Contacts of the strand formed by residues 1047 - 1053 (chain B) in PDB entry 2IUI
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 TYR1047 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004B ASN* 5.1 6.9 + - - +
1007B LEU* 3.4 19.1 - - + +
1013B TYR* 3.8 23.3 + + - -
1036B VAL* 3.9 14.1 - - + -
1037B ARG 3.3 12.3 - - - +
1038B ASP* 3.3 26.7 - - - -
1039B ALA 3.6 1.8 - - - +
1043B MET* 5.1 9.7 - - + +
1045B GLY* 3.4 25.9 - - - -
1046B ASP* 1.3 76.8 - - - +
1048B THR* 1.3 62.5 + - - +
1061B LYS* 3.3 8.3 + - - -
1062B ILE* 2.9 38.7 + - + +
1069B TYR* 4.0 13.4 + + - -
1080B VAL* 3.8 27.6 - - + -
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Residues in contact with THR1048 (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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1036B VAL* 3.4 7.1 - - - -
1037B ARG* 2.8 54.7 + - - +
1039B ALA* 3.5 3.3 - - - -
1047B TYR* 1.3 72.4 - - - +
1049B LEU* 1.3 73.4 + - - +
1050B THR* 3.8 2.6 + - - +
1059B LEU* 3.7 18.6 - - + -
1060B ILE 3.6 2.9 - - - +
1061B LYS* 2.5 23.1 + - - +
1204D PTR 2.9 38.3 + - + +
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Residues in contact with LEU1049 (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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1034B PHE* 3.8 32.3 - - + -
1035B LEU 3.6 15.7 - - - +
1036B VAL* 4.1 8.1 - - + -
1048B THR* 1.3 76.4 - - - +
1050B THR* 1.3 64.3 + - - +
1051B LEU* 4.7 1.6 - - + -
1058B LYS 3.5 0.3 - - - +
1059B LEU* 3.8 0.2 - - - -
1060B ILE* 2.8 68.1 + - + +
1062B ILE* 4.0 18.3 - - + +
1071B PHE* 3.9 26.0 - - + -
1084B ILE* 4.1 7.6 - - + -
1092B LEU* 5.1 1.1 - - + -
1103B LEU* 4.3 19.7 - - + -
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Residues in contact with THR1050 (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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1022B VAL* 3.8 24.3 - - + +
1023B ASN* 5.6 0.7 - - - +
1026B LEU* 3.4 24.5 - - + +
1034B PHE* 3.2 6.1 - - - +
1035B LEU* 3.0 35.3 + - - +
1037B ARG* 4.5 6.2 + - - +
1048B THR* 3.8 5.9 + - - +
1049B LEU* 1.3 75.0 - - - +
1051B LEU* 1.3 62.8 + - - +
1057B ASN* 3.7 19.1 - - + -
1058B LYS 3.3 5.6 - - - +
1059B LEU* 3.5 24.9 - - + +
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Residues in contact with LEU1051 (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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1026B LEU* 4.4 2.0 - - - -
1032B GLY* 4.1 20.6 - - - -
1033B THR 3.5 9.9 - - - +
1034B PHE* 4.2 3.8 - - + -
1049B LEU* 4.7 3.8 - - + -
1050B THR* 1.3 76.3 - - - +
1052B ARG* 1.3 72.7 + - - +
1053B LYS* 3.5 2.8 + - + -
1057B ASN* 3.4 3.3 - - - -
1058B LYS* 2.7 42.5 + - + +
1060B ILE* 4.0 17.5 - - + -
1092B LEU* 3.8 20.2 - - + -
1099B LEU* 4.1 12.1 - - + -
1101B VAL* 3.7 26.5 - - + -
1102B LYS 4.5 0.9 - - - +
1103B LEU* 3.7 21.5 - - + -
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Residues in contact with ARG1052 (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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1026B LEU* 3.3 22.4 + - + +
1027B ARG* 4.7 2.4 - - - +
1028B ASP* 3.3 27.1 + - - +
1029B THR* 3.1 31.1 + - - +
1030B ALA 3.1 26.7 - - - +
1031B ASP* 3.2 5.4 - - - +
1032B GLY* 2.8 27.9 + - - -
1033B THR* 2.8 19.3 + - - +
1051B LEU* 1.3 72.9 - - - +
1053B LYS* 1.3 62.9 + - - +
1055B GLY* 3.3 37.5 + - - -
1056B ASN* 3.6 6.3 - - - +
1057B ASN* 3.0 26.3 + - - +
1101B VAL* 4.9 0.2 - - - +
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Residues in contact with LYS1053 (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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1031B ASP* 3.5 13.9 + - - +
1051B LEU* 3.5 7.2 + - + +
1052B ARG* 1.3 76.8 - - - +
1054B GLY* 1.3 69.3 + - - +
1055B GLY 3.3 0.4 - - - -
1056B ASN* 3.0 28.2 + - - +
1058B LYS* 3.5 32.0 + - + -
1098B LYS 3.4 27.4 - - - +
1099B LEU* 4.4 4.3 - - + -
1100B ASP* 3.5 29.3 + - - +
1101B VAL* 3.6 33.7 - - + +
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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