Contacts of the strand formed by residues 898 - 912 (chain A) in PDB entry 2XDP
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 ARG 898 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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897A CYS* 1.3 75.0 - - - +
899A VAL* 1.3 70.7 + - - +
900A MET* 3.3 32.3 + - - +
968A VAL* 3.2 6.1 - - - -
969A GLU* 2.9 42.6 + - + +
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Residues in contact with VAL 899 (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 CYS 5.4 2.0 - - - +
898A ARG* 1.3 80.0 + - - +
900A MET* 1.3 63.6 + - - +
901A ALA 3.9 18.8 - - - +
902A VAL* 4.1 17.0 - - + -
966A TYR* 4.3 15.5 - - + -
967A GLN 3.6 5.4 - - - +
968A VAL* 4.5 12.1 - - + -
983A ILE* 5.7 9.2 - - + -
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Residues in contact with MET 900 (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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898A ARG* 3.6 50.0 - - - +
899A VAL* 1.3 74.1 - - - +
901A ALA* 1.3 59.8 + - + +
967A GLN* 2.7 26.4 + - + +
968A VAL 4.2 1.3 - - - -
969A GLU* 3.7 40.2 - - + +
975A GLN* 4.3 13.2 - - - +
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Residues in contact with ALA 901 (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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899A VAL* 3.6 4.2 - - - +
900A MET* 1.3 82.1 - - + +
902A VAL* 1.3 65.7 + - - +
903A THR* 4.2 13.5 - - + -
965A MET 3.9 0.2 - - - +
966A TYR* 3.5 3.6 - - - -
967A GLN* 2.9 40.5 + - + +
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Residues in contact with VAL 902 (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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899A VAL* 4.1 10.1 - - + -
901A ALA* 1.3 78.3 - - - +
903A THR* 1.3 66.5 + - - +
964A HIS* 3.8 35.3 - - + -
965A MET 3.4 2.7 - - - +
966A TYR* 3.7 29.8 - - + +
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Residues in contact with THR 903 (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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901A ALA* 4.7 11.7 - - + -
902A VAL* 1.3 81.3 - - - +
904A SER* 1.3 66.5 + - - +
964A HIS* 3.0 13.6 - - - +
965A MET* 2.9 46.5 + - - +
967A GLN* 6.3 0.9 - - + -
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Residues in contact with SER 904 (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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903A THR* 1.3 80.8 + - - +
905A GLN* 1.3 62.9 + - - +
962A ILE* 4.0 18.1 - - - +
963A ALA 3.3 5.8 - - - -
964A HIS* 4.2 11.9 + - - -
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Residues in contact with GLN 905 (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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904A SER* 1.3 76.9 - - - +
906A THR* 1.3 86.5 + - - +
907A PHE* 3.5 29.3 - - + -
922A PHE* 4.1 13.3 - - - -
923A PRO* 3.9 14.3 - - - +
924A GLU* 4.7 5.0 + - - -
962A ILE* 3.4 5.1 - - - +
963A ALA 2.7 36.0 + - - +
965A MET* 3.6 27.2 - - + +
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Residues in contact with THR 906 (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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905A GLN* 1.3 96.7 + - - +
907A PHE* 1.3 67.7 + - - +
908A TYR* 4.2 20.2 - - + -
923A PRO* 3.2 16.6 - - + +
960A SER* 4.2 9.2 - - - +
961A ASN 3.4 11.0 - - - +
962A ILE* 4.3 13.4 - - + +
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Residues in contact with PHE 907 (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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905A GLN* 3.5 36.3 - - + -
906A THR* 1.3 75.9 - - - +
908A TYR* 1.3 63.8 + - - +
919A ARG 3.6 17.9 - - - +
920A ASP* 3.6 34.8 - - + -
921A THR 3.5 8.3 - - - +
922A PHE* 3.6 24.2 - + - -
960A SER* 3.2 6.2 - - - -
961A ASN* 2.8 39.2 + - - +
963A ALA* 3.6 29.4 - - + -
964A HIS 3.8 10.5 - - - -
965A MET* 3.7 18.6 - - - -
979A LYS* 4.1 10.8 - - + -
980A ARG 6.1 0.2 - - - -
1995A SO4 5.2 0.2 - - - -
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Residues in contact with TYR 908 (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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906A THR* 4.2 10.8 - - + -
907A PHE* 1.3 82.4 - - - +
909A GLU* 1.3 63.1 + - - +
910A VAL* 4.0 4.3 - - + -
918A SER 3.7 0.7 - - - +
919A ARG 3.5 8.0 - - - -
921A THR* 2.7 47.7 + - - +
922A PHE 4.8 0.2 - - - -
923A PRO* 3.6 36.8 - - + +
926A ILE* 3.8 18.6 - - + -
931A CYS* 3.3 39.2 + - - +
935A GLY 4.2 0.3 - - - -
936A PRO* 3.4 23.7 - - + +
937A PRO* 4.0 5.2 - - + -
957A TYR* 3.5 31.9 - + + -
959A GLY 3.6 1.3 - - - -
960A SER* 3.9 6.1 - - - -
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Residues in contact with GLU 909 (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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908A TYR* 1.3 73.3 - - - +
910A VAL* 1.3 63.1 + - - +
917A PHE* 3.7 25.5 - - + -
918A SER 3.2 5.2 - - - +
919A ARG* 4.0 22.3 + - - +
957A TYR* 3.9 0.9 - - - -
958A PHE* 2.9 31.0 + - - +
959A GLY* 2.8 24.0 + - - +
960A SER* 4.1 8.5 - - - +
961A ASN* 2.8 40.5 + - - +
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Residues in contact with VAL 910 (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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908A TYR* 4.0 6.5 - - + -
909A GLU* 1.3 79.3 - - - +
911A MET* 1.3 59.2 + - - +
912A PHE* 3.8 26.6 + - + -
917A PHE* 3.4 7.3 - - - -
918A SER* 2.9 34.5 + - - -
921A THR* 3.7 21.8 - - + +
926A ILE* 4.5 20.0 - - + -
943A VAL* 4.6 4.5 - - + -
945A VAL* 4.6 2.9 - - + -
955A ALA* 4.1 12.3 - - + -
956A LYS 3.3 13.5 - - - +
957A TYR* 4.2 16.4 - - + -
958A PHE 4.6 0.2 - - - +
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Residues in contact with MET 911 (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 VAL* 1.3 71.1 - - - +
912A PHE* 1.3 68.6 + - - +
913A ASP* 4.7 0.5 - - - +
915A GLY* 3.2 38.6 - - - +
916A SER 3.6 5.4 - - - +
917A PHE* 3.7 24.2 - - + -
955A ALA* 3.2 1.9 - - - -
956A LYS* 2.9 33.3 + - + +
958A PHE* 3.7 27.8 - - + -
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Residues in contact with PHE 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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910A VAL* 3.9 15.0 - - + -
911A MET* 1.3 80.0 - - - +
913A ASP* 1.3 54.3 + - - +
914A ASP* 2.9 22.2 - - - +
915A GLY* 2.8 27.4 + - - -
916A SER* 2.9 28.1 + - - +
918A SER* 3.7 25.4 - - - -
921A THR* 4.7 2.9 - - - -
945A VAL* 4.0 27.4 - - + -
947A TRP* 5.3 13.9 - + - -
953A TYR* 3.8 32.8 - + + -
954A GLY 3.6 13.9 - - - +
955A ALA* 3.9 4.5 - - + -
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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