Contacts of the helix formed by residues 1239 - 1247 (chain A) in PDB entry 1Y8Z
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 ALA1239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1205A THR* 3.1 33.6 - - + +
1211A PHE* 5.2 4.5 - - + -
1237A SER* 3.0 5.3 + - - +
1238A PRO* 1.3 80.8 - - - +
1240A PHE* 1.3 61.3 + - - +
1241A ILE 3.1 1.3 + - - -
1242A ALA* 3.3 21.0 + - - +
1243A ILE* 4.3 2.4 + - - +
6C T 3.2 41.7 - - + +
8D A 3.8 2.7 + - - -
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Residues in contact with PHE1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205A THR* 3.6 11.9 - - + +
1215A PHE* 6.0 0.4 - + - -
1234A LEU* 4.2 13.7 - - + -
1235A GLU 3.7 16.6 - - - +
1236A ARG* 3.6 32.8 - - + +
1237A SER 2.7 15.1 + - - +
1239A ALA* 1.3 76.5 - - - +
1241A ILE* 1.3 64.8 + - - +
1242A ALA 3.1 0.2 - - - -
1243A ILE* 3.1 40.0 + - + +
1244A LYS* 3.4 22.2 + - + +
1250A TYR* 3.6 43.5 - + - -
1252A TYR* 4.3 12.8 - + - -
1271A ILE* 5.1 1.1 - - + -
7D G 3.8 14.1 - - - +
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Residues in contact with ILE1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A PRO* 2.9 19.7 + - + +
1240A PHE* 1.3 77.9 - - - +
1242A ALA* 1.3 62.1 + - - +
1244A LYS* 3.0 14.9 + - + +
1245A GLU* 3.0 39.7 + - + +
7D G 3.5 58.6 - - + +
8D A 3.5 50.5 - - + +
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Residues in contact with ALA1242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A PHE* 6.0 0.7 - - + -
1212A TYR* 3.4 18.8 - - - +
1238A PRO 4.4 0.2 + - - -
1239A ALA 3.3 12.6 + - - +
1240A PHE 3.1 0.6 - - - -
1241A ILE* 1.3 79.8 - - - +
1243A ILE* 1.3 61.3 + - + +
1245A GLU* 3.2 14.9 + - - +
1246A LYS* 2.9 38.9 + - - +
3C T 5.5 3.6 - - - +
5C C 6.4 0.4 - - - +
6C T 5.6 0.9 - - - +
8D A 4.4 12.4 - - - +
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Residues in contact with ILE1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1205A THR* 4.5 2.7 - - + -
1211A PHE* 3.4 44.0 - - + -
1212A TYR* 4.5 4.9 - - + +
1215A PHE* 4.1 8.5 - - + -
1234A LEU* 3.9 15.7 - - + -
1239A ALA 4.9 0.7 - - - +
1240A PHE* 3.1 41.1 + - + +
1242A ALA* 1.3 77.0 - - - +
1244A LYS* 1.3 61.2 + - - +
1246A LYS* 3.6 5.6 + - - +
1247A GLY 3.5 2.8 + - - -
1248A ILE* 3.5 43.8 + - + +
1250A TYR* 4.2 20.0 - - + -
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Residues in contact with LYS1244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1236A ARG* 6.0 1.8 - - - +
1240A PHE* 3.5 33.2 - - + +
1241A ILE* 3.0 9.1 + - + +
1243A ILE* 1.3 78.5 - - - +
1245A GLU* 1.3 63.2 + - + +
1247A GLY* 3.2 13.3 + - - -
1248A ILE 5.9 0.2 - - - -
1250A TYR* 4.0 19.5 - - - +
5001A GOL 6.1 1.9 - - - -
6D T 5.6 3.8 + - - +
7D G 2.9 47.3 + - + +
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Residues in contact with GLU1245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1241A ILE* 3.0 30.7 + - + +
1242A ALA* 3.2 18.1 + - - +
1244A LYS* 1.3 78.2 - - + +
1246A LYS* 1.3 71.9 + - + +
1247A GLY* 3.4 0.9 + - - -
8D A 5.2 4.7 + - - +
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Residues in contact with LYS1246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212A TYR* 3.9 21.1 - - + +
1242A ALA* 2.9 30.8 + - - +
1243A ILE 4.0 4.9 - - - +
1244A LYS 3.3 0.2 - - - -
1245A GLU* 1.3 86.8 + - - +
1247A GLY* 1.3 61.9 + - - +
1248A ILE* 4.1 14.4 - - + +
1C G 3.4 28.6 + - - +
3C T 3.6 28.4 + - + +
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Residues in contact with GLY1247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243A ILE 3.5 0.6 + - - -
1244A LYS 3.2 13.2 + - - -
1245A GLU 3.1 4.4 - - - -
1246A LYS* 1.3 80.6 - - - +
1248A ILE* 1.3 64.8 + - - +
1249A PRO* 3.5 5.0 - - - +
5001A GOL 3.1 27.9 + - - -
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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