Contacts of the helix formed by residues 1049 - 1059 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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984A ILE* 4.1 10.3 - - + -
985A CYS 3.8 22.2 - - - +
991A MET* 3.8 19.1 - - + -
1027A ILE* 4.0 11.2 - - - +
1028A SER 3.9 5.7 + - - -
1048A ASN* 1.3 73.9 - - - +
1050A GLU* 1.3 58.6 + - + +
1051A PHE 3.1 0.2 - - - -
1052A VAL* 2.9 23.0 + - - +
1053A LEU* 3.0 21.6 + - + +
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Residues in contact with GLU1050 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A ARG* 2.9 26.6 + - - -
1048A ASN* 2.9 20.5 + - - +
1049A ALA* 1.3 75.1 - - + +
1051A PHE* 1.3 66.6 + - - +
1053A LEU* 3.5 12.7 - - - +
1054A THR* 2.6 48.3 + - - +
1055A GLY 3.3 3.8 + - - -
1066A TYR* 3.5 26.8 - - + -
142C TYR 4.1 4.2 - - - +
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Residues in contact with PHE1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A PHE* 4.1 15.2 - + - -
978A PHE* 3.8 30.5 - + - -
1025A ILE* 3.9 21.1 - - + -
1027A ILE* 4.2 7.6 - - + -
1047A HIS* 3.9 27.4 - + + -
1048A ASN 3.0 15.1 + - - +
1050A GLU* 1.3 77.6 - - - +
1052A VAL* 1.3 59.0 + - + +
1055A GLY* 3.3 19.6 - - - -
1060A THR 4.7 1.2 - - - +
1061A LEU* 4.1 15.3 - - + -
1062A ASP 3.3 38.1 + - - +
1063A TYR* 3.8 27.4 - + - -
1066A TYR* 3.7 14.7 - - + -
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Residues in contact with VAL1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A PHE* 4.3 10.8 - - + -
978A PHE* 4.0 30.1 - - + -
980A ILE* 5.3 0.2 - - + -
991A MET* 3.7 26.0 - - + +
994A ILE* 3.7 27.4 - - + -
995A VAL* 4.1 21.1 - - + -
1027A ILE* 4.4 8.7 - - + -
1049A ALA 2.9 9.5 + - - +
1051A PHE* 1.3 79.0 - - + +
1053A LEU* 1.3 61.1 + - + +
1056A VAL* 2.8 32.2 + - - +
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Residues in contact with LEU1053 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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910A ARG* 3.5 29.6 + - - +
915A LEU* 3.7 33.2 - - + +
985A CYS 5.0 0.2 - - - +
986A PRO* 3.9 26.9 - - + -
991A MET* 4.3 13.2 - - - -
994A ILE* 3.7 20.0 - - + -
1049A ALA* 3.0 24.3 + - + +
1050A GLU* 3.5 14.6 - - - +
1052A VAL* 1.3 78.5 - - + +
1054A THR* 1.3 63.6 + - - +
1056A VAL* 4.1 1.0 - - - -
1057A LEU* 3.2 19.6 + - - +
142C TYR* 4.0 11.7 - - + +
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Residues in contact with THR1054 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A ARG* 3.2 12.8 + - - +
956A PHE* 4.3 20.3 - - + +
1050A GLU* 2.6 39.3 + - - +
1053A LEU* 1.3 71.9 - - - +
1055A GLY* 1.3 66.1 + - - +
1057A LEU* 3.3 2.4 + - - -
1058A THR* 2.9 44.5 + - + +
1066A TYR* 3.4 24.8 + - + +
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Residues in contact with GLY1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A LEU* 3.3 8.5 - - - +
1050A GLU 3.3 6.5 + - - -
1051A PHE 3.3 14.8 - - - -
1052A VAL 3.3 2.0 + - - -
1053A LEU 3.3 0.6 - - - -
1054A THR* 1.3 77.1 - - - +
1056A VAL* 1.3 52.1 + - - +
1058A THR* 4.2 2.2 - - - -
1059A GLN* 2.7 32.2 + - - -
1060A THR* 3.0 28.1 + - - -
1062A ASP* 6.0 1.1 - - - -
1066A TYR* 5.4 2.1 - - - -
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Residues in contact with VAL1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915A LEU* 3.2 29.4 - - + +
918A ILE* 3.4 18.1 - - + +
919A SER* 3.7 11.0 - - - +
972A LEU* 4.0 3.1 - - + -
973A PHE* 3.7 26.5 - - + -
994A ILE* 3.8 17.7 - - + -
998A ALA* 4.0 13.2 - - + -
1052A VAL 2.8 23.2 + - - +
1053A LEU 4.2 2.5 - - - +
1055A GLY* 1.3 72.8 - - - +
1057A LEU* 1.3 63.7 + - - +
1059A GLN* 2.8 28.1 + - - +
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Residues in contact with LEU1057 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908A VAL* 4.0 15.9 - - + -
910A ARG* 4.3 16.4 - - + +
914A PHE* 4.0 22.0 - - + -
915A LEU* 4.1 12.3 - - + +
918A ILE* 3.4 17.3 - - + +
956A PHE* 3.8 48.7 - - + -
958A PHE* 3.4 25.8 - - + -
960A LEU* 4.9 0.2 - - + -
963A SER* 2.7 21.8 + - - -
1053A LEU 3.2 15.2 + - - +
1054A THR* 3.3 5.6 + - - +
1056A VAL* 1.3 78.6 - - - +
1058A THR* 1.3 54.3 + - + +
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Residues in contact with THR1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956A PHE* 3.8 18.2 - - + +
957A SER 5.3 0.4 - - - +
958A PHE* 3.7 34.1 - - + +
962A GLU* 5.9 0.2 - - - +
963A SER* 3.5 11.2 + - - -
966A ARG* 3.0 19.9 + - - -
1054A THR* 2.9 32.2 + - + +
1055A GLY 3.6 0.7 + - - -
1057A LEU* 1.3 78.7 - - + +
1059A GLN* 1.3 67.1 + - - +
1060A THR* 2.9 24.7 + - - +
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Residues in contact with GLN1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A ILE* 4.5 4.1 + - + +
919A SER* 3.5 26.2 + - - +
963A SER* 3.4 28.9 - - - +
966A ARG* 3.1 37.2 + - + +
967A ALA* 3.6 26.3 + - - +
970A SER 4.5 0.2 - - - +
972A LEU* 3.5 39.4 + - + +
1055A GLY 2.7 11.5 + - - -
1056A VAL* 2.8 30.4 + - - +
1058A THR* 1.3 77.9 - - - +
1060A THR* 1.3 56.0 + - - +
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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