Contacts of the helix formed by residues 1044 - 1049 (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 PHE1044 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A ARG* 3.5 42.2 - - + -
1010A GLY* 3.9 8.7 - - - -
1011A LEU 3.7 17.9 - - - +
1012A GLU* 3.6 38.4 - - + +
1014A CME 5.3 6.1 - - + -
1042A LYS* 3.4 47.8 - - + -
1043A SER* 1.3 79.9 - - - +
1045A THR* 1.3 63.6 + - - +
1046A ARG 3.4 0.4 - - - +
1047A THR* 2.9 27.0 + - + +
7C 5HU 6.3 5.2 - - + -
2D T 5.9 1.0 - - - +
3D A 4.8 1.9 + - - -
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Residues in contact with THR1045 (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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1044A PHE* 1.3 74.0 - - - +
1046A ARG* 1.3 64.0 + - + +
1047A THR 3.3 4.7 + - - -
1048A SER* 4.6 1.4 + - - -
1235A GLU* 6.4 2.5 - - + -
1273A ASP* 5.6 5.4 - - - +
1274A CME 3.7 26.7 - - + -
7C 5HU 4.6 13.0 + - - -
3D A 3.6 20.4 + - + +
4D T 3.8 30.2 - - + +
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Residues in contact with ARG1046 (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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1012A GLU 3.6 15.2 + - - +
1013A GLY* 3.3 7.2 - - - -
1014A CME 3.4 35.3 - - - -
1044A PHE* 3.4 1.0 - - - +
1045A THR* 1.3 80.3 - - - +
1047A THR* 1.3 62.6 + - - +
1048A SER 3.1 3.1 - - - -
1049A SER* 2.8 31.1 + - - +
1204A ARG* 3.9 7.4 - - - +
1233A GLY 3.3 13.7 + - - -
1235A GLU* 2.7 40.0 + - - +
1273A ASP 3.7 1.0 + - - -
1274A CME 3.3 36.3 - - + +
3006A UDP 2.7 46.5 + - - +
7C 5HU 3.0 16.9 + - - -
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Residues in contact with THR1047 (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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1011A LEU* 3.3 35.1 - - + +
1012A GLU 4.4 0.2 + - - -
1038A TYR* 6.2 1.6 - - + -
1043A SER* 5.1 1.3 - - - -
1044A PHE* 2.9 34.3 + - + +
1045A THR 3.3 2.0 + - - -
1046A ARG* 1.3 76.4 - - - +
1048A SER* 1.3 66.0 + - - +
1049A SER 3.7 0.2 + - - -
1050A HIS 4.0 1.7 + - - +
1052A HIS* 2.8 32.1 + - - -
1053A LYS* 4.4 10.7 + - - -
2D T 4.9 17.5 + - - +
3D A 4.1 10.4 + - - -
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Residues in contact with SER1048 (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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1045A THR 4.6 1.4 + - - -
1046A ARG 3.1 1.0 - - - -
1047A THR* 1.3 80.8 + - - +
1049A SER* 1.3 65.0 + - - +
1050A HIS 3.2 10.8 + - - +
1053A LYS* 3.8 22.4 + - - +
1274A CME 5.3 5.8 - - - -
1276A ILE* 3.4 24.4 - - - +
2D T 5.1 0.3 + - - -
3D A 3.6 21.8 + - - -
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Residues in contact with SER1049 (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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1013A GLY 2.9 20.1 + - - -
1046A ARG* 2.8 27.3 + - - -
1048A SER* 1.3 79.8 - - - +
1050A HIS* 1.3 65.4 + - - +
1051A ASP 4.4 0.2 + - - -
1274A CME 4.3 5.1 - - - +
1275A TYR 3.3 23.6 - - - -
1276A ILE* 3.7 10.6 - - - +
1277A ASN* 2.9 27.0 + - - +
1278A SER 4.8 0.2 + - - -
3006A UDP 3.5 16.8 - - - -
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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