Contacts of the strand formed by residues 1028 - 1033 (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 SER1028 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020A LEU* 3.8 12.8 - - - +
1023A THR* 3.0 33.1 + - - +
1025A LEU* 3.0 27.1 + - - +
1026A ASP 3.3 0.8 + - - -
1027A GLY* 1.3 78.8 - - - +
1029A TYR* 1.3 62.5 + - - +
1045A VAL* 3.4 0.7 - - - -
1046A LEU* 3.0 29.1 + - - -
1100A TYR* 3.2 19.8 + - - +
1102A VAL* 4.5 3.5 - - - +
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Residues in contact with TYR1029 (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 VAL* 3.8 22.0 - - + +
1020A LEU* 3.8 7.1 - - - +
1027A GLY 3.4 14.4 - - - +
1028A SER* 1.3 76.4 - - - +
1030A LEU* 1.3 64.5 + - - +
1043A LEU* 4.1 10.1 - - + -
1044A CYS 3.1 12.8 - - - +
1045A VAL* 4.2 2.0 - - + -
1084A ILE* 3.8 13.5 - - + +
1088A GLN* 3.2 23.4 + - - -
1098A LEU* 3.6 54.1 - - + -
1099A GLN 3.6 9.0 - - - -
1100A TYR 3.1 11.8 + - - -
1101A PRO* 3.4 35.0 - - + +
1102A VAL* 2.9 25.7 + - - +
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Residues in contact with LEU1030 (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 VAL* 3.6 17.7 - - - +
1008A HIS* 4.0 12.8 - - + -
1011A ILE* 5.1 3.6 - - + -
1016A GLY* 3.8 28.0 - - - +
1019A LEU* 4.0 23.3 - - + -
1020A LEU* 3.8 20.0 - - + -
1029A TYR* 1.3 76.4 - - - +
1031A LEU* 1.3 73.5 + - - +
1032A ARG* 4.0 18.4 - - + +
1043A LEU* 3.6 8.1 - - - +
1044A CYS* 2.8 46.1 + - + +
1102A VAL* 4.3 5.8 - - + -
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Residues in contact with LEU1031 (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 VAL* 4.8 6.1 - - + -
1006A VAL* 2.9 20.4 + - + +
1007A TYR* 3.4 27.9 - - + -
1008A HIS* 2.9 27.2 + - - +
1030A LEU* 1.3 77.1 - - - +
1032A ARG* 1.3 60.9 + - - +
1041A TYR* 3.9 26.9 - - + -
1042A CYS 3.4 22.0 - - - +
1043A LEU* 3.8 18.2 - - + +
1056A VAL* 4.3 10.8 - - + -
1064A TRP* 6.1 0.4 - - + -
1080A ILE* 4.3 23.6 - - + -
1084A ILE* 5.1 6.3 - - + -
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Residues in contact with ARG1032 (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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1007A TYR* 4.3 4.3 - - - -
1008A HIS 3.7 14.1 - - - +
1011A ILE* 4.6 9.4 - - + +
1012A SER 4.2 7.2 - - - -
1013A ARG* 3.5 49.3 + - - +
1016A GLY* 4.8 5.6 - - - -
1017A GLU* 4.8 2.8 + - - +
1030A LEU* 4.0 11.7 - - + -
1031A LEU* 1.3 74.2 - - - +
1033A ASP* 1.3 78.9 + - - +
1035A GLU* 4.4 0.6 - - - +
1041A TYR* 3.3 6.8 - - - +
1042A CYS* 2.8 55.0 + - + +
1044A CYS* 3.4 18.9 - - - -
1053A THR* 3.9 12.7 + - - +
5001A SO4 2.7 43.2 + - - -
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Residues in contact with ASP1033 (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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1007A TYR* 2.5 32.1 + - - -
1008A HIS 4.3 1.2 + - - -
1009A GLY* 4.1 0.7 - - - -
1010A LYS* 3.1 38.0 + - - +
1011A ILE 4.8 8.7 + - - +
1032A ARG* 1.3 94.5 + - - +
1034A SER* 1.3 67.7 + - - +
1035A GLU* 3.4 5.6 + - + +
1040A VAL 4.1 4.9 - - - +
1041A TYR* 3.6 7.7 - - - -
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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