Contacts of the helix formed by residues 1746 - 1755 (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 THR1746 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1743B ALA* 2.8 35.4 + - + +
1744B GLU 5.2 0.7 - - - +
1745B GLY* 1.4 74.2 - - - +
1747B PRO* 1.4 68.8 - - + +
1748B GLU* 3.6 18.2 - - + +
1749B TYR* 3.2 16.0 + - - +
1750B ASP* 2.9 31.8 + - - +
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Residues in contact with PRO1747 (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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1745B GLY 4.7 1.1 - - - +
1746B THR* 1.4 84.9 - - + +
1748B GLU* 1.3 71.5 + - - +
1750B ASP* 3.8 9.2 - - + +
1751B GLU* 3.0 28.1 + - - +
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Residues in contact with GLU1748 (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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1739B ARG* 3.5 42.8 + - - +
1742B PRO* 3.9 10.3 - - + -
1743B ALA 5.6 0.2 - - - +
1746B THR* 3.6 18.6 - - + +
1747B PRO* 1.3 87.2 - - - +
1749B TYR* 1.3 58.2 + - - +
1751B GLU* 3.6 5.1 + - - +
1752B MET* 3.1 27.9 + - - +
1759B ALA* 5.2 0.2 - - - +
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Residues in contact with TYR1749 (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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1500B VAL* 3.6 26.3 - - + +
1504B ILE* 4.9 5.2 - - + -
1742B PRO* 3.6 17.2 - - + +
1743B ALA 3.5 5.4 - - - +
1744B GLU* 3.1 54.0 + - + -
1745B GLY* 3.7 11.4 - - - -
1746B THR* 3.2 22.2 + - - +
1748B GLU* 1.3 78.5 - - - +
1750B ASP* 1.3 70.5 + - - +
1752B MET* 3.5 27.7 + - + +
1753B VAL* 3.4 23.2 + - + +
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Residues in contact with ASP1750 (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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1745B GLY* 3.7 12.7 - - - +
1746B THR 2.9 23.2 + - - +
1747B PRO* 4.2 7.0 - - + +
1748B GLU 3.4 0.2 - - - -
1749B TYR* 1.3 83.8 - - - +
1751B GLU* 1.3 61.4 + - - +
1752B MET 3.1 0.7 + - - -
1753B VAL* 3.1 10.9 + - - +
1754B LYS* 3.0 51.4 + - - +
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Residues in contact with GLU1751 (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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1739B ARG* 3.1 27.5 + - - -
1747B PRO 3.0 20.0 + - - +
1748B GLU* 3.9 4.3 - - - +
1750B ASP* 1.3 73.7 - - - +
1752B MET* 1.3 55.9 + - - +
1753B VAL 3.5 0.2 - - - -
1754B LYS* 4.4 9.7 - - - +
1755B ASN* 2.8 34.1 + - + +
1758B LYS* 3.4 33.8 - - + +
1759B ALA* 4.6 4.7 + - - +
1762B ARG* 3.9 20.1 + - - -
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Residues in contact with MET1752 (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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1500B VAL* 4.0 14.8 - - + -
1503B THR* 3.6 20.8 - - + +
1504B ILE* 3.3 28.5 - - + -
1507B LEU* 3.4 9.9 - - - -
1742B PRO* 3.1 24.5 - - + -
1748B GLU 3.1 16.6 + - - +
1749B TYR* 3.5 41.5 - - + +
1750B ASP 3.1 0.6 - - - -
1751B GLU* 1.3 75.9 - - - +
1753B VAL* 1.3 59.2 + - - +
1755B ASN 3.8 0.2 - - - -
1756B PRO* 3.1 28.4 - - - +
1759B ALA* 3.6 22.9 - - + -
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Residues in contact with VAL1753 (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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1500B VAL* 4.3 29.4 - - + +
1503B THR* 5.5 1.8 - - - -
1749B TYR* 3.4 10.7 + - + +
1750B ASP* 3.1 26.1 + - - +
1752B MET* 1.3 77.4 - - - +
1754B LYS* 1.3 81.3 + - + +
1755B ASN 3.4 0.2 + - - -
1756B PRO* 4.1 8.5 - - - +
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Residues in contact with LYS1754 (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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1750B ASP* 3.0 48.5 + - - +
1751B GLU* 4.3 6.7 - - - +
1753B VAL* 1.3 91.0 - - + +
1755B ASN* 1.3 61.3 + - + +
1756B PRO* 4.0 2.6 - - - +
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Residues in contact with ASN1755 (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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1308B GLU* 5.0 9.6 + - - +
1751B GLU* 2.8 27.8 + - + +
1752B MET 3.4 1.1 - - - -
1754B LYS* 1.3 84.6 - - + +
1756B PRO* 1.3 67.9 - - - +
1757B GLN* 3.6 11.1 + - - +
1758B LYS* 3.2 33.0 + - + +
1759B ALA* 3.1 15.9 + - - +
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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