Contacts of the helix formed by residues 911 - 918 (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 THR 911 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872A THR* 2.8 27.2 + - - +
873A GLY* 5.4 2.7 - - - +
909A THR* 2.9 24.5 + - - +
910A ARG* 1.3 77.7 - - - +
912A VAL* 1.3 65.9 + - - +
913A LYS 3.7 1.4 + - - -
914A PHE* 3.2 18.4 + - - +
915A LEU* 3.0 24.3 + - - +
139C SEP 3.9 28.0 - - - +
140C GLN 3.6 19.3 - - - +
141C GLU* 4.0 3.4 - - + -
142C TYR* 5.0 1.1 - - - -
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Residues in contact with VAL 912 (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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911A THR* 1.3 74.2 - - - +
913A LYS* 1.3 61.3 + - + +
915A LEU* 3.2 3.8 + - - -
916A THR* 2.8 43.6 + - + +
990A THR* 3.8 42.0 - - + +
993A ALA* 5.1 4.9 - - + -
994A ILE* 4.8 4.3 - - + -
140C GLN 4.5 1.7 + - - +
142C TYR* 4.1 17.2 - - + +
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Residues in contact with LYS 913 (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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870A LEU* 4.5 27.9 - - + +
871A PHE* 2.7 32.8 + - - +
872A THR* 4.1 6.3 - - - -
903A LEU* 4.5 6.5 - - + -
911A THR* 3.2 3.2 + - - +
912A VAL* 1.3 80.6 - - + +
914A PHE* 1.3 58.0 + - - +
916A THR* 3.2 5.2 + - - -
917A ALA* 2.9 35.1 + - - +
139C SEP 2.6 41.0 + - - +
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Residues in contact with PHE 914 (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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872A THR* 4.2 4.0 - - + -
903A LEU* 3.6 24.8 - - + +
905A ALA* 4.0 7.6 - - + -
907A LYS 3.7 18.8 - - - -
908A VAL* 4.1 14.1 - - + -
909A THR* 2.9 40.8 - - + +
911A THR* 3.2 11.7 + - - +
913A LYS* 1.3 79.2 - - - +
915A LEU* 1.3 62.4 + - + +
917A ALA* 4.0 0.3 - - - +
918A ILE* 2.9 39.3 + - + +
924A ILE* 4.2 17.5 - - + -
947A LEU* 4.0 12.3 - - + -
960A LEU* 4.4 15.5 - - + -
1057A LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 915 (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* 4.1 34.1 - - + +
911A THR 3.0 21.8 + - - +
912A VAL 4.1 0.4 - - - +
914A PHE* 1.3 79.7 - - + +
916A THR* 1.3 61.8 + - - +
918A ILE* 3.7 4.1 - - + +
919A SER* 4.5 1.2 + - - -
994A ILE* 3.7 28.3 - - + +
1053A LEU* 3.7 50.5 - - + +
1056A VAL* 3.2 24.8 - - + +
1057A LEU* 4.1 26.9 - - + +
142C TYR* 5.4 3.6 - - + -
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Residues in contact with THR 916 (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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897A ALA* 3.3 23.5 - - + +
912A VAL* 2.8 27.5 + - + +
913A LYS* 3.2 8.5 + - - -
915A LEU* 1.3 76.8 - - - +
917A ALA* 1.3 71.3 + - - +
918A ILE 3.2 0.9 + - - -
919A SER* 3.2 10.9 + - - -
920A VAL* 3.9 3.6 - - - +
993A ALA* 3.6 38.8 - - + +
994A ILE* 3.9 9.4 - - + +
997A CYS* 3.5 26.0 - - - +
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Residues in contact with ALA 917 (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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870A LEU* 4.6 9.6 - - + -
897A ALA* 4.2 3.4 - - - -
900A CYS* 5.1 0.2 - - - -
903A LEU* 3.9 23.8 - - + -
913A LYS 2.9 17.3 + - - +
914A PHE 4.0 1.6 - - - +
916A THR* 1.3 83.1 + - - +
918A ILE* 1.3 58.2 + - - +
920A VAL* 2.8 26.3 + - - -
921A VAL* 2.9 35.1 + - + +
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Residues in contact with ILE 918 (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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914A PHE* 2.9 25.0 + - + +
915A LEU* 3.7 6.7 - - + +
917A ALA* 1.3 75.9 - - - +
919A SER* 1.3 61.7 + - - +
920A VAL 3.3 0.4 - - - -
921A VAL* 4.5 8.0 + - - +
924A ILE* 4.3 16.8 - - + -
960A LEU* 3.7 23.6 - - + -
963A SER* 3.9 10.3 - - - -
964A LEU* 3.8 15.5 - - + +
967A ALA* 3.7 14.2 - - - +
1056A VAL* 3.4 35.9 - - + +
1057A LEU* 3.4 35.9 - - + +
1059A GLN* 4.5 1.8 - - - +
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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