581B LYS* 3.1 23.6 + - - +
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Residues in contact with ILE1578 (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 17.9 - - + +
1285B LEU* 4.7 2.7 - - + -
1286B SER* 4.6 8.7 - - - -
1290B ILE* 4.1 26.9 - - + -
1571B SER 3.5 10.1 + - - +
1572B LEU* 3.4 29.0 + - + -
1577B GLY* 1.3 71.8 - - - +
1579B ILE* 1.3 61.0 + - + +
1581B LYS* 3.8 1.8 - - - +
1582B SER* 2.7 42.1 + - - +
1772B ILE* 3.9 10.3 - - + -
1776B VAL* 3.4 41.1 - - + -
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Residues in contact with ILE1579 (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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1521B GLN* 4.3 21.5 - - + +
1522B LEU* 4.0 27.6 - - + -
1572B LEU* 2.9 48.9 + - + +
1573B ILE* 4.0 15.7 - - + -
1578B ILE* 1.3 79.9 - - + +
1580B GLU* 1.3 57.1 + - + +
1583B PHE* 2.8 62.9 + - + +
1589B SER* 4.4 6.1 + - - -
1590B ILE* 5.0 0.9 - - + -
1776B VAL* 5.2 3.8 - - + -
1780B LEU* 5.6 5.6 - - + -
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Residues in contact with GLU1580 (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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1227B ARG* 3.2 34.5 + - - -
1572B LEU 5.1 0.2 - - - +
1573B ILE* 3.8 11.7 - - - +
1574B ASN 3.0 28.5 - - - +
1575B ALA* 3.6 1.0 - - - -
1576B ASP* 3.6 11.7 + - - +
1577B GLY 3.4 9.7 + - - +
1578B ILE 3.3 0.4 - - - -
1579B ILE* 1.3 74.3 - - + +
1581B LYS* 1.3 65.1 + - - +
1583B PHE 3.4 14.4 - - - +
1586B GLY* 3.4 32.3 - - - +
1587B LYS* 3.3 19.3 + - - +
1589B SER* 4.3 9.0 - - - -
1590B ILE* 5.2 4.1 - - + +
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Residues in contact with LYS1581 (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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1290B ILE* 6.2 1.6 - - + -
1576B ASP* 3.9 26.9 + - - +
1577B GLY 3.1 17.5 + - - +
1578B ILE* 3.8 3.8 - - - +
1580B GLU* 1.3 79.4 - - - +
1582B SER* 1.3 60.5 - - - +
1736B LEU* 4.2 7.6 - - - +
1768B PHE* 4.4 11.7 - - + -
1769B GLU* 3.5 40.2 + - - +
1772B ILE* 4.1 23.3 - - + -
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Residues in contact with SER1582 (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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1578B ILE* 2.7 26.3 + - - +
1581B LYS* 1.3 76.2 - - - +
1583B PHE* 1.3 73.7 + - - +
1735B THR* 2.7 28.4 + - - -
1736B LEU* 3.0 7.1 - - - +
1769B GLU* 4.8 9.2 - - - -
1772B ILE* 3.0 26.0 - - - +
1773B ASP* 3.9 18.1 + - - -
1776B VAL* 5.8 0.2 - - - -
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Residues in contact with PHE1583 (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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1517B SER* 3.7 35.9 - - - -
1518B GLY* 4.4 5.6 - - - -
1521B GLN* 3.8 34.1 - - + -
1522B LEU* 5.2 3.4 - - + -
1579B ILE* 2.8 50.8 + - + +
1580B GLU 3.4 8.5 - - - +
1581B LYS 3.6 0.2 - - - -
1582B SER* 1.3 86.7 - - - +
1584B LEU* 1.3 66.9 + - - +
1585B PRO* 3.5 10.1 - - + -
1586B GLY* 3.1 14.0 + - - -
1589B SER* 4.2 2.0 + - - +
1735B THR* 3.8 23.8 - - + -
1736B LEU* 3.6 6.6 - - - +
1773B ASP* 3.8 16.6 - - - -
1776B VAL* 6.0 2.5 - - + -
1777B ILE* 4.5 8.7 - - + -
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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