Contacts of the helix formed by residues 1420 - 1428 (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 THR1420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1413B GLU* 3.3 20.2 - - - +
1416B MET* 3.5 1.6 - - - -
1418B GLY 4.0 4.0 + - - +
1419B VAL* 1.3 80.9 - - - +
1421B VAL* 1.3 65.0 + - - +
1422B GLU* 3.8 10.7 + - - +
1423B GLU* 3.0 30.2 + - - +
1424B ALA 2.9 19.6 + - - -
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Residues in contact with VAL1421 (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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1389B PHE* 3.6 37.9 - - + -
1409B LYS* 3.6 36.6 - - + +
1412B LEU* 3.6 23.3 - - + -
1413B GLU* 3.2 11.2 + - + +
1416B MET* 3.4 12.4 - - + +
1420B THR* 1.3 70.4 - - - +
1422B GLU* 1.3 56.8 + - - +
1424B ALA* 3.1 5.1 + - - +
1425B LEU* 2.9 32.8 + - + +
1430B LEU* 3.7 13.5 - - + -
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Residues in contact with GLU1422 (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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1409B LYS* 5.7 5.4 - - - +
1413B GLU* 5.0 0.4 + - - -
1420B THR* 3.1 9.3 + - - +
1421B VAL* 1.3 78.5 - - - +
1423B GLU* 1.3 64.0 + - - +
1425B LEU* 3.4 14.1 + - + +
1426B SER* 3.2 22.7 + - - -
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Residues in contact with GLU1423 (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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1418B GLY 4.7 2.4 - - - +
1419B VAL* 3.8 25.1 - - + +
1420B THR* 3.0 30.7 + - - +
1422B GLU* 1.3 80.5 + - - +
1424B ALA* 1.3 51.5 + - - +
1426B SER* 3.3 7.0 + - - -
1427B THR* 2.6 47.3 + - + +
1429B ARG* 5.5 0.9 + - - -
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Residues in contact with ALA1424 (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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1416B MET* 4.6 0.7 - - + -
1419B VAL* 3.8 7.1 - - + +
1420B THR 2.9 11.6 + - - +
1421B VAL* 3.1 11.4 + - - +
1423B GLU* 1.3 74.3 - - - +
1425B LEU* 1.3 58.2 + - - +
1427B THR* 3.2 6.4 + - - -
1428B GLN 2.8 9.5 + - - -
1429B ARG* 2.8 31.5 + - + -
1430B LEU* 3.9 15.9 + - + -
1462B PHE* 3.7 29.6 - - + -
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Residues in contact with LEU1425 (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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1385B ARG* 5.4 0.7 - - - -
1386B LEU* 4.2 25.7 - - + +
1387B GLN* 4.4 16.4 - - - +
1388B GLU* 4.6 7.0 - - - +
1389B PHE* 4.2 27.4 - - + +
1421B VAL* 2.9 23.3 + - + +
1422B GLU* 3.6 16.4 - - + +
1424B ALA* 1.3 76.0 - - - +
1426B SER* 1.3 61.4 + - - +
1428B GLN* 3.4 17.0 + - - +
1430B LEU* 3.8 25.1 - - + +
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Residues in contact with SER1426 (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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1422B GLU* 3.2 10.9 + - - -
1423B GLU* 3.4 13.5 - - - -
1424B ALA 3.2 0.2 - - - -
1425B LEU* 1.3 80.8 - - - +
1427B THR* 1.3 61.2 + - - +
1428B GLN* 3.4 7.7 - - - +
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Residues in contact with THR1427 (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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1419B VAL* 5.4 0.7 - - - +
1423B GLU* 2.6 35.0 + - + +
1424B ALA* 3.2 12.1 + - - -
1426B SER* 1.3 76.8 - - - +
1428B GLN* 1.4 77.2 + - - +
1429B ARG* 3.5 20.8 + - - +
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Residues in contact with GLN1428 (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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1385B ARG* 3.9 39.0 + - + +
1386B LEU 5.6 0.7 - - - -
1424B ALA 2.8 7.8 + - - -
1425B LEU* 3.4 14.2 + - - +
1426B SER 4.4 6.7 + - - +
1427B THR* 1.4 85.8 + - - +
1429B ARG* 1.3 57.6 + - - +
1430B LEU 3.6 3.8 - - - +
1431B PHE* 3.5 20.7 - - - -
1463B LEU* 4.5 5.7 - - - +
1618B ILE* 3.4 26.1 - - - +
1630B VAL* 3.9 24.2 + - + +
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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