Contacts of the strand formed by residues 1033 - 1042 (chain B) in PDB entry 2OOQ
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 ILE1033 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B TRP* 4.1 31.9 - - + +
995B ARG* 4.7 6.1 - - + +
998B TRP* 3.8 22.7 - - + -
1028B GLU 3.8 0.5 - - - +
1029B VAL* 3.3 2.4 - - - +
1030B TYR* 2.9 43.9 + - - +
1031B GLY 3.7 0.4 - - - -
1032B ASP* 1.3 93.3 - - - +
1034B LYS* 1.3 59.4 + - - +
1035B VAL* 3.7 11.5 + - + -
1053B VAL* 3.5 32.3 - - + -
1054B GLN 3.5 2.2 - - - +
1055B LYS* 3.7 28.0 - - + +
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Residues in contact with LYS1034 (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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1027B THR* 3.6 25.8 - - - +
1028B GLU 3.6 3.4 - - - -
1029B VAL* 4.2 16.4 - - + -
1032B ASP 3.7 2.0 + - - -
1033B ILE* 1.3 69.2 - - - +
1035B VAL* 1.3 62.8 + - - +
1036B THR* 3.8 11.6 + - - +
1052B THR* 3.7 1.9 + - - +
1053B VAL* 3.4 3.8 - - - +
1054B GLN* 2.7 54.2 + - + +
1056B LYS* 4.1 24.7 - - + +
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Residues in contact with VAL1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B TRP* 3.7 42.4 - - + -
1024B PRO* 3.4 15.7 - - + +
1027B THR* 3.2 3.8 + - - -
1028B GLU 3.0 31.1 + - - -
1030B TYR* 3.9 24.2 - - + -
1033B ILE* 4.0 9.4 - - + -
1034B LYS* 1.3 77.1 - - - +
1036B THR* 1.3 64.0 + - - +
1051B PHE* 3.5 35.2 - - + -
1052B THR 3.3 4.3 - - - +
1053B VAL* 4.4 3.8 - - + -
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Residues in contact with THR1036 (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 ASP* 3.3 15.3 - - - +
1027B THR* 3.0 21.4 + - - -
1034B LYS* 3.8 15.6 + - - +
1035B VAL* 1.3 73.6 - - - +
1037B LEU* 1.3 75.1 + - - +
1038B ILE* 3.4 7.1 + - + +
1051B PHE* 3.0 7.3 - - - -
1052B THR* 2.9 49.2 + - - +
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Residues in contact with LEU1037 (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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1024B PRO* 4.1 10.9 - - - +
1025B ASP* 3.2 26.7 - - - +
1026B ASP* 2.9 19.9 + - - +
1036B THR* 1.3 78.1 - - - +
1038B ILE* 1.3 61.9 + - - +
1039B GLU* 3.5 26.9 - - - +
1040B THR* 3.8 18.6 - - - +
1049B ARG* 4.1 10.8 - - + -
1050B THR 3.5 7.6 - - - +
1051B PHE* 3.6 27.1 - - + -
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Residues in contact with ILE1038 (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 THR* 3.4 16.1 + - + +
1037B LEU* 1.3 80.0 - - - +
1039B GLU* 1.3 59.9 + - + +
1050B THR* 2.8 44.3 + - + +
1051B PHE* 4.2 4.0 - - - +
1052B THR* 4.1 28.3 - - + -
1063B GLU* 4.0 12.6 - - - +
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Residues in contact with GLU1039 (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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301B B3P 2.9 55.8 + - - +
1037B LEU* 3.5 10.4 - - - +
1038B ILE* 1.3 82.8 - - + +
1040B THR* 1.3 73.6 + - - +
1041B GLU* 4.3 5.3 - - - +
1048B ILE 4.6 0.2 - - - -
1049B ARG* 3.5 0.5 - - - -
1050B THR* 2.8 41.4 + - + +
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Residues in contact with THR1040 (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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1037B LEU* 3.8 23.2 - - - +
1039B GLU* 1.3 83.9 + - - +
1041B GLU* 1.3 61.0 + - - +
1042B PRO* 3.4 18.9 - - + +
1047B VAL* 3.6 24.5 - - + -
1048B ILE 3.6 2.9 - - - -
1049B ARG* 4.4 10.2 - - + +
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Residues in contact with GLU1041 (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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301B B3P 2.6 92.1 + - + +
1039B GLU* 4.3 5.1 - - - +
1040B THR* 1.3 72.8 - - - +
1042B PRO* 1.3 60.1 - - + +
1043B LEU* 3.3 28.8 - - + +
1047B VAL* 3.5 2.8 - - - -
1048B ILE* 2.8 43.4 + - + +
1090B GLN* 4.6 10.5 + - - +
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Residues in contact with PRO1042 (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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1040B THR* 3.4 18.8 - - + +
1041B GLU* 1.3 83.7 - - + +
1043B LEU* 1.3 64.9 + - - +
1047B VAL* 3.7 19.0 - - + -
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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