Contacts of the helix formed by residues 1288 - 1298 (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 ASP1288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283B LYS 4.5 0.5 - - - +
1284B SER* 3.0 33.5 + - - +
1286B SER 3.5 2.4 + - - -
1287B HIS* 1.3 92.0 + - - +
1289B VAL* 1.3 65.6 + - - +
1290B ILE 3.5 1.8 - - - -
1291B PRO* 3.3 15.2 - - - +
1292B LEU* 3.4 20.8 - - + +
1334B LEU* 3.8 28.6 - - + +
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Residues in contact with VAL1289 (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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1284B SER 3.3 6.2 + - - +
1285B LEU* 3.7 14.3 + - + -
1288B ASP* 1.3 75.1 - - - +
1290B ILE* 1.3 54.9 + - - +
1291B PRO 3.5 0.2 - - - -
1292B LEU* 3.1 6.5 + - + +
1293B PHE* 2.7 67.8 + - + -
1331B ILE* 3.9 28.5 - - + -
1334B LEU* 4.1 10.1 - - + -
1337B LEU* 3.4 33.2 - - + -
1341B PHE* 4.2 9.4 - - + -
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Residues in contact with ILE1290 (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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1285B LEU* 3.3 45.9 + - + +
1286B SER* 4.6 4.7 - - - +
1289B VAL* 1.3 78.0 - - - +
1291B PRO* 1.4 62.8 - - + +
1293B PHE* 3.3 9.5 + - + -
1294B LYS* 3.1 22.8 + - - +
1578B ILE* 4.1 17.7 - - + -
1581B LYS* 6.2 1.6 - - + -
1768B PHE* 3.4 24.3 - - + -
1772B ILE* 4.0 42.6 - - + +
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Residues in contact with PRO1291 (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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1286B SER 3.9 14.4 - - - +
1287B HIS* 4.1 12.1 - - - +
1288B ASP* 3.3 22.2 - - - +
1290B ILE* 1.4 93.7 - - + +
1292B LEU* 1.3 56.7 + - - -
1294B LYS* 3.3 17.6 - - + +
1295B SER* 2.8 31.9 + - - -
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Residues in contact with LEU1292 (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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1288B ASP* 3.4 22.5 + - + +
1289B VAL* 3.1 14.2 + - + +
1291B PRO* 1.3 71.5 - - - +
1293B PHE* 1.3 67.9 + - - +
1295B SER* 3.4 6.6 + - - +
1296B ALA* 3.0 23.4 + - - +
1327B ILE* 3.8 41.1 - - + +
1330B GLN* 4.1 28.5 - - + +
1331B ILE* 3.4 42.6 - - + +
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Residues in contact with PHE1293 (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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1285B LEU* 4.7 4.5 - - + -
1289B VAL* 2.7 48.0 + - + +
1290B ILE* 3.3 13.6 + - + +
1292B LEU* 1.3 73.3 - - - +
1294B LYS* 1.3 56.1 + - - +
1296B ALA* 3.2 5.8 + - - +
1297B ILE* 3.0 35.7 + - + +
1323B LEU* 4.2 13.0 - - + -
1331B ILE* 4.3 2.9 - - + -
1341B PHE* 4.0 17.3 - + - -
1349B LEU* 3.5 25.8 - - + -
1351B PHE* 4.6 1.1 - + - -
1768B PHE* 3.7 20.6 - + + -
1771B LEU* 3.8 44.0 - - + -
1772B ILE 4.7 0.7 - - - -
1775B SER* 3.8 17.3 - - - -
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Residues in contact with LYS1294 (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* 3.1 15.3 + - - +
1291B PRO* 3.3 19.7 - - + +
1293B PHE* 1.3 72.5 - - - +
1295B SER* 1.4 66.0 + - - +
1296B ALA 3.0 1.9 + - - -
1297B ILE 3.1 1.3 + - - +
1298B PHE* 2.9 41.5 + - + -
1299B GLN* 3.7 2.6 + - - -
1768B PHE* 3.5 26.2 - - + -
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Residues in contact with SER1295 (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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1291B PRO 2.8 21.4 + - - -
1292B LEU* 3.8 8.6 - - - +
1294B LYS* 1.4 71.1 - - - +
1296B ALA* 1.3 56.4 + - - +
1299B GLN* 3.2 37.9 + - - -
1300B LEU* 2.8 36.4 + - - +
1327B ILE* 4.6 12.3 - - - -
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Residues in contact with ALA1296 (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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1292B LEU 3.0 14.5 + - - +
1293B PHE 3.4 9.6 - - - +
1294B LYS 3.0 0.4 + - - -
1295B SER* 1.3 77.3 - - - +
1297B ILE* 1.3 61.9 + - + +
1300B LEU* 4.6 2.2 - - - -
1301B ARG 4.3 0.4 - - - -
1302B VAL* 3.0 41.3 + - + +
1303B THR 3.3 5.9 + - - -
1323B LEU* 3.5 31.9 - - + -
1327B ILE* 4.9 7.4 - - + -
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Residues in contact with ILE1297 (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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1293B PHE* 3.0 17.3 + - + +
1296B ALA* 1.3 85.2 - - + +
1298B PHE* 1.3 78.1 + - + +
1299B GLN 3.8 0.4 - - - -
1301B ARG* 3.5 22.8 + - - +
1303B THR* 3.6 20.3 - - - +
1304B SER 3.8 6.3 - - - +
1305B SER* 3.5 36.8 + - - -
1323B LEU* 5.8 1.6 - - + -
1767B LYS* 4.3 11.9 - - + -
1768B PHE* 3.9 35.4 - - + +
1771B LEU* 4.5 12.8 - - + -
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Residues in contact with PHE1298 (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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1294B LYS* 2.9 31.0 + - + +
1297B ILE* 1.3 95.2 - - + +
1299B GLN* 1.3 62.2 + - - +
1301B ARG* 3.7 27.8 + - - +
1305B SER* 4.4 18.8 - - - -
1766B PRO* 6.5 1.3 - - + -
1768B PHE* 4.0 30.7 - + + -
1769B GLU* 5.8 1.8 - - - -
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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