Contacts of the helix formed by residues 1049 - 1059 (chain B) in PDB entry 3SQD
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 ALA1049 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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984B ILE* 4.0 10.3 - - + -
985B CYS 3.7 23.6 - - - +
991B MET* 3.9 18.8 - - + -
1027B ILE* 4.0 12.7 - - - +
1028B SER 4.1 2.8 + - - -
1048B ASN* 1.3 75.0 - - - +
1050B GLU* 1.3 58.1 + - + +
1051B PHE 3.1 0.4 - - - -
1052B VAL* 2.8 22.3 + - - +
1053B LEU* 2.9 23.1 + - + +
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Residues in contact with GLU1050 (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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910B ARG* 2.8 32.8 + - - -
1048B ASN* 2.8 19.2 + - - +
1049B ALA* 1.3 74.8 - - + +
1051B PHE* 1.3 65.9 + - - +
1053B LEU* 4.0 8.3 - - - +
1054B THR* 2.9 46.8 + - - -
1055B GLY 3.4 3.5 + - - -
1066B TYR* 3.4 25.5 - - + -
142D TYR 4.4 1.0 - - - +
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Residues in contact with PHE1051 (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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973B PHE* 3.9 17.2 - + - -
976B LYS* 6.2 0.9 - - + -
978B PHE* 3.9 29.8 - + - -
1025B ILE* 4.1 10.1 - - + -
1027B ILE* 3.9 10.3 - - + -
1047B HIS* 3.7 29.4 - + + -
1048B ASN 3.0 15.5 + - - +
1050B GLU* 1.3 78.3 - - - +
1052B VAL* 1.3 58.9 + - + +
1055B GLY* 3.3 19.6 - - - -
1060B THR 5.1 0.3 - - - +
1061B LEU* 4.3 12.5 - - + +
1062B ASP 3.4 38.1 + - - -
1063B TYR* 4.0 33.9 - + - -
1066B TYR* 3.6 16.0 - + + -
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Residues in contact with VAL1052 (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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973B PHE* 4.1 11.0 - - + -
978B PHE* 3.8 31.9 - - + -
980B ILE* 5.5 0.2 - - + -
991B MET* 3.8 28.0 - - + -
994B ILE* 3.8 26.5 - - + -
995B VAL* 3.9 21.1 - - + -
1027B ILE* 4.5 8.3 - - + -
1049B ALA 2.8 8.5 + - - +
1051B PHE* 1.3 81.4 - - + +
1053B LEU* 1.3 66.5 - - + +
1056B VAL* 2.9 25.1 + - - +
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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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910B ARG* 3.7 27.2 + - - +
915B LEU* 3.9 17.3 - - + +
986B PRO* 3.7 27.1 - - + -
991B MET* 4.0 17.5 - - - -
994B ILE* 3.7 28.9 - - + -
1049B ALA* 2.9 22.1 + - + +
1050B GLU* 3.8 16.6 - - - +
1052B VAL* 1.3 78.0 - - + +
1054B THR* 1.3 61.4 + - - +
1056B VAL* 3.6 5.7 - - - +
1057B LEU* 3.4 20.4 + - - +
142D TYR* 4.0 12.1 - - + +
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Residues in contact with THR1054 (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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910B ARG* 3.3 11.4 + - - +
956B PHE* 4.1 17.9 - - + +
1050B GLU* 2.9 34.6 + - - +
1053B LEU* 1.3 72.9 - - - +
1055B GLY* 1.3 67.5 + - - +
1057B LEU* 4.4 4.3 - - - -
1058B THR* 2.9 44.9 + - + +
1060B THR* 5.6 0.7 - - - +
1066B TYR* 3.0 26.6 + - - +
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Residues in contact with GLY1055 (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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972B LEU* 3.4 8.9 - - - +
1050B GLU 3.4 7.7 + - - -
1051B PHE 3.3 17.5 + - - -
1053B LEU 3.4 0.2 - - - -
1054B THR* 1.3 79.2 - - - +
1056B VAL* 1.3 51.9 + - - +
1058B THR* 4.2 1.3 - - - -
1059B GLN* 2.6 36.0 + - - -
1060B THR* 3.1 21.9 + - - -
1062B ASP 6.1 0.2 - - - -
1066B TYR* 5.0 3.0 + - - -
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Residues in contact with VAL1056 (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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915B LEU* 3.7 25.6 - - + +
918B ILE* 3.7 6.1 - - + +
919B SER* 4.4 2.7 - - - +
972B LEU* 3.9 3.6 - - + -
973B PHE* 3.6 27.6 - - + -
994B ILE* 3.7 28.9 - - + +
998B ALA* 4.2 13.9 - - + -
1052B VAL 2.9 25.4 + - - +
1053B LEU 3.6 7.4 - - - +
1055B GLY* 1.3 68.8 - - - +
1057B LEU* 1.3 69.7 + - - +
1059B GLN* 2.9 36.3 + - - +
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Residues in contact with LEU1057 (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 VAL* 4.2 9.4 - - + -
910B ARG* 4.2 20.9 - - + +
914B PHE* 3.9 30.3 - - + -
915B LEU* 4.1 9.4 - - + -
918B ILE* 3.3 17.7 - - + +
956B PHE* 3.9 39.3 - - + -
958B PHE* 3.6 25.4 - - + -
960B LEU* 4.3 2.7 - - + -
963B SER* 2.8 15.6 + - - -
1053B LEU 3.4 14.1 + - - +
1054B THR* 3.3 6.3 + - - +
1056B VAL* 1.3 82.2 - - - +
1058B THR* 1.3 60.3 + - + +
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Residues in contact with THR1058 (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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956B PHE* 3.9 16.8 - - + +
958B PHE* 3.7 34.3 - - + +
963B SER* 3.5 11.1 + - - -
966B ARG* 3.2 19.1 + - - -
1054B THR* 2.9 34.8 + - + +
1055B GLY 3.6 0.3 + - - -
1057B LEU* 1.3 79.8 - - + +
1059B GLN* 1.3 69.4 + - - +
1060B THR* 2.9 25.4 + - - -
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Residues in contact with GLN1059 (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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918B ILE* 4.4 5.8 + - + +
919B SER* 3.5 25.7 + - - +
963B SER* 3.2 31.4 - - - +
966B ARG* 3.7 24.3 + - + +
967B ALA* 3.7 26.9 + - + +
970B SER 4.6 0.7 - - - +
972B LEU* 3.5 39.3 + - - +
1055B GLY 2.6 17.0 + - - -
1056B VAL* 2.9 26.8 + - - +
1058B THR* 1.3 76.6 - - - +
1060B THR* 1.3 58.1 + - - +
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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