Contacts of the helix formed by residues 849 - 864 (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 TRP 849 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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845A LEU* 3.3 17.6 + - + +
846A ALA 3.0 15.5 + - - +
847A LYS 4.7 0.7 - - - -
848A SER* 1.3 77.9 - - - +
850A PRO* 1.3 106.6 - - + +
851A THR* 3.5 7.2 - - - +
852A LEU* 3.8 35.2 - - + -
853A ASN* 3.2 11.8 + - - +
1323A ASN* 3.5 22.2 + - - -
1326A LEU* 3.4 54.3 - - + -
1327A VAL* 3.9 17.0 - - + -
1330A ILE* 4.3 17.9 - - + -
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Residues in contact with PRO 850 (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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848A SER 3.8 4.2 - - - +
849A TRP* 1.3 111.8 - - + +
851A THR* 1.3 69.8 + - - +
853A ASN* 3.4 8.0 - - + +
854A MET* 3.4 18.5 + - - +
1323A ASN* 4.8 4.5 - - - +
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Residues in contact with THR 851 (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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849A TRP* 4.0 8.3 - - - -
850A PRO* 1.3 81.2 - - - +
852A LEU* 1.3 61.7 + - - +
853A ASN 3.1 1.6 - - - -
854A MET* 2.8 35.0 + - + +
855A LEU* 3.1 6.4 + - - +
1323A ASN* 3.5 23.9 + - - +
1324A VAL* 4.6 12.8 - - + +
1327A VAL* 3.1 28.9 - - + -
1451A LEU* 4.6 12.6 - - + -
1455A VAL* 5.8 2.2 - - + -
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Residues in contact with LEU 852 (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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843A PHE* 4.1 20.4 - - + +
845A LEU* 4.2 11.4 - - + -
846A ALA* 3.5 33.7 - - + +
849A TRP* 3.7 40.2 + - + -
850A PRO 3.5 0.6 - - - -
851A THR* 1.3 78.1 - - - +
853A ASN* 1.3 63.3 + - - +
855A LEU* 3.1 14.3 + - + +
856A ILE* 3.0 29.1 + - + +
1327A VAL* 3.1 32.0 - - + +
1330A ILE* 5.4 9.2 - - + -
1331A PHE* 6.0 1.3 - - + +
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Residues in contact with ASN 853 (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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808A TRP* 5.6 3.8 - - - -
846A ALA* 3.7 12.7 + - - +
847A LYS* 3.8 24.2 + - - +
849A TRP 3.2 9.7 + - - +
850A PRO* 3.4 13.8 - - + +
851A THR 3.1 0.2 - - - -
852A LEU* 1.3 79.8 - - - +
854A MET* 1.3 55.9 + - - +
856A ILE* 3.3 13.3 + - - +
857A LYS* 2.9 28.4 + - - +
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Residues in contact with MET 854 (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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850A PRO 3.4 9.2 + - - +
851A THR* 2.8 22.0 + - + +
853A ASN* 1.3 77.7 - - - +
855A LEU* 1.3 57.9 + - - +
857A LYS* 3.1 29.0 + - - +
858A ILE* 2.9 37.0 + - + +
970A SER* 4.2 18.2 - - - +
971A PHE* 6.1 1.3 - - - -
1451A LEU* 4.0 25.1 - - + -
1455A VAL* 6.0 5.2 - - + -
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Residues in contact with LEU 855 (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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843A PHE* 4.9 8.3 - - + -
851A THR 3.1 6.4 + - - +
852A LEU* 3.1 15.2 + - + +
854A MET* 1.3 73.7 - - - +
856A ILE* 1.3 68.2 + - - +
858A ILE* 3.2 8.2 + - + +
859A ILE* 3.2 32.7 + - + +
1327A VAL* 4.1 22.7 - - + -
1331A PHE* 3.4 42.6 - - + -
1447A PHE* 4.6 20.6 - - + +
1448A THR* 5.1 3.4 - - + +
1451A LEU* 3.7 27.3 - - + +
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Residues in contact with ILE 856 (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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808A TRP* 5.4 12.6 - - + -
843A PHE* 3.8 34.3 - - + -
846A ALA* 3.9 20.0 - - + -
852A LEU* 3.0 19.5 + - + +
853A ASN* 3.5 14.4 - - - +
