Contacts of the strand formed by residues 1052 - 1057 (chain B) in PDB entry 2QRA
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 PHE1052 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029B ARG* 3.9 7.6 - - - +
1033B PHE* 3.1 16.7 - - + -
1047B LEU* 2.9 35.2 + - + +
1048B ALA* 3.6 10.0 + - - -
1050B ALA* 3.6 15.5 - - + -
1051B GLY* 1.3 77.8 - - - +
1053B LEU* 1.3 60.7 - - - +
1061B VAL* 3.3 32.8 - - + -
1062B ARG 3.5 14.6 - - - -
1063B CYS* 3.6 9.4 - - + -
1068B ALA 3.8 20.0 - - - -
1070B VAL* 3.9 21.3 - - + -
1073B TRP* 4.2 9.4 - + - -
1079B ALA 3.6 21.3 - - - -
1083B HIS* 3.6 26.2 - + + -
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Residues in contact with LEU1053 (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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1023B PHE* 3.4 44.2 - - + -
1029B ARG* 3.2 44.9 - - + -
1032B THR* 3.6 11.0 - - + +
1033B PHE* 3.8 2.9 - - - -
1052B PHE* 1.3 73.7 - - - +
1054B TYR* 1.3 65.8 + - - +
1055B THR* 3.3 2.3 + - - +
1061B VAL* 3.3 1.0 - - - -
1062B ARG* 2.7 40.1 + - + +
1063B CYS 5.3 0.2 - - - -
1064B PHE* 3.9 20.2 - - + -
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Residues in contact with TYR1054 (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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1032B THR* 3.4 27.5 + - - +
1033B PHE* 3.3 30.7 - - + -
1034B ALA 3.8 12.8 - - - -
1035B ASN 3.3 12.2 + - - -
1036B PHE* 3.3 46.4 - + + -
1037B PRO* 3.6 6.8 - - + +
1053B LEU* 1.3 72.6 - - - +
1055B THR* 1.3 61.7 + - - +
1056B GLY* 3.0 24.7 + - - -
1057B GLU* 3.0 41.5 + - - -
1058B GLY 2.8 22.8 + - - -
1060B THR 3.5 8.5 - - - -
1061B VAL* 4.2 2.5 - - - -
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Residues in contact with THR1055 (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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1053B LEU 4.2 0.4 - - - +
1054B TYR* 1.3 73.5 - - - +
1056B GLY* 1.3 59.9 + - - +
1057B GLU* 3.3 29.4 + - - +
1060B THR* 2.6 34.6 + - + +
1061B VAL 4.1 1.6 - - - -
1062B ARG* 3.7 42.6 - - + +
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Residues in contact with GLY1056 (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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1032B THR 5.8 0.2 - - - -
1034B ALA 5.7 0.9 - - - -
1054B TYR* 3.0 32.4 + - - -
1055B THR* 1.3 78.2 - - - +
1057B GLU* 1.3 58.9 + - - +
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Residues in contact with GLU1057 (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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1054B TYR* 3.0 7.1 - - - -
1055B THR* 3.3 23.6 - - - +
1056B GLY* 1.3 80.8 - - - +
1058B GLY* 1.3 72.2 + - - +
1060B THR* 3.0 24.7 + - - +
3085D LYS* 4.0 26.5 - - - +
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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