Contacts of the helix formed by residues 927 - 940 (chain A) in PDB entry 6J8H
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 GLU 927 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A ASP* 3.4 12.1 - - - +
362A TYR 6.0 0.3 + - - -
922A ARG* 2.8 65.5 + - + +
923A VAL* 4.9 2.1 - - - +
925A CYS* 2.8 16.9 + - + -
926A GLY* 1.3 78.3 - - - +
928A TRP* 1.3 62.1 + - - +
929A ILE 3.5 3.1 + - - -
930A GLU* 4.0 11.3 + - - +
931A THR* 4.3 10.0 + - - -
1405A PHE* 3.6 13.7 - - + +
1406A LYS* 5.5 2.1 + - - -
1408A TRP* 4.1 14.8 + - + -
2007A 9SL 3.6 38.0 + - - +
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Residues in contact with TRP 928 (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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352A LEU* 4.1 6.7 - - + -
355A PHE* 3.7 28.3 - + - -
356A ARG* 3.7 27.8 - - + -
359A THR* 3.2 20.2 + - - -
361A ASP* 3.5 14.9 + - + +
923A VAL* 3.9 32.3 - - + +
926A GLY* 4.3 5.2 - - - -
927A GLU* 1.3 76.6 - - - +
929A ILE* 1.3 101.1 + - + +
930A GLU 3.5 0.3 + - - -
931A THR* 3.7 5.1 + - - -
932A MET* 3.2 47.9 + - + +
948A TYR* 4.1 12.1 - + + -
949A MET* 4.1 12.8 - - + -
952A MET* 3.2 33.9 - - + -
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Residues in contact with ILE 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.7 11.9 - - + -
356A ARG* 4.2 22.0 - - + +
361A ASP* 2.5 51.5 + - - +
362A TYR* 3.9 16.2 - - + -
928A TRP* 1.3 107.1 - - + +
930A GLU* 1.3 71.7 + - + +
932A MET* 3.3 18.7 + - + +
933A TRP* 3.4 40.4 + - + +
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Residues in contact with GLU 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ASP* 5.3 2.2 - - - +
362A TYR* 3.7 36.8 + - + -
922A ARG* 4.1 23.8 + - - +
927A GLU* 4.0 7.9 + - - +
928A TRP 3.5 1.0 - - - -
929A ILE* 1.3 83.4 - - + +
931A THR* 1.3 62.3 + - - +
933A TRP* 3.7 25.4 + - + +
934A ASP* 4.0 10.0 + - - +
2007A 9SL 2.9 37.7 + - + +
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Residues in contact with THR 931 (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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892A TYR* 4.6 3.4 - - - +
908A TRP* 4.8 6.5 - - + +
919A ILE* 3.5 35.0 - - + +
922A ARG* 3.4 29.9 + - - +
923A VAL* 5.8 2.3 - - - +
927A GLU 4.3 3.4 + - - -
928A TRP* 3.7 8.2 + - - -
929A ILE 3.3 0.2 - - - -
930A GLU* 1.3 76.8 - - - +
932A MET* 1.3 64.8 + - - +
934A ASP* 3.1 17.4 + - + +
935A CYS 3.2 10.0 + - - -
948A TYR* 2.9 27.7 + - + +
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Residues in contact with MET 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.3 13.2 - - + -
928A TRP* 3.2 47.2 + - + +
929A ILE* 3.3 15.0 + - + +
931A THR* 1.3 76.8 - - - +
933A TRP* 1.3 67.9 + - + +
935A CYS* 3.2 1.6 + - - +
936A MET* 3.0 37.9 + - + +
944A CYS* 4.3 12.6 - - - -
945A LEU* 4.4 14.8 - - - -
948A TYR* 4.0 32.5 - - + -
949A MET* 4.1 17.0 - - + -
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Residues in contact with TRP 933 (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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338A ASP* 3.5 34.8 - - + -
339A TYR* 3.8 23.3 - + + -
341A TYR* 3.8 36.4 - + + +
342A THR* 3.7 17.6 + - - -
352A LEU* 5.7 2.9 - - + +
356A ARG* 3.9 19.5 - - - -
362A TYR* 4.4 14.6 - + - -
365A ASN* 5.6 0.9 - - - -
929A ILE* 3.4 37.8 + - + +
930A GLU* 4.0 29.2 - - - +
931A THR 3.3 0.6 - - - -
