Contacts of the strand formed by residues 1050 - 1058 (chain A) in PDB entry 1D1Z
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 TYR1050 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1021A LEU* 5.0 0.2 - - - -
1046A LEU* 3.4 7.2 - - - +
1047A TYR 2.9 29.3 + - - +
1048A HIS 3.5 11.7 - - - -
1049A GLY* 1.3 88.5 - - - +
1051A ILE* 1.3 64.4 + - - +
1052A TYR* 3.5 25.6 - - + +
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Residues in contact with ILE1051 (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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1017A GLU* 4.1 39.6 - - + +
1020A LEU* 3.6 28.9 - - + -
1021A LEU* 4.1 16.6 - - + -
1044A CYS* 4.0 21.8 - - + -
1045A VAL 3.4 2.9 - - - +
1046A LEU* 3.5 29.4 - - + -
1050A TYR* 1.3 77.6 - - - +
1052A TYR* 1.3 64.8 + - - +
1053A THR* 3.9 18.8 + - - +
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Residues in contact with TYR1052 (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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1043A LEU 3.5 2.3 - - - +
1044A CYS* 3.4 2.8 - - - -
1045A VAL* 2.8 37.7 + - + +
1047A TYR* 3.5 35.5 + + + -
1048A HIS* 5.7 0.5 - - - +
1050A TYR* 3.5 36.8 - - + +
1051A ILE* 1.3 73.5 - - - +
1053A THR* 1.3 60.8 + - - +
1054A TYR* 3.6 27.2 - + + +
1095A VAL* 3.6 31.8 - - + +
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Residues in contact with THR1053 (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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1017A GLU* 4.3 8.7 + - - -
1032A ARG* 3.9 12.5 + - - +
1042A CYS* 3.6 34.3 - - + -
1043A LEU 3.4 2.5 - - - -
1044A CYS* 4.1 7.8 - - - -
1051A ILE* 3.9 16.5 + - - +
1052A TYR* 1.3 74.4 + - - +
1054A TYR* 1.3 72.1 + - - +
1055A ARG* 4.3 4.1 + - + +
5001A SO4 4.8 2.7 - - - +
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Residues in contact with TYR1054 (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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1042A CYS* 3.6 2.3 - - - -
1043A LEU* 2.8 57.6 + - + +
1045A VAL* 4.2 13.9 - - + -
1052A TYR* 3.6 30.5 - + + +
1053A THR* 1.3 78.3 - - - +
1055A ARG* 1.3 66.8 + - - +
1056A VAL 3.5 0.2 + - - -
1066A ALA* 5.0 5.6 - - + -
1067A GLU 3.6 20.9 - - - +
1068A THR* 4.4 6.3 - - - -
1069A ALA 5.3 0.2 - - - -
1093A GLY 4.3 5.4 - - - -
1094A ILE* 3.5 39.9 - - + -
1095A VAL* 2.9 33.1 + - - +
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Residues in contact with ARG1055 (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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1034A SER* 4.1 4.2 + - - -
1036A SER* 3.7 15.4 + - - -
1037A VAL* 3.7 26.1 - - - +
1040A VAL* 3.9 24.3 - - + +
1041A TYR 3.4 1.8 - - - -
1042A CYS* 3.9 17.9 - - - -
1053A THR* 4.3 3.9 + - + +
1054A TYR* 1.3 74.1 - - - +
1056A VAL* 1.3 59.8 - - - +
1057A SER* 4.2 1.1 - - - -
1065A SER 4.1 0.3 - - - +
1066A ALA* 3.3 2.9 - - - -
1067A GLU* 2.9 46.5 + - + +
5001A SO4 4.2 13.9 + - - -
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Residues in contact with VAL1056 (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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1031A LEU* 4.3 6.1 - - + -
1040A VAL* 3.5 0.9 - - - +
1041A TYR* 2.8 49.5 + - + +
1043A LEU* 3.8 28.7 - - + -
1054A TYR 3.9 1.1 - - - +
1055A ARG* 1.3 78.5 - - - +
1057A SER* 1.3 66.4 + - - +
1064A TRP* 3.9 11.7 - - + -
1065A SER 3.5 8.7 - - - +
1066A ALA* 4.0 16.2 - - + -
1080A ILE* 3.6 30.1 - - + -
1083A LEU* 4.1 13.5 - - + -
1084A ILE* 6.2 0.2 - - + -
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Residues in contact with SER1057 (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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1039A GLY 5.2 0.7 - - - -
1040A VAL* 4.0 26.2 - - - +
1041A TYR* 5.1 0.9 - - - -
1055A ARG* 4.2 0.9 - - - -
1056A VAL* 1.3 78.9 - - - +
1058A GLN* 1.3 66.7 + - - +
1059A THR* 4.2 2.1 + - - +
1063A SER 3.9 0.2 - - - +
1064A TRP* 3.4 10.2 - - - -
1065A SER* 3.0 37.9 + - - -
1067A GLU* 6.1 0.7 - - - +
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Residues in contact with GLN1058 (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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1039A GLY 5.2 3.6 + - - -
1041A TYR* 5.9 0.4 - - + -
1057A SER* 1.3 80.4 - - - +
1059A THR* 1.3 71.5 + - - +
1062A GLY* 2.9 28.1 + - - +
1063A SER 3.0 14.8 - - - +
1064A TRP* 3.5 40.9 - - + +
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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