Contacts of the helix formed by residues 1548 - 1555 (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 HIS1548 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1174B THR* 4.2 0.9 - - - -
1175B TYR 3.8 3.1 - - - -
1176B LEU* 3.8 6.5 - - + +
1177B PRO* 3.7 10.3 - - + +
1188B ARG* 3.5 15.6 - - - +
1544B LEU* 4.2 14.8 - - + +
1545B SER 2.9 20.0 + - - +
1547B LEU* 1.3 78.6 - - - +
1549B PRO* 1.4 62.0 - - + +
1550B ILE* 3.1 32.6 + - + +
1551B TYR* 3.1 7.2 + - + +
1552B LYS* 2.9 27.4 + - - +
1659B TYR* 3.1 26.9 - - - -
1668B ASP* 3.1 22.6 + - - -
1670B GLU* 3.4 23.6 - - + -
1671B LEU* 4.7 1.6 - - + -
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Residues in contact with PRO1549 (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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1174B THR* 3.5 26.2 - - + -
1175B TYR 4.0 13.9 - - - +
1176B LEU* 3.5 24.7 - - + +
1547B LEU 3.7 2.0 - - - +
1548B HIS* 1.4 88.9 - - + +
1550B ILE* 1.3 59.5 + - + +
1552B LYS* 4.2 0.7 - - + -
1553B LEU 2.8 15.1 + - - -
1654B TYR* 2.7 36.3 + - + +
1658B TYR* 3.7 30.1 - - + -
1659B TYR* 4.2 2.2 - - - +
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Residues in contact with ILE1550 (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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1544B LEU* 3.9 15.7 - - + +
1548B HIS* 3.1 10.8 + - + +
1549B PRO* 1.3 74.8 - - - +
1551B TYR* 1.3 67.5 + - - +
1553B LEU* 3.8 11.4 - - + -
1554B LEU* 3.0 28.9 + - + +
1654B TYR* 4.4 5.4 - - + -
1655B VAL* 3.6 31.0 - - + -
1659B TYR* 3.3 35.9 - - + +
1671B LEU* 4.0 20.2 - - + -
1674B TRP* 4.6 3.6 - - + -
1701B LEU* 4.2 4.7 - - + -
1705B CYS* 4.2 19.5 - - - -
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Residues in contact with TYR1551 (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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1540B THR* 4.3 17.5 - - + -
1541B ASN* 4.0 27.4 + - - -
1544B LEU* 3.4 35.2 - - + +
1545B SER 3.1 19.5 - - - +
1546B VAL* 3.5 44.7 - - + +
1548B HIS* 3.1 6.6 + - - +
1550B ILE* 1.3 79.0 - - - +
1552B LYS* 1.4 63.2 + - + +
1555B TYR* 2.8 61.7 + + + +
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Residues in contact with LYS1552 (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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1171B VAL 4.3 10.1 + - - -
1172B ASN* 3.9 8.5 - - - +
1173B ASP 3.5 17.2 + - - -
1174B THR* 3.0 31.6 - - - +
1546B VAL* 2.7 28.9 + - - +
1547B LEU* 3.6 4.8 - - - +
1548B HIS 2.9 17.3 + - - +
1551B TYR* 1.4 73.4 - - + +
1553B LEU* 1.3 56.6 + - - +
1555B TYR* 3.2 18.7 - - + -
1654B TYR* 3.6 16.6 - - - +
1793B ARG* 2.8 31.0 + - - -
1798B TRP* 3.3 35.2 - - + +
1799B THR* 4.6 2.2 - - - -
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Residues in contact with LEU1553 (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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1549B PRO 2.8 20.6 + - - +
1550B ILE* 3.8 17.9 - - + +
1551B TYR 3.0 0.8 + - - -
1552B LYS* 1.3 72.9 - - - +
1554B LEU* 1.3 67.6 + - + +
1556B PRO* 3.5 7.8 - - - +
1557B HIS* 3.6 13.6 - - + -
1650B TRP* 3.7 38.8 - - + +
1651B VAL* 4.2 18.8 - - + -
1654B TYR* 3.8 22.4 + - + -
1655B VAL* 4.5 0.4 - - + -
1705B CYS* 3.9 34.1 - - + -
1709B VAL* 5.5 1.6 - - + -
1793B ARG* 3.1 18.3 + - - +
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Residues in contact with LEU1554 (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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1540B THR* 4.8 4.5 - - + +
1550B ILE* 3.0 15.6 + - + +
1551B TYR 3.0 7.3 + - - -
1553B LEU* 1.3 83.9 - - + +
1555B TYR* 1.3 61.5 + - - -
1556B PRO* 3.1 5.4 - - - -
1557B HIS* 3.4 17.1 + - - +
1558B TYR* 3.3 37.6 - - + +
1674B TRP* 3.9 24.5 - - + -
1705B CYS* 4.2 22.9 - - - +
1708B ILE* 3.8 20.6 - - + -
1709B VAL* 3.8 29.4 - - + -
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Residues in contact with TYR1555 (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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1152B VAL* 5.4 3.1 - - - +
1154B ASN* 6.2 0.7 - - - -
1540B THR* 5.3 1.3 - - - +
1551B TYR* 2.8 51.2 + + + +
1552B LYS* 3.2 42.0 - - + -
1554B LEU* 1.3 69.4 - - - +
1556B PRO* 1.4 67.6 - - + +
1557B HIS 3.5 0.6 + - - -
1558B TYR* 3.9 21.5 + - - +
1559B ARG* 4.4 4.0 + - - +
1793B ARG* 3.3 24.7 + - + +
1794B GLU* 5.2 18.8 - - + +
1795B THR* 4.3 9.0 + - - -
1798B TRP* 3.5 24.3 - + + +
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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