Contacts of the helix formed by residues 935 - 947 (chain A) in PDB entry 1RJB
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 SER 935 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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803A GLU* 5.2 5.6 - - - -
871A VAL* 4.7 2.5 - - - -
934A PRO* 1.3 74.3 - - - +
936A PHE* 1.3 59.5 + - - +
937A PRO* 3.3 16.2 - - - +
938A ASN* 2.8 46.7 + - - +
939A LEU* 2.8 31.1 + - - +
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Residues in contact with PHE 936 (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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796A ALA* 4.2 11.7 - - - +
799A MET* 3.5 35.7 - - + -
800A GLU* 4.0 14.8 - - - +
803A GLU* 4.0 6.8 + - - +
867A ILE* 3.6 50.0 - - + -
870A ASP* 3.6 28.3 - - + -
871A VAL* 3.7 8.0 - - + +
874A TYR* 3.8 26.0 - + + -
935A SER* 1.3 69.5 - - - +
937A PRO* 1.3 78.0 - - + +
939A LEU* 3.0 17.6 + - + +
940A THR* 2.7 28.6 + - - -
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Residues in contact with PRO 937 (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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800A GLU* 3.2 31.1 - - + +
803A GLU* 3.3 22.2 - - - +
935A SER* 3.3 17.3 - - - +
936A PHE* 1.3 91.5 - - + +
938A ASN* 1.3 62.3 + - - +
940A THR* 3.4 2.5 + - - +
941A SER* 3.3 21.7 + - - -
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Residues in contact with ASN 938 (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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934A PRO* 3.8 7.8 - - + +
935A SER* 2.8 48.0 + - - +
937A PRO* 1.3 77.5 - - - +
939A LEU* 1.3 64.1 + - - +
941A SER* 3.0 15.0 + - - -
942A PHE* 3.1 43.5 + - + -
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Residues in contact with LEU 939 (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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796A ALA* 4.4 10.3 - - + -
871A VAL* 4.1 19.5 - - + -
874A TYR* 3.8 23.1 - - + -
921A ILE* 3.6 31.0 - - + -
925A CYS* 4.1 4.5 - - - -
934A PRO* 3.7 20.2 - - + -
935A SER 2.8 21.2 + - - +
936A PHE* 3.0 30.0 + - + +
938A ASN* 1.3 73.6 - - - +
940A THR* 1.3 62.3 + - - +
942A PHE* 4.1 9.4 - - + -
943A LEU* 3.0 32.5 + - + +
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Residues in contact with THR 940 (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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793A TYR* 3.0 29.2 - - + +
796A ALA* 3.5 29.6 + - - +
797A LYS* 3.2 41.2 + - - +
800A GLU* 3.7 12.4 + - - +
936A PHE 2.7 21.0 + - - -
937A PRO 3.7 5.6 - - - -
938A ASN 3.2 0.2 - - - -
939A LEU* 1.3 73.6 - - - +
941A SER* 1.3 57.2 + - - +
944A GLY* 2.9 22.2 + - - -
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Residues in contact with SER 941 (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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937A PRO 3.3 10.3 + - - -
938A ASN* 3.0 10.7 + - - -
940A THR* 1.3 75.3 - - - +
942A PHE* 1.3 73.8 + - - +
944A GLY* 3.1 1.2 + - - -
945A CYS* 2.7 34.9 + - - -
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Residues in contact with PHE 942 (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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921A ILE* 3.8 28.3 - - + -
924A SER* 5.9 1.3 - - - -
934A PRO* 4.3 15.7 - - + -
938A ASN* 3.4 41.3 - - + -
939A LEU* 3.8 16.6 - - + +
941A SER* 1.3 78.5 - - - +
943A LEU* 1.3 60.1 + - + +
945A CYS* 3.2 6.9 + - - +
946A GLN* 2.8 30.7 + - - +
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Residues in contact with LEU 943 (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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789A LEU* 3.4 29.2 - - + +
792A ALA* 3.6 21.8 - - + +
793A TYR* 3.9 18.8 - - + +
796A ALA* 4.1 3.8 - - + -
874A TYR* 2.8 36.1 - - + +
878A LEU* 4.8 6.5 - - + -
882A PHE* 6.3 0.2 - - + -
918A ILE* 5.2 5.8 - - + -
921A ILE* 4.1 24.9 - - + -
939A LEU* 3.0 23.8 + - + +
942A PHE* 1.3 73.2 - - + +
944A GLY* 1.3 66.2 + - - +
945A CYS 3.0 1.6 - - - -
946A GLN* 3.1 4.8 + - + -
947A LEU* 2.8 20.8 + - - +
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Residues in contact with GLY 944 (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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793A TYR* 3.4 27.7 - - - -
940A THR 2.9 15.2 + - - -
941A SER* 3.1 1.5 + - - -
943A LEU* 1.3 75.3 - - - +
945A CYS* 1.3 62.6 + - - +
947A LEU* 3.2 23.8 - - - +
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Residues in contact with CYS 945 (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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941A SER* 2.7 24.9 + - - +
942A PHE* 3.3 11.2 - - - +
944A GLY* 1.3 74.2 - - - +
946A GLN* 1.3 68.9 + - - +
947A LEU 2.8 9.8 + - - +
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Residues in contact with GLN 946 (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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785A PHE* 5.2 5.8 - - - -
789A LEU* 4.0 21.7 - - + +
915A THR* 3.8 14.6 + - - +
917A GLU* 3.6 40.7 + - + +
918A ILE* 4.0 13.6 - - + +
921A ILE* 4.9 9.9 - - + -
942A PHE 2.8 21.3 + - - +
943A LEU* 3.6 10.3 - - + +
945A CYS* 1.3 71.2 - - - +
947A LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 947 (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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786A GLU* 4.2 24.5 - - + +
789A LEU* 3.3 21.7 - - + +
790A CYS* 4.2 16.8 - - + +
793A TYR* 3.9 39.0 - - + -
943A LEU 2.8 8.1 + - - +
944A GLY* 3.2 17.9 - - - +
945A CYS 2.8 7.0 + - - +
946A GLN* 1.3 83.5 - - - +
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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