Contacts of the strand formed by residues 1100 - 1108 (chain B) in PDB entry 1CJY
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 GLU1100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032B LYS* 3.6 22.2 + - - +
1092B MET* 3.3 5.3 - - - -
1093B ASP* 2.7 49.4 + - + +
1095B ASN* 3.5 14.2 + - - +
1098B MET 3.4 1.5 + - - +
1099B ASP* 1.3 72.9 - - - +
1101B THR* 1.3 69.7 + - + +
1102B LEU* 3.6 18.9 + - - +
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Residues in contact with THR1101 (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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1090B THR* 3.7 13.9 - - - +
1091B LEU 3.7 0.2 - - - -
1092B MET* 3.6 26.9 - - + -
1099B ASP 4.1 1.7 + - - +
1100B GLU* 1.3 82.7 - - + +
1102B LEU* 1.3 60.5 + - - +
1103B GLY* 3.9 5.7 + - - -
1104B THR* 4.0 9.5 + - - -
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Residues in contact with LEU1102 (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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1030B VAL* 3.8 28.7 - - + -
1031B THR 4.5 5.4 - - - +
1032B LYS* 3.5 36.1 - - + -
1042B PRO* 4.8 3.4 - - + -
1044B PRO* 5.6 0.4 - - + -
1091B LEU* 2.9 24.8 + - + +
1092B MET 4.5 7.6 - - - +
1093B ASP* 4.1 22.7 - - + -
1100B GLU* 3.8 22.2 - - - +
1101B THR* 1.3 73.5 - - - +
1103B GLY* 1.3 58.0 + - - +
1124B PHE* 5.1 0.7 - - - -
1125B ASN* 3.0 37.8 + - - +
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Residues in contact with GLY1103 (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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1090B THR* 3.4 6.4 - - - +
1091B LEU* 3.0 26.9 + - - +
1101B THR* 3.5 3.5 + - - -
1102B LEU* 1.3 83.0 - - - +
1104B THR* 1.3 64.4 + - - -
1124B PHE* 3.4 24.8 - - - -
1125B ASN* 5.1 1.6 - - - -
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Residues in contact with THR1104 (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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1088B GLU* 5.5 9.4 - - + +
1089B ILE 3.4 9.6 - - - +
1090B THR* 4.4 9.4 + - - +
1101B THR* 4.0 10.4 + - - -
1103B GLY* 1.3 79.2 + - - -
1105B ALA* 1.3 73.9 + - - +
1124B PHE* 3.7 4.9 - - - -
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Residues in contact with ALA1105 (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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1088B GLU* 3.7 4.2 - - - +
1089B ILE* 2.8 35.6 + - + +
1104B THR* 1.3 83.8 - - - +
1106B THR* 1.3 62.8 + - - +
1122B PHE* 3.6 28.0 - - + -
1124B PHE* 3.8 18.4 - - + -
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Residues in contact with THR1106 (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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1086B VAL* 4.1 17.3 - - - +
1087B LEU 3.3 11.1 + - - -
1088B GLU* 5.2 3.1 - - - +
1089B ILE* 4.4 0.9 - - - -
1105B ALA* 1.3 76.2 - - - +
1107B PHE* 1.3 68.5 + - - +
1108B THR* 4.4 7.5 + - - +
1122B PHE* 3.1 22.2 - - - -
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Residues in contact with PHE1107 (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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1020B PHE* 3.8 21.8 - + - -
1086B VAL* 4.5 0.2 - - - -
1087B LEU* 2.7 40.2 + - + +
1089B ILE* 4.2 5.4 - - + -
1106B THR* 1.3 81.3 + - - +
1108B THR* 1.3 62.7 + - - +
1109B VAL* 3.5 12.8 + - - +
1111B SER* 4.0 19.5 - - - -
1112B MET* 4.0 20.4 - - - -
1118B LYS* 4.8 7.0 - - - -
1120B VAL* 3.8 25.4 - - + -
1122B PHE* 4.1 10.8 - + + -
1134B MET* 3.2 47.3 - - + -
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Residues in contact with THR1108 (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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1084B GLU* 6.0 2.9 - - + -
1085B ASN 3.9 7.0 - - - +
1086B VAL* 4.0 22.6 - - + +
1106B THR* 4.4 8.5 + - - +
1107B PHE* 1.3 73.4 + - - +
1109B VAL* 1.3 68.4 + - - +
1110B SER* 3.5 21.5 - - - +
1111B SER* 2.9 31.3 + - - +
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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