Contacts of the helix formed by residues 1278 - 1287 (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 LEU1278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1275B SER 3.8 16.6 - - - +
1276B ASP* 2.8 21.6 + - - +
1277B PHE* 1.3 68.3 - - - +
1279B THR* 1.3 59.9 + - - +
1281B GLY* 3.0 19.0 + - - +
1282B ILE* 3.1 12.1 + - - +
1336B ALA 5.7 4.3 - - - +
1339B GLU* 5.8 1.3 - - - +
1340B ILE* 5.1 8.3 - - + -
1779B ILE* 3.5 40.2 - - + +
1782B ARG* 4.0 24.9 - - + +
1783B HIS 4.9 0.7 - - - -
1784B ALA* 4.3 20.0 - - + +
1864B ILE* 4.1 20.2 - - + -
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Residues in contact with THR1279 (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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1277B PHE* 4.2 4.9 - - - +
1278B LEU* 1.3 74.9 - - + +
1280B TYR* 1.3 74.1 + - - +
1281B GLY 3.1 0.6 + - - -
1282B ILE* 3.2 13.5 + - - +
1283B LYS* 3.2 34.8 + - - +
1560B ASP* 5.6 3.1 - - - +
1563B ASN* 4.3 21.3 - - - +
1564B ILE* 4.1 25.6 - - + -
1567B LEU* 4.3 19.6 - - + +
1864B ILE* 5.4 0.8 - - + +
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Residues in contact with TYR1280 (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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1024B ASP* 5.8 1.7 - - - +
1025B PHE* 3.7 50.6 + + + +
1026B ASN* 5.4 1.2 + - + -
1268B ASN* 5.9 5.4 - - - -
1277B PHE* 2.9 44.7 + + + +
1279B THR* 1.3 89.2 + - - +
1281B GLY* 1.3 55.8 + - - +
1283B LYS* 3.8 33.1 + - + +
1284B SER* 3.0 25.2 + - - -
1336B ALA* 3.2 7.3 - - + +
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Residues in contact with GLY1281 (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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1277B PHE 3.6 0.6 + - - -
1278B LEU 3.0 10.3 + - - -
1280B TYR* 1.3 78.8 - - - +
1282B ILE* 1.3 53.6 + - - +
1283B LYS 3.4 0.2 - - - -
1284B SER* 3.5 3.8 - - - -
1285B LEU* 2.8 32.9 + - - +
1336B ALA* 3.6 26.9 - - - +
1337B LEU* 3.7 2.9 - - - +
1779B ILE* 3.3 15.7 - - - +
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Residues in contact with ILE1282 (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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1278B LEU 3.1 13.1 + - - +
1279B THR* 3.2 10.7 + - - +
1281B GLY* 1.3 76.7 - - - +
1283B LYS* 1.3 55.7 + - - +
1285B LEU* 3.3 8.0 + - - +
1286B SER* 2.7 26.5 + - - -
1564B ILE* 4.9 6.5 - - + -
1567B LEU* 3.4 32.1 - - + -
1571B SER* 4.5 6.1 - - - -
1572B LEU* 3.7 26.2 - - + -
1578B ILE* 4.5 6.0 - - + +
1776B VAL* 4.8 5.8 - - + -
1779B ILE* 4.0 16.4 - - + -
1780B LEU* 4.1 24.0 - - + -
1864B ILE* 4.3 14.6 - - + -
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Residues in contact with LYS1283 (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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1279B THR* 3.2 16.8 + - - +
1280B TYR* 3.8 51.1 + - + +
1282B ILE* 1.3 74.1 - - - +
1284B SER* 1.3 59.5 + - - +
1285B LEU 3.3 0.7 - - - -
1286B SER* 3.7 10.8 - - - -
1287B HIS* 3.1 29.4 + - + +
1288B ASP* 4.5 0.3 - - - +
1567B LEU* 4.1 21.9 - - + +
1571B SER* 4.7 6.1 - - - +
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Residues in contact with SER1284 (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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1280B TYR 3.0 22.1 + - - -
1281B GLY* 3.3 7.6 + - - -
1282B ILE 3.2 0.4 - - - -
1283B LYS* 1.3 76.7 - - - +
1285B LEU* 1.3 60.1 + - - +
1286B SER 3.4 0.2 - - - -
1288B ASP* 3.0 42.4 + - - +
1289B VAL* 3.3 7.1 + - - +
1334B LEU* 3.6 12.0 - - - +
1335B PRO* 5.8 0.7 - - - +
1336B ALA* 4.4 4.3 - - - +
1337B LEU* 3.1 20.9 - - - +
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Residues in contact with LEU1285 (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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1281B GLY 2.8 14.9 + - - +
1282B ILE* 3.5 6.5 - - - +
1284B SER* 1.3 80.3 - - - +
1286B SER* 1.3 60.3 + - - +
1289B VAL* 3.7 18.9 + - + +
1290B ILE* 3.3 55.3 + - + +
1293B PHE* 4.7 1.3 - - + -
1337B LEU* 4.5 1.3 - - + -
1341B PHE* 4.3 8.1 - - + -
1578B ILE* 4.7 2.5 - - + -
1772B ILE 4.7 0.2 - - - +
1775B SER* 3.5 26.5 - - - +
1776B VAL* 3.3 45.8 - - + +
1779B ILE* 3.9 12.3 - - + -
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Residues in contact with SER1286 (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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1282B ILE 2.7 17.3 + - - -
1283B LYS* 3.9 9.0 - - - -
1284B SER 3.4 0.2 - - - -
1285B LEU* 1.3 79.8 - - - +
1287B HIS* 1.3 59.3 + - - +
1290B ILE* 4.6 9.5 - - - +
1291B PRO* 3.9 12.0 - - - +
1571B SER* 4.4 23.8 + - - -
1578B ILE* 4.6 9.9 - - - +
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Residues in contact with HIS1287 (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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1283B LYS* 3.1 19.1 + - + +
1286B SER* 1.3 79.1 - - - +
1288B ASP* 1.3 72.4 + - - +
1291B PRO* 4.1 10.3 - - - +
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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