Contacts of the strand formed by residues 1044 - 1051 (chain A) in PDB entry 3E0D
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 LYS1044 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1039A LEU* 5.3 1.7 - - - +
1042A LYS 5.7 0.7 - - - -
1043A PRO* 1.3 78.8 - - - +
1045A VAL* 1.3 70.5 + - - +
1102A LEU* 5.2 8.5 - - + -
1103A ALA 3.3 8.3 - - - +
1104A GLU* 3.6 27.1 - - + -
1116A GLN* 4.1 24.7 - - - +
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Residues in contact with VAL1045 (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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1026A SER* 4.9 7.9 - - - +
1027A CYS* 6.4 0.4 - - + -
1032A LEU* 4.1 11.4 - - + -
1035A PHE* 4.0 28.7 - - + -
1036A VAL* 4.5 11.4 - - + -
1039A LEU* 5.4 2.9 - - + -
1043A PRO* 5.8 0.4 - - + -
1044A LYS* 1.3 80.0 - - - +
1046A LEU* 1.3 66.5 + - - +
1047A LEU* 3.8 33.0 - - + -
1101A VAL 3.5 0.9 - - - +
1102A LEU* 3.4 8.9 - - - +
1103A ALA* 2.8 34.3 + - + +
1105A VAL* 4.4 13.0 - - + -
1202A ARG* 5.0 3.6 - - - +
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Residues in contact with LEU1046 (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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1024A VAL* 4.2 16.8 - - + +
1025A ALA* 4.6 2.1 - - - -
1026A SER* 2.1 48.5 + - - +
1045A VAL* 1.3 75.9 - - - +
1047A LEU* 1.3 66.1 + - - +
1100A LEU* 4.1 30.5 - - + -
1101A VAL 3.0 9.0 - - - +
1102A LEU* 3.8 21.3 - - + -
1119A TRP* 5.9 0.2 - - + -
1202A ARG* 2.8 55.9 - - + +
1205A PHE* 5.3 7.0 - - + -
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Residues in contact with LEU1047 (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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1025A ALA* 5.5 1.3 - - - -
1027A CYS* 4.8 16.6 - - + +
1029A ILE* 4.3 23.8 - - + +
1032A LEU* 3.9 42.2 - - + -
1045A VAL* 3.8 15.7 + - + +
1046A LEU* 1.3 78.6 - - - +
1048A SER* 1.3 59.4 + - - +
1070A LEU* 4.1 15.7 - - + -
1072A ASP* 6.0 0.2 - - - +
1077A LEU* 4.0 14.8 - - + -
1099A LEU 4.0 0.3 - - - +
1100A LEU* 4.1 1.8 - - - -
1101A VAL* 2.7 47.6 + - + +
1103A ALA* 5.7 2.7 - - + -
1113A VAL* 4.8 13.9 - - + -
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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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1021A LEU* 4.8 17.6 + - - +
1022A ARG* 5.6 2.6 + - - -
1025A ALA* 3.6 21.2 - - - +
1047A LEU* 1.3 76.4 - - - +
1049A GLY* 1.3 58.0 + - - +
1070A LEU* 4.1 2.5 - - - -
1072A ASP* 2.8 21.2 - - - +
1099A LEU 3.3 11.9 - - - -
1100A LEU* 3.7 20.6 - - - -
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Residues in contact with GLY1049 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048A SER* 1.3 73.7 - - - +
1050A MET* 1.3 63.6 - - - +
1070A LEU* 3.7 15.3 - - - +
1071A SER 3.4 13.0 - - - -
1072A ASP* 3.8 4.5 - - - -
1098A PRO* 3.4 8.5 - - - +
1099A LEU 3.2 27.6 + - - -
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Residues in contact with MET1050 (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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1009A TYR* 5.3 15.5 - - + +
1014A PRO* 6.4 1.6 - - + -
1049A GLY* 1.3 75.8 - - - +
1051A VAL* 1.3 67.3 + - - +
1052A GLU* 4.5 5.4 - - + +
1069A THR 3.1 1.9 - - - +
1070A LEU* 3.1 10.2 - - - -
1071A SER* 3.0 45.5 + - - +
1095A GLU* 5.9 0.2 - - - +
1096A ASP* 4.2 24.5 - - - +
1097A ILE 3.7 8.3 - - - -
1098A PRO* 3.6 38.8 - - + -
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Residues in contact with VAL1051 (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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1050A MET* 1.3 76.7 - - - +
1052A GLU* 1.3 70.8 + - - +
1053A GLU 4.1 11.2 - - - +
1068A PHE* 3.8 31.0 - - + -
1069A THR 3.4 2.0 - - - -
1070A LEU* 4.3 1.3 - - + -
1094A LYS* 3.6 24.7 - - - +
1095A GLU* 3.4 1.4 - - - -
1096A ASP* 3.2 24.3 + - - -
1097A ILE* 3.4 19.9 + - + +
1099A LEU* 3.6 34.5 - - + -
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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