Contacts of the strand formed by residues 1033 - 1039 (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 GLU1033 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A SER* 6.1 1.6 - - - +
1001A MET 3.0 11.6 + - - +
1002A ARG* 3.1 37.8 + - + +
1003A ILE* 2.7 33.4 + - - +
1031A GLY 5.5 1.1 - - - +
1032A HIS* 1.3 75.1 - - - +
1034A VAL* 1.3 57.8 + - - +
1035A THR* 6.0 0.2 - - - -
5002A GOL 4.7 12.0 + - - +
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Residues in contact with VAL1034 (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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1003A ILE* 3.2 14.8 - - + +
1005A ILE* 3.9 18.8 - - + -
1024A ARG* 3.8 35.4 + - + +
1027A PHE* 3.5 32.1 - - + -
1028A ILE* 3.9 21.6 - - + +
1032A HIS 4.0 1.1 + - - +
1033A GLU* 1.3 81.2 - - - +
1035A THR* 1.3 79.5 + - - +
1036A LEU* 4.4 0.6 + - - +
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Residues in contact with THR1035 (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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1002A ARG* 3.7 37.6 + - + +
1003A ILE 2.9 7.5 + - - +
1004A CYS* 3.4 26.0 - - - +
1005A ILE 2.9 23.4 + - - +
1034A VAL* 1.3 80.7 - - - +
1036A LEU* 1.3 59.3 + - - +
1037A VAL* 3.9 8.8 + - - +
1057A ILE* 4.7 14.8 - - + -
1071A LEU* 5.1 7.5 + - + +
1074A ASP 5.4 0.3 + - - -
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Residues in contact with LEU1036 (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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1005A ILE* 3.5 36.1 - - + +
1007A MET* 3.8 25.8 - - + -
1011A LEU* 5.3 0.7 - - + -
1020A SER* 4.0 7.4 - - - +
1021A LEU* 3.5 32.8 - - + -
1024A ARG* 4.4 17.2 - - + +
1034A VAL* 4.2 1.3 - - + +
1035A THR* 1.3 71.9 - - - +
1037A VAL* 1.3 56.6 + - - +
1038A TYR* 5.8 0.4 - - + -
1052A HIS* 5.0 0.7 - - + -
1055A PHE* 3.6 25.2 + - + +
1056A SER* 3.4 15.1 - - - -
1057A ILE* 2.8 35.6 + - - +
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Residues in contact with VAL1037 (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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1004A CYS* 4.0 22.0 - - - -
1005A ILE 2.8 13.0 + - - +
1006A PHE* 3.3 21.9 - - + -
1007A MET* 2.9 24.1 + - - +
1035A THR* 4.5 7.0 - - - +
1036A LEU* 1.3 82.3 - - - +
1038A TYR* 1.3 65.2 + - - +
1057A ILE* 3.3 17.9 - - + +
1059A VAL* 4.0 14.8 - - + -
1068A ALA* 6.1 0.7 - - - -
1071A LEU* 4.0 39.0 - - + -
1072A VAL* 5.8 2.5 - - + -
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Residues in contact with TYR1038 (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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1006A PHE* 4.5 0.7 - - - -
1007A MET* 3.2 24.7 - - + +
1011A LEU* 3.6 49.4 - - + +
1036A LEU* 5.1 0.9 - - + -
1037A VAL* 1.3 77.2 - - - +
1039A ALA* 1.3 68.9 + - - +
1040A LYS* 4.2 17.3 + - + -
1047A THR* 6.2 2.0 - - + -
1052A HIS* 4.2 9.1 + - - -
1053A LYS* 5.5 1.9 + - - -
1056A SER* 3.4 30.6 + - - -
1057A ILE 3.0 12.2 + - - -
1058A PRO* 3.3 35.9 - - + +
1059A VAL* 2.9 27.7 + - - +
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Residues in contact with ALA1039 (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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1006A PHE* 4.2 2.2 - - + -
1007A MET 3.0 8.1 + - - -
1008A ALA* 3.5 27.1 - - - +
1009A ARG 4.3 1.1 - - - -
1010A GLY* 2.9 26.3 - - - -
1038A TYR* 1.3 72.6 - - - +
1040A LYS* 1.3 59.6 + - - +
1041A ASP* 3.3 20.4 + - + +
1042A LYS 4.2 1.4 + - - +
1059A VAL* 3.1 9.6 - - - -
1061A LEU* 3.6 21.5 - - + -
1092A THR* 5.7 0.4 - - + -
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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