Contacts of the helix formed by residues 1366 - 1373 (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 THR1366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1361B LYS* 4.7 8.7 - - + +
1362B SER* 2.7 41.2 + - - +
1364B VAL 2.9 7.3 + - - +
1365B MET* 1.3 73.6 - - + +
1367B ASP* 1.3 51.0 + - - +
1368B GLU* 3.1 18.4 - - + +
1369B GLU* 2.9 20.3 + - - +
1370B PHE* 2.7 34.1 + - - +
1509B LYS* 4.1 1.6 - - - -
1837B PRO* 4.1 6.5 - - + +
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Residues in contact with ASP1367 (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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1365B MET 3.9 0.5 + - - +
1366B THR* 1.3 65.8 - - - +
1368B GLU* 1.3 77.1 + - - +
1370B PHE* 3.7 9.2 - - - -
1371B ALA* 2.8 35.5 + - - +
1470B LYS* 5.3 5.2 + - + -
1471B PRO* 3.2 20.1 - - + +
1495B PRO* 4.2 13.9 - - - +
1496B ALA 5.2 1.6 + - - -
1505B TRP* 3.4 22.5 - - - -
1509B LYS* 3.1 26.5 + - - -
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Residues in contact with GLU1368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366B THR* 4.2 13.8 - - + +
1367B ASP* 1.3 97.3 + - - +
1369B GLU* 1.3 57.4 + - - +
1371B ALA* 3.8 1.2 - - - +
1372B ARG* 2.9 28.9 + - - +
1468B THR* 6.1 5.8 - - + -
1469B LEU 4.4 9.3 - - - +
1470B LYS* 5.2 10.2 + - + +
1837B PRO* 3.9 22.7 - - + -
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Residues in contact with GLU1369 (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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1362B SER* 3.8 9.9 - - - +
1363B GLY 4.1 4.3 - - - +
1364B VAL 5.1 0.7 - - - +
1366B THR* 2.9 22.9 + - - +
1368B GLU* 1.3 77.0 - - - +
1370B PHE* 1.3 66.7 + - - +
1372B ARG* 3.0 45.7 + - - -
1373B GLU* 2.7 49.6 + - - +
1726B TYR* 4.0 1.0 - - - -
1732B ASN* 5.2 0.2 - - - +
1837B PRO* 3.6 13.7 - - + +
1838B VAL* 3.3 35.0 - - + +
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Residues in contact with PHE1370 (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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1364B VAL 5.2 3.7 + - - +
1366B THR 2.7 19.3 + - - +
1367B ASP* 3.7 4.9 - - - +
1369B GLU* 1.3 76.1 - - - +
1371B ALA* 1.3 66.3 + - - +
1373B GLU* 3.5 13.1 + - - +
1374B VAL* 3.8 10.2 - - - +
1433B LEU* 5.9 1.6 - - + -
1459B THR* 3.8 17.7 - - + -
1461B LEU* 5.3 1.3 - - + -
1471B PRO* 3.4 40.2 - - + -
1474B ILE* 3.9 20.2 - - + -
1505B TRP* 4.1 14.1 - + - -
1509B LYS* 3.9 29.6 - - + +
1512B VAL* 4.2 9.6 - - + -
1513B ILE* 3.7 34.3 - - + +
1732B ASN* 6.2 0.4 - - - -
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Residues in contact with ALA1371 (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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1367B ASP 2.8 23.3 + - - +
1370B PHE* 1.3 74.2 - - - +
1372B ARG* 1.3 61.0 + - - +
1374B VAL* 3.5 21.7 + - - +
1461B LEU* 4.0 11.2 - - + -
1469B LEU* 3.3 45.0 - - + +
1471B PRO* 3.4 16.6 - - + -
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Residues in contact with ARG1372 (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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1368B GLU 2.9 22.5 + - - +
1369B GLU* 3.0 41.4 + - - +
1370B PHE 3.4 0.2 - - - -
1371B ALA* 1.3 71.5 - - - +
1373B GLU* 1.3 58.6 + - - +
1374B VAL 3.1 0.4 - - - -
1375B ILE* 3.0 19.7 + - - +
1376B ALA* 3.0 36.3 + - - +
1469B LEU* 4.8 3.3 + - - +
1726B TYR* 3.0 28.6 + - - -
1832B ARG 5.0 0.2 - - - +
1833B ASN* 3.2 41.6 + - + +
1834B ARG 3.8 8.5 + - - -
1835B THR 3.5 15.1 + - - -
1836B GLY* 3.5 16.3 - - - +
1837B PRO* 5.5 0.9 - - + -
1838B VAL* 3.7 8.1 - - - +
1840B LEU* 3.1 20.0 + - - +
1842B TYR* 4.7 3.8 - - - -
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Residues in contact with GLU1373 (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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1356B VAL* 4.2 1.2 - - - +
1369B GLU* 2.7 46.5 + - - +
1370B PHE* 3.7 6.1 - - - +
1371B ALA 3.3 0.6 - - - -
1372B ARG* 1.3 80.3 - - - +
1374B VAL* 1.3 60.1 + - - +
1375B ILE 3.3 0.4 - - - -
1376B ALA 4.1 0.7 - - - -
1377B GLY* 3.1 29.1 + - - +
1378B VAL 4.4 1.6 + - - -
1379B ASN 4.1 7.1 + - - +
1726B TYR* 3.4 34.8 - - + +
1732B ASN* 3.4 31.8 + - - +
1733B ARG* 4.4 17.4 + - - +
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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