Contacts of the helix formed by residues 911 - 921 (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 THR 911 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B THR* 2.6 29.3 + - - +
873B GLY* 5.3 2.2 - - - +
909B THR* 2.9 28.4 + - + +
910B ARG* 1.3 76.5 - - - +
912B VAL* 1.3 65.6 + - - +
913B LYS 3.7 1.7 + - - -
914B PHE* 3.3 15.4 + - - +
915B LEU* 2.9 23.4 + - - +
139D SEP 3.8 21.3 - - - +
140D GLN 3.5 20.9 - - - +
141D GLU* 4.2 7.4 - - + -
142D TYR* 4.5 2.9 - - - -
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Residues in contact with VAL 912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911B THR* 1.3 75.1 - - - +
913B LYS* 1.3 56.7 + - + +
915B LEU* 4.5 3.6 - - - +
916B THR* 2.5 50.8 + - + -
990B THR* 3.9 29.2 - - + +
993B ALA* 4.8 6.7 - - + -
994B ILE* 4.6 4.9 - - + -
140D GLN* 5.3 1.1 - - + +
142D TYR* 3.5 29.4 - - + +
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Residues in contact with LYS 913 (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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870B LEU* 4.4 26.8 - - + +
871B PHE* 2.8 27.6 + - - +
872B THR* 4.1 6.1 - - - -
897B ALA* 5.6 0.4 - - - -
903B LEU* 4.7 7.2 - - + -
911B THR* 3.2 5.5 + - - +
912B VAL* 1.3 79.2 - - + +
914B PHE* 1.3 50.6 + - - +
916B THR* 3.1 5.1 + - - -
917B ALA* 2.7 43.4 + - - +
139D SEP 2.5 39.8 + - - +
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Residues in contact with PHE 914 (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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872B THR* 3.9 18.8 + - + -
903B LEU* 4.0 17.8 - - + +
905B ALA* 4.4 3.4 - - + -
907B LYS 3.9 5.2 - - - -
908B VAL* 3.7 20.2 - - + -
909B THR* 3.0 42.8 - - + +
910B ARG* 4.8 0.4 - - - -
911B THR* 3.2 11.6 + - - +
912B VAL 3.2 0.2 - - - -
913B LYS* 1.3 80.3 - - - +
915B LEU* 1.3 62.7 + - + +
917B ALA* 4.0 0.2 - - - +
918B ILE* 3.0 31.5 + - + +
924B ILE* 4.3 12.1 - - + -
947B LEU* 4.2 6.7 - - + -
960B LEU* 3.9 29.2 - - + -
1057B LEU* 3.9 27.1 - - + -
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Residues in contact with LEU 915 (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* 4.0 34.5 - - + +
911B THR 2.9 20.4 + - - +
912B VAL 4.2 0.2 - - - +
914B PHE* 1.3 79.1 - - + +
916B THR* 1.3 63.0 + - - +
918B ILE* 3.3 14.8 - - + +
919B SER* 4.2 3.8 + - - -
994B ILE* 3.7 36.2 - - + +
1053B LEU* 3.9 38.4 - - + +
1056B VAL* 3.7 20.1 - - + +
1057B LEU* 4.1 21.5 - - + -
142D TYR* 5.0 4.9 - - + -
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Residues in contact with THR 916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B ALA* 3.6 12.8 - - - +
912B VAL* 2.5 35.4 + - + +
913B LYS* 3.1 6.9 + - - -
915B LEU* 1.3 76.0 - - - +
917B ALA* 1.3 70.9 + - - +
919B SER* 3.0 17.0 + - - -
920B VAL* 3.6 11.2 - - - +
993B ALA* 3.9 10.3 - - + +
994B ILE* 3.9 24.9 - - + +
997B CYS* 3.6 32.1 - - - +
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Residues in contact with ALA 917 (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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870B LEU* 4.3 13.5 - - + -
897B ALA* 4.1 4.0 - - - +
903B LEU* 4.0 21.3 - - + -
913B LYS 2.7 26.7 + - - +
914B PHE 4.0 2.0 - - - +
916B THR* 1.3 74.5 + - - +
918B ILE* 1.3 56.6 + - - +
920B VAL* 2.9 24.0 + - - -
921B VAL* 2.9 35.1 + - + +
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Residues in contact with ILE 918 (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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914B PHE* 3.0 19.1 + - + +
915B LEU* 3.3 22.9 - - + +
917B ALA* 1.3 75.9 - - - +
919B SER* 1.3 67.4 + - - +
921B VAL* 4.7 1.2 + - - +
924B ILE* 4.2 24.0 - - + +
960B LEU* 3.9 19.1 - - + -
963B SER* 3.9 11.4 - - - -
964B LEU* 4.0 16.0 - - + +
967B ALA* 3.7 13.5 - - - +
1056B VAL* 3.7 20.4 - - + +
1057B LEU* 3.3 34.8 - - + +
1059B GLN* 4.4 3.9 + - + +
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Residues in contact with SER 919 (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 4.2 4.5 + - - -
916B THR 3.0 11.1 + - - -
917B ALA 2.9 0.2 + - - -
918B ILE* 1.3 81.9 - - - +
920B VAL* 1.3 62.3 + - - +
921B VAL 4.0 0.7 - - - -
967B ALA* 4.0 22.7 - - - +
971B PRO* 6.1 0.7 - - - +
972B LEU 6.3 0.2 - - - -
994B ILE 5.1 0.5 + - - -
997B CYS* 3.4 25.4 - - - +
998B ALA* 3.6 18.4 + - - +
1056B VAL* 4.4 2.8 - - - +
1059B GLN* 3.5 17.6 + - - +
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Residues in contact with VAL 920 (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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897B ALA* 3.1 31.4 - - + +
898B GLN* 4.4 21.4 - - + +
900B CYS 3.8 7.3 - - - +
916B THR 3.6 12.3 - - - +
917B ALA* 2.9 13.4 + - - +
919B SER* 1.3 85.6 - - - +
921B VAL* 1.3 58.6 + - + +
922B LYS* 5.4 1.7 - - - +
968B HIS* 5.9 1.6 - - - -
997B CYS* 3.6 26.2 - - + +
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Residues in contact with VAL 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B ALA 4.3 2.2 - - - +
900B CYS* 3.4 43.5 - - + +
901B THR 3.9 7.6 - - - +
902B HIS 4.4 0.2 - - - +
903B LEU* 4.4 5.8 - - + +
917B ALA* 2.9 33.6 + - + +
918B ILE 4.7 0.5 - - - +
919B SER 5.4 0.3 - - - -
920B VAL* 1.3 81.6 + - - +
922B LYS* 1.3 61.1 + - - +
923B HIS 3.4 24.9 - - - +
924B ILE* 4.1 13.0 - - + -
964B LEU* 3.6 16.6 - - + +
968B HIS* 3.7 10.7 - - - -
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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