854A MET 3.2 0.2 - - - -
855A LEU* 1.3 77.1 - - + +
857A LYS* 1.3 63.5 + - - +
859A ILE* 3.5 12.0 + - + +
860A GLY* 3.3 17.7 + - - -
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Residues in contact with LYS 857 (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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853A ASN 2.9 14.2 + - - +
854A MET* 3.1 32.6 + - - +
856A ILE* 1.3 78.9 - - - +
858A ILE* 1.3 61.9 + - - +
860A GLY* 3.2 3.4 + - - +
861A ASN* 3.2 35.8 + - - +
970A SER* 4.0 30.6 + - - +
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Residues in contact with ILE 858 (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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854A MET* 2.9 22.7 + - + +
855A LEU* 3.2 10.3 + - + +
857A LYS* 1.3 76.0 - - - +
859A ILE* 1.3 62.8 + - - +
861A ASN* 3.4 10.5 + - - -
862A SER* 3.6 4.2 + - - -
966A LEU* 3.5 31.7 - - + +
970A SER* 3.8 23.8 - - - +
1447A PHE* 4.0 23.5 - - + +
1450A ASN* 4.2 25.1 - - + +
1451A LEU* 4.0 37.7 - - + +
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Residues in contact with ILE 859 (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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843A PHE* 5.9 4.5 - - + -
855A LEU* 3.2 28.6 + - + +
856A ILE* 3.9 13.5 - - + +
857A LYS 3.3 0.2 - - - -
858A ILE* 1.3 76.4 - - - +
860A GLY* 1.3 61.6 + - - +
862A SER* 2.9 25.1 + - - +
863A VAL* 3.8 7.8 + - + +
1331A PHE* 4.6 10.3 - - + -
1443A PHE* 3.8 36.1 - - + -
1447A PHE* 4.2 26.9 - - + -
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Residues in contact with GLY 860 (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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856A ILE 3.3 8.5 + - - -
857A LYS 3.2 6.8 + - - -
858A ILE 3.2 0.8 - - - -
859A ILE* 1.3 78.6 - - - +
861A ASN* 1.3 52.3 + - - +
863A VAL* 3.2 10.4 + - - +
864A GLY* 2.7 35.6 + - - -
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Residues in contact with ASN 861 (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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857A LYS* 3.2 24.4 + - - +
858A ILE 3.6 2.9 - - - +
859A ILE 3.3 0.4 - - - -
860A GLY* 1.3 76.6 - - - +
862A SER* 1.3 61.0 + - - +
864A GLY* 3.2 5.6 + - - +
865A ALA* 4.5 11.9 + - - +
866A LEU* 2.9 36.3 + - + +
966A LEU* 3.6 19.9 - - + +
969A SER* 3.4 24.5 + - - -
970A SER* 4.0 23.0 - - - +
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Residues in contact with SER 862 (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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858A ILE 3.6 1.8 + - - -
859A ILE* 2.9 16.2 + - - +
860A GLY 3.2 0.2 - - - -
861A ASN* 1.3 79.3 - - - +
863A VAL* 1.3 64.9 + - - +
866A LEU* 3.2 6.9 - - - +
867A GLY* 3.1 6.1 + - - -
870A THR* 2.5 43.7 - - - +
962A LEU* 5.4 4.0 - - - -
966A LEU* 4.0 22.8 - - - +
1447A PHE* 4.0 18.6 - - - -
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Residues in contact with VAL 863 (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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859A ILE* 4.4 7.6 - - + +
860A GLY* 3.2 10.9 + - - +
862A SER* 1.3 90.7 + - - +
864A GLY* 1.3 63.4 + - - +
867A GLY* 4.0 9.3 - - - -
870A THR* 4.5 4.9 - - + +
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Residues in contact with GLY 864 (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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860A GLY 2.7 16.7 + - - -
861A ASN* 3.2 3.0 + - - -
863A VAL* 1.3 81.6 - - - +
865A ALA* 1.3 65.5 + - - +
867A GLY* 3.1 9.5 + - - -
868A ASN 4.9 0.3 + - - -
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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