932A MET* 1.3 80.9 - - + +
934A ASP* 1.3 64.2 + - - +
936A MET* 3.4 7.5 + - - +
937A GLU* 3.1 26.7 + - - +
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Residues in contact with ASP 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A TYR* 3.9 18.7 + - - -
892A TYR* 4.1 11.9 - - + +
899A ILE* 3.6 27.1 - - + +
906A PRO* 4.0 24.0 - - - +
908A TRP* 4.3 5.9 - - - +
930A GLU 4.0 6.9 + - - +
931A THR* 3.1 15.4 + - + +
932A MET 3.1 0.2 - - - -
933A TRP* 1.3 81.3 - - - +
935A CYS* 1.3 62.8 + - - +
937A GLU* 3.4 7.3 + - - -
938A VAL* 3.3 16.5 + - - +
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Residues in contact with CYS 935 (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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888A PHE* 3.9 32.3 - - - -
892A TYR* 3.7 17.0 + - + +
910A MET* 5.4 0.4 - - - -
931A THR 3.2 2.2 + - - +
932A MET 3.2 3.6 + - - +
934A ASP* 1.3 78.2 - - - +
936A MET* 1.3 52.2 + - - +
938A VAL* 3.2 6.3 - - - +
939A ALA* 2.6 39.3 + - - +
944A CYS* 2.0 47.1 - - - -
948A TYR* 3.9 20.6 - - - +
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Residues in contact with MET 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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341A TYR* 3.7 40.7 + - + +
349A TRP* 5.0 9.2 - - + -
352A LEU* 5.4 2.9 - - + -
932A MET* 3.0 36.0 + - + +
933A TRP* 3.7 6.3 - - - +
935A CYS* 1.3 75.2 - - - +
937A GLU* 1.3 66.3 + - - +
940A GLY* 2.9 29.3 + - - +
941A GLN* 4.0 17.4 - - + +
944A CYS* 3.7 14.8 - - + -
945A LEU* 2.8 48.5 - - + -
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Residues in contact with GLU 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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339A TYR* 3.7 40.6 - - + +
341A TYR* 2.8 31.8 + - - -
898A LYS* 3.1 53.1 + - + +
899A ILE* 4.1 12.6 - - + -
933A TRP 3.1 14.4 + - - +
934A ASP* 3.7 7.6 - - - +
935A CYS 3.3 0.4 - - - -
936A MET* 1.3 79.3 - - - +
938A VAL* 1.3 62.6 + - - +
940A GLY* 4.4 0.9 + - - -
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Residues in contact with VAL 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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891A SER* 4.0 16.2 + - - +
892A TYR* 4.3 25.4 - - + -
895A CYS* 3.0 47.7 - - + -
896A VAL 4.4 0.4 - - - +
898A LYS* 4.7 1.8 - - + -
899A ILE* 3.2 32.5 - - + -
934A ASP 3.3 10.5 - - - +
935A CYS* 3.2 14.8 - - - +
937A GLU* 1.3 80.2 - - - +
939A ALA* 1.3 63.5 + - + +
940A GLY 3.6 0.2 - - - -
55C CYS* 4.5 3.1 - - - -
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Residues in contact with ALA 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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888A PHE* 3.4 39.7 - - + -
891A SER* 4.6 9.2 - - - +
935A CYS* 2.6 24.0 + - - +
938A VAL* 1.3 77.2 - - + +
940A GLY* 1.3 60.1 - - - +
943A MET* 3.4 23.6 + - + +
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Residues in contact with GLY 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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936A MET* 2.9 19.7 + - - -
937A GLU 4.4 1.0 + - - -
938A VAL 3.6 1.8 + - - -
939A ALA* 1.3 81.4 - - - +
941A GLN* 1.3 65.5 + - - -
942A ALA 3.6 2.0 - - - -
943A MET 4.0 0.6 + - - -
944A CYS* 3.5 20.8 + - - +
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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