Contacts of the strand formed by residues 801 - 808 (chain A) in PDB entry 6DMY
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 TYR 801 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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794A GLN* 6.3 0.7 - - - -
795A PHE* 4.0 22.6 - + - -
798A PHE 5.7 2.0 - - - -
799A SER* 4.0 4.9 + - - -
800A PHE* 1.3 91.7 - - - +
802A ASN* 1.3 61.4 + - - +
803A MET 3.9 0.2 - - - -
977A TYR* 3.5 10.9 - - - +
978A LEU* 3.0 42.3 + - + -
981A LEU* 3.9 17.7 - - + -
987A PHE* 3.5 29.5 - + - -
1013A TYR* 4.9 18.2 - + + -
1014A PRO* 3.8 34.3 - - + -
1018A TRP* 3.8 23.9 - + - -
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Residues in contact with ASN 802 (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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153A PHE* 4.2 11.8 - - - -
800A PHE* 6.3 0.9 - - + -
801A TYR* 1.3 74.6 - - - +
803A MET* 1.3 64.1 + - - +
804A TYR* 3.5 43.3 + - + -
938A GLN* 5.6 0.6 + - - -
975A PRO* 5.2 1.0 - - - +
976A PHE 3.7 4.2 + - - +
977A TYR* 3.3 31.2 + - + -
1012A GLY* 3.8 19.9 - - - -
1013A TYR* 4.4 5.2 + - + +
1014A PRO* 5.3 1.2 - - - +
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Residues in contact with MET 803 (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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801A TYR 3.9 1.0 + - - -
802A ASN* 1.3 72.5 - - - +
804A TYR* 1.3 70.6 + - - +
805A ILE* 3.7 27.1 + - + -
826A PHE* 5.8 2.7 - - + -
829A VAL* 5.9 0.4 - - + -
832A VAL* 4.6 13.2 - - + -
975A PRO 3.7 0.2 - - - -
976A PHE* 2.7 64.6 + - + +
978A LEU* 3.6 34.8 - - + -
994A VAL* 4.4 11.9 - - + -
1011A ASN 3.9 4.0 - - - +
1012A GLY* 5.1 0.7 - - - -
1014A PRO* 6.1 1.8 - - + -
1015A PHE* 3.6 36.6 - - + -
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Residues in contact with TYR 804 (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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151A ALA* 5.1 14.4 - - + -
152A MET* 6.3 1.6 - - + -
153A PHE* 3.2 35.2 - + - -
802A ASN* 3.5 29.2 + - + -
803A MET* 1.3 75.9 - - - +
805A ILE* 1.3 65.1 + - - +
806A VAL* 5.8 0.9 - - + -
938A GLN* 3.6 25.1 + - + -
973A GLN* 3.5 44.6 - - + +
974A PHE 4.2 3.4 - - - -
975A PRO* 4.1 16.6 - - + -
1011A ASN* 3.2 44.1 + - + +
1012A GLY* 6.0 0.9 - - - -
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Residues in contact with ILE 805 (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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803A MET* 3.7 36.1 - - + +
804A TYR* 1.3 80.7 - - - +
806A VAL* 1.3 64.8 + - - +
822A LEU* 5.0 2.2 - - + -
826A PHE* 3.5 43.5 - - + -
973A GLN* 3.6 0.8 - - - -
974A PHE* 3.1 51.9 + - + +
976A PHE* 4.5 3.6 - - + -
994A VAL* 4.1 10.1 - - + -
998A CYS* 4.4 10.8 - - - -
1008A SER* 5.1 4.5 - - - -
1009A TYR 4.1 9.2 - - - +
1010A PRO* 4.1 10.8 - - + -
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Residues in contact with VAL 806 (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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143A THR* 4.9 1.8 - - + -
804A TYR* 5.4 0.4 - - + -
805A ILE* 1.3 76.5 - - - +
807A THR* 1.3 75.1 + - - +
971A TYR* 3.5 32.1 - - + +
972A ALA 3.3 12.3 - - - +
973A GLN* 4.0 10.8 - - + +
1008A SER* 3.7 3.1 - - - -
1009A TYR* 3.2 66.7 + - + +
1011A ASN* 4.1 14.6 - - + +
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Residues in contact with THR 807 (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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805A ILE 4.2 0.8 + - - -
806A VAL* 1.3 86.0 - - - +
808A GLN* 1.3 71.8 + - - +
810A ALA* 4.5 0.3 - - - +
812A TYR* 2.9 28.7 + - + +
819A LEU* 5.0 6.7 - - + -
844A TRP* 5.0 4.9 - - + +
971A TYR* 3.8 3.6 - - - -
972A ALA* 2.9 38.1 + - + +
974A PHE* 4.9 16.0 - - + -
1006A LEU* 3.6 26.4 - - - +
1007A SER 3.6 8.7 + - - -
1008A SER* 4.4 4.9 - - - -
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Residues in contact with GLN 808 (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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142A TYR* 3.2 52.3 + - + +
807A THR* 1.3 84.6 + - - +
809A LYS* 1.3 67.9 + - + +
810A ALA* 2.9 14.5 + - - +
812A TYR* 3.5 1.5 + - - -
970A GLU 3.8 5.4 - - - -
1007A SER* 2.6 46.5 + - - +
1008A SER 5.1 0.2 + - - -
1009A TYR* 3.2 27.4 - - + -
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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