Contacts of the helix formed by residues 1044 - 1052 (chain B) in PDB entry 3U44
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 ASP1044 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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953B LYS* 4.7 17.8 + - - +
1042B LEU* 3.1 21.1 + - + +
1043B GLY* 1.3 79.4 - - - +
1045B GLN* 1.3 64.6 + - - +
1046B GLU* 3.9 9.5 + - - +
1047B VAL* 3.0 37.0 + - - +
1048B VAL* 3.6 14.4 + - - +
1073B LEU* 4.1 5.9 - - - +
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Residues in contact with GLN1045 (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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1044B ASP* 1.3 75.7 - - - +
1046B GLU* 1.3 72.6 + - - +
1048B VAL* 3.5 5.4 + - - +
1049B ARG* 2.7 60.9 + - - +
1067B LEU* 4.8 10.4 - - + +
1071B GLY* 3.7 26.5 - - - +
1072B SER* 5.5 1.6 - - - -
1073B LEU* 4.9 2.6 - - - +
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Residues in contact with GLU1046 (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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951B SER* 3.3 28.6 + - - -
952B SER* 3.3 31.1 + - - -
953B LYS* 4.4 6.8 + - - +
1044B ASP* 3.4 10.0 + - - +
1045B GLN* 1.3 87.8 + - - +
1047B VAL* 1.3 68.9 + - + +
1049B ARG* 2.8 24.3 + - + +
1050B LEU* 2.8 34.8 + - + +
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Residues in contact with VAL1047 (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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909B PHE* 5.1 1.3 - - + -
956B LEU* 3.9 27.4 - - + -
1004B ALA* 3.9 29.8 - - + +
1041B LEU* 5.4 0.4 - - + -
1042B LEU* 3.9 29.8 - - + +
1044B ASP* 3.0 33.1 + - - +
1046B GLU* 1.3 76.0 - - + +
1048B VAL* 1.3 64.6 + - + +
1050B LEU* 3.3 7.9 + - - +
1051B MET* 3.0 40.8 + - + +
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Residues in contact with VAL1048 (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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1041B LEU* 4.6 10.8 - - + -
1042B LEU 4.9 4.3 - - - +
1044B ASP 3.6 10.6 + - - +
1045B GLN* 3.5 11.1 + - - +
1046B GLU 3.1 0.2 - - - -
1047B VAL* 1.3 80.2 - - + +
1049B ARG* 1.3 65.9 + - + +
1051B MET* 2.9 11.1 + - - +
1052B ASP* 2.8 28.4 + - + +
1055B LEU* 4.2 25.1 - - + -
1063B ILE* 5.2 4.7 - - + +
1065B ALA* 3.7 28.5 - - + -
1066B GLY 5.0 2.2 - - - +
1067B LEU* 4.6 11.0 - - + -
1073B LEU* 4.3 15.3 - - + -
1079B ALA* 5.8 0.4 - - + -
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Residues in contact with ARG1049 (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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1045B GLN* 2.7 56.7 + - - +
1046B GLU* 2.8 18.8 + - + +
1048B VAL* 1.3 78.3 - - + +
1050B LEU* 1.3 61.2 + - + +
1051B MET 3.3 0.2 - - - -
1052B ASP 3.1 20.4 - - - +
1053B THR* 3.1 22.2 - - - +
1055B LEU* 4.3 13.7 + - + +
1056B GLN* 6.4 0.2 - - - +
1067B LEU* 4.2 22.9 - - + -
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Residues in contact with LEU1050 (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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908B GLY* 2.6 37.6 + - - +
909B PHE* 3.7 12.6 + - + -
949B ALA* 3.8 14.4 - - + -
950B GLU 3.6 22.9 - - - +
951B SER* 3.9 2.9 - - - -
956B LEU* 3.6 29.8 - - + -
1046B GLU* 2.8 48.9 + - + +
1047B VAL 3.7 7.9 - - - +
1048B VAL 3.2 0.2 - - - -
1049B ARG* 1.3 80.0 - - + +
1051B MET* 1.3 59.2 + - - +
1053B THR* 4.2 3.8 - - - +
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Residues in contact with MET1051 (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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907B SER* 3.4 21.7 + - - -
909B PHE* 3.6 20.2 - - + -
958B ARG* 3.1 34.9 + - + +
1004B ALA* 4.8 2.9 - - - +
1005B GLY* 6.3 0.2 - - - -
1007B LEU* 3.2 22.4 - - + -
1041B LEU* 3.3 38.6 - - + -
1047B VAL* 3.0 28.7 - - - +
1048B VAL* 2.9 8.4 + - - +
1050B LEU* 1.3 79.7 - - - +
1052B ASP* 1.3 58.0 + - - +
1053B THR 4.1 0.2 - - - -
1062B ILE* 4.2 13.5 - - - +
1063B ILE* 3.4 20.2 - - + -
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Residues in contact with ASP1052 (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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906B ALA* 3.8 9.4 - - - +
1048B VAL* 2.8 9.9 + - + +
1049B ARG* 3.1 18.5 - - - +
1051B MET* 1.3 77.7 - - + +
1053B THR* 1.3 60.9 + - - +
1054B THR* 3.0 26.5 + - - -
1055B LEU* 3.2 35.0 + - + +
1060B SER* 2.8 32.7 + - - +
1061B ASN 4.4 2.6 + - - -
1062B ILE* 4.1 14.4 - - + +
1063B ILE* 5.4 2.7 - - + +
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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