Contacts of the strand formed by residues 1076 - 1082 (chain B) 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 PHE1076 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986B GLU* 3.8 36.1 - - + -
989B ALA* 3.6 16.4 - - + -
990B ALA* 3.6 31.2 - - + +
1012B PHE* 4.0 22.4 - + - -
1029B PHE* 4.0 10.1 - - + -
1030B ILE 3.2 20.6 - - - -
1031B LYS* 3.6 22.7 - - + -
1032B LYS* 4.0 7.0 - - - +
1072B GLU* 3.3 6.2 - - - +
1073B ASN* 2.9 33.9 + - - +
1074B GLN 3.7 0.6 - - - -
1075B GLY* 1.3 98.3 - - - +
1077B PHE* 1.3 64.3 + - - +
1078B GLN* 3.9 10.5 - - - +
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Residues in contact with PHE1077 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028B LYS 3.8 0.4 - - - +
1029B PHE* 3.7 3.5 - - - -
1030B ILE* 2.9 55.1 + - + -
1032B LYS* 3.9 27.6 - - + -
1048B LYS* 3.4 36.3 - - - -
1049B VAL* 3.7 24.7 - - + -
1050B THR* 4.5 7.9 - - - -
1053B ILE* 3.6 28.0 - - + -
1070B ILE* 4.9 4.5 - - + -
1071B PHE 3.4 7.9 - - - +
1072B GLU* 3.4 28.0 - - + -
1076B PHE* 1.3 76.2 - - - +
1078B GLN* 1.3 63.0 + - - +
1079B LEU 4.0 0.2 - - - -
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Residues in contact with GLN1078 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990B ALA 2.7 29.6 - - - +
992B GLU 4.3 2.2 + - - +
995B TYR* 3.8 36.0 - - + +
1027B VAL* 4.0 5.4 - - + -
1028B LYS 3.7 4.3 - - - -
1029B PHE* 3.8 15.5 - - + -
1069B ASP 3.7 0.3 - - - +
1070B ILE* 3.4 6.8 - - - -
1071B PHE* 3.0 61.1 + - + +
1072B GLU* 3.4 7.5 + - - +
1073B ASN* 3.1 22.3 + - - -
1076B PHE* 3.9 4.7 - - - +
1077B PHE* 1.3 74.8 - - - +
1079B LEU* 1.3 61.2 + - - +
1080B VAL* 3.5 3.4 + - + +
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Residues in contact with LEU1079 (chain B).
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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1026B VAL 3.5 2.1 - - - +
1027B VAL* 3.3 1.7 - - - -
1028B LYS* 2.8 45.9 + - + +
1030B ILE* 3.9 22.4 - - + -
1052B GLU* 4.2 20.2 - - + +
1053B ILE* 4.3 21.5 - - + +
1056B LEU* 3.9 23.3 - - + -
1057B SER* 5.8 1.1 - - - +
1067B VAL* 4.1 30.7 - - + -
1069B ASP 4.0 0.9 - - - -
1070B ILE* 4.6 9.9 - - + +
1077B PHE 4.0 1.2 - - - -
1078B GLN* 1.3 69.6 - - - +
1080B VAL* 1.3 62.5 + - - +
1081B MET* 3.6 19.5 - - + +
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Residues in contact with VAL1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995B TYR* 3.8 33.7 - - + -
999B TYR* 3.6 33.0 - - + +
1025B VAL* 3.7 25.6 - - + -
1026B VAL 3.3 4.3 - - - +
1027B VAL* 4.0 5.8 - - + -
1067B VAL* 3.7 6.8 - - - +
1068B LEU* 2.8 25.4 + - + -
1069B ASP* 2.8 32.0 + - + +
1071B PHE* 4.6 2.0 - - + -
1078B GLN 4.2 5.6 - - - +
1079B LEU* 1.3 75.2 - - - +
1081B MET* 1.3 62.7 + - - +
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Residues in contact with MET1081 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ADP 3.9 24.5 - - - +
1013B VAL* 5.6 0.2 - - + -
1025B VAL* 3.5 7.6 - - - +
1026B VAL* 2.6 45.7 + - + +
1028B LYS* 3.8 26.7 - - + +
1056B LEU* 4.5 9.2 - - + -
1065B ILE* 4.0 20.6 - - + -
1066B LYS 3.3 13.9 - - - +
1067B VAL* 4.5 8.3 - - + -
1068B LEU* 3.6 5.8 - - - +
1079B LEU* 3.6 33.4 - - + +
1080B VAL* 1.3 76.6 - - - +
1082B GLU* 1.3 73.3 + - - +
1145B ILE* 5.4 2.5 - - - -
1146B ASP 6.0 1.8 - - - -
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Residues in contact with GLU1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ADP 3.0 23.2 + - - -
1025B VAL* 5.2 0.2 - - - -
1026B VAL 4.5 0.2 - - - -
1065B ILE* 3.5 15.7 - - + +
1066B LYS* 2.9 52.9 + - + +
1068B LEU* 3.5 21.0 - - + +
1081B MET* 1.3 72.9 - - - +
1083B LYS* 1.3 64.9 + - - +
1084B HIS* 4.5 8.0 + - - +
1143B LYS* 3.4 30.2 + - - -
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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