Contacts of the strand formed by residues 1105 - 1111 (chain B) in PDB entry 2IUK
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 ASP1105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1016B VAL* 4.8 1.6 - - - -
1017B LEU* 3.1 26.1 + - + +
1019B PRO* 3.8 24.9 - - + +
1058B ALA* 4.5 13.7 - - - +
1061B PHE* 5.0 0.5 - - - -
1093B HIS* 4.0 8.1 - - + -
1097B LEU* 3.3 28.8 - - + +
1102B ALA 3.9 1.0 - - - +
1103B ARG 3.7 11.3 - - - +
1104B GLN* 1.3 75.4 - - - +
1106B ALA* 1.3 58.8 + - - +
1107B PHE* 3.4 28.5 - - + -
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Residues in contact with ALA1106 (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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1014B THR* 4.7 9.6 - - + -
1015B VAL 3.7 5.6 - - - +
1016B VAL* 4.5 17.2 - - + +
1093B HIS* 3.8 4.3 - - - -
1094B LEU* 2.8 39.8 + - + +
1097B LEU* 3.3 10.3 - - - +
1098B PRO* 3.8 28.5 - - + -
1104B GLN 3.9 2.0 + - - -
1105B ASP* 1.3 70.8 - - - +
1107B PHE* 1.3 60.6 + - - +
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Residues in contact with PHE1107 (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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1014B THR* 3.6 4.3 - - - -
1015B VAL* 2.7 40.7 + - - +
1017B LEU* 3.7 17.3 - - + -
1058B ALA 3.7 2.5 - - - -
1059B THR 2.9 29.6 - - - -
1061B PHE* 3.4 22.9 - + + -
1062B LEU* 3.6 22.7 - - + -
1090B LEU* 3.9 28.7 - - + -
1092B LYS 3.4 5.8 - - - +
1093B HIS* 3.3 32.3 - + - -
1094B LEU* 4.2 6.5 - - - +
1105B ASP* 3.4 30.1 - - + -
1106B ALA* 1.3 76.4 - - - +
1108B SER* 1.3 59.8 + - - +
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Residues in contact with SER1108 (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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1012B LYS* 4.9 3.8 - - - +
1013B GLY 3.6 7.2 + - - -
1090B LEU* 3.8 5.0 - - - +
1091B GLU* 3.0 22.7 + - - -
1092B LYS* 2.6 31.1 + - - +
1094B LEU* 3.4 28.2 - - - +
1107B PHE* 1.3 74.1 - - - +
1109B ILE* 1.3 65.6 + - - +
1110B PHE* 3.4 24.9 - - - -
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Residues in contact with ILE1109 (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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1012B LYS* 3.3 2.4 - - - -
1013B GLY* 2.7 48.1 + - - +
1015B VAL* 3.7 23.8 - - + -
1066B ILE 4.8 0.9 - - - +
1068B MET* 4.5 8.7 - - + -
1088B VAL* 3.4 32.3 - - + +
1089B TYR 3.6 24.2 - - - +
1090B LEU* 3.8 12.6 - - + +
1091B GLU* 3.8 3.6 - - - +
1108B SER* 1.3 81.7 + - - +
1110B PHE* 1.3 65.9 + - - +
1111B PHE* 3.5 35.9 - - + -
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Residues in contact with PHE1110 (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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1010B LYS* 4.0 31.9 - - + +
1011B ILE 3.6 2.5 - - - +
1012B LYS* 3.5 34.8 - - + -
1088B VAL* 3.3 20.1 - - - +
1091B GLU* 3.0 39.0 + - + +
1092B LYS* 4.6 13.9 - - - -
1108B SER* 3.4 25.8 - - - -
1109B ILE* 1.3 71.9 - - - +
1111B PHE* 1.3 63.9 + - - +
1112B GLU* 4.0 0.9 + - - +
1142B ASP* 5.6 2.0 - - - -
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Residues in contact with PHE1111 (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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1010B LYS* 3.6 8.1 - - - -
1011B ILE* 2.9 50.5 + - + +
1012B LYS 4.3 3.6 - - - -
1013B GLY* 3.9 11.0 - - - -
1068B MET* 3.6 42.4 - - + -
1070B LEU* 4.3 27.4 - - + -
1086B LYS 5.0 2.0 - - - -
1088B VAL* 3.9 18.8 - - + -
1109B ILE* 3.5 51.4 - - + -
1110B PHE* 1.3 73.9 - - - +
1112B GLU* 1.3 70.6 + - - +
1140B LEU* 4.1 11.2 - - + -
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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