Contacts of the strand formed by residues 1067 - 1072 (chain A) in PDB entry 3DLS
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 VAL1067 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056A LEU* 3.9 53.1 + - + +
1057A SER* 4.6 14.4 - - - +
1065A ILE 4.0 0.2 + - - -
1066A LYS* 1.3 89.9 + - - +
1068A LEU* 1.3 62.8 + - - +
1069A ASP 3.8 19.5 - - - +
1070A ILE* 4.8 6.5 - - + +
1079A LEU* 4.0 13.2 - - + -
1080A VAL 3.6 10.8 - - - +
1081A MET* 4.3 1.6 - - + +
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Residues in contact with LEU1068 (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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999A TYR* 4.1 11.7 - - - +
1023A LYS* 3.9 21.5 - - - +
1025A VAL* 3.5 32.5 - - + -
1066A LYS* 3.9 28.0 - - + +
1067A VAL* 1.3 75.6 - - - +
1069A ASP* 1.3 69.3 + - - +
1080A VAL* 2.6 15.9 + - + +
1081A MET 3.7 1.6 - - - -
1082A GLU* 3.5 32.8 - - + +
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Residues in contact with ASP1069 (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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998A LYS* 3.3 18.9 + - - -
999A TYR* 2.6 26.8 + - - +
1067A VAL* 3.7 7.9 - - - +
1068A LEU* 1.3 85.2 - - - +
1070A ILE* 1.3 64.0 + - - +
1071A PHE* 3.5 36.0 - - + -
1078A GLN 4.3 0.9 - - - -
1079A LEU* 4.0 0.2 - - - -
1080A VAL* 2.9 34.5 + - + +
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Residues in contact with ILE1070 (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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1046A LEU* 4.0 29.6 - - + +
1049A VAL* 3.8 19.3 - - + -
1053A ILE* 3.2 39.9 - - + -
1057A SER* 4.9 3.8 - - - +
1067A VAL* 5.0 8.7 - - + -
1069A ASP* 1.3 77.4 + - - +
1071A PHE* 1.3 78.0 + - - +
1072A GLU* 6.2 0.2 - - + -
1077A PHE* 4.3 9.2 - - + -
1078A GLN 3.5 8.1 - - - +
1079A LEU* 5.1 4.7 - - + -
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Residues in contact with PHE1071 (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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994A GLU* 3.4 48.7 - - + +
995A TYR* 3.6 36.8 - + + +
998A LYS* 3.7 17.3 - - + -
999A TYR* 3.6 24.7 - + - -
1069A ASP* 3.5 35.7 - - + -
1070A ILE* 1.3 80.0 - - - +
1072A GLU* 1.3 62.0 + - - +
1077A PHE* 3.3 11.2 - - - -
1078A GLN* 2.9 45.6 + - - +
1080A VAL* 4.7 0.7 - - + -
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Residues in contact with GLU1072 (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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994A GLU* 5.7 4.9 + - - +
1032A LYS* 3.1 37.9 + - - +
1040A TRP* 5.9 0.2 - - - -
1048A LYS* 4.4 9.1 - - - +
1071A PHE* 1.3 78.3 - - - +
1073A ASN* 1.3 65.4 + - - +
1074A GLN* 4.0 3.0 - - - +
1076A PHE 3.3 5.4 - - - -
1077A PHE* 3.6 24.4 - - + -
1078A GLN* 4.0 3.1 - - - +
